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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Species limits in <italic>Diaporthe</italic>: molecular re-assessment of <italic>D. citri</italic>, <italic>D. cytosporella</italic>, <italic>D. foeniculina</italic> and <italic>D. rudis</italic></title><author><name sortKey="Udayanga, D" sort="Udayanga, D" uniqKey="Udayanga D" first="D." last="Udayanga">D. Udayanga</name><affiliation><nlm:aff id="A1"><xref ref-type="author-notes" rid="fn1">*</xref>Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705 USA;</nlm:aff></affiliation><affiliation><nlm:aff id="A2"> Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand.</nlm:aff></affiliation><affiliation><nlm:aff id="A3"> School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.</nlm:aff></affiliation></author><author><name sortKey="Castlebury, L A" sort="Castlebury, L A" uniqKey="Castlebury L" first="L. A." last="Castlebury">L. A. Castlebury</name><affiliation><nlm:aff id="A1"><xref ref-type="author-notes" rid="fn1">*</xref>Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705 USA;</nlm:aff></affiliation></author><author><name sortKey="Rossman, A Y" sort="Rossman, A Y" uniqKey="Rossman A" first="A. Y." last="Rossman">A. Y. Rossman</name><affiliation><nlm:aff id="A1"><xref ref-type="author-notes" rid="fn1">*</xref>Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705 USA;</nlm:aff></affiliation></author><author><name sortKey="Hyde, K D" sort="Hyde, K D" uniqKey="Hyde K" first="K. D." last="Hyde">K. D. Hyde</name><affiliation><nlm:aff id="A2"> Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand.</nlm:aff></affiliation><affiliation><nlm:aff id="A3"> School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25264384</idno><idno type="pmc">4150081</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150081</idno><idno type="RBID">PMC:4150081</idno><idno type="doi">10.3767/003158514X679984</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">001244</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Species limits in <italic>Diaporthe</italic>: molecular re-assessment of <italic>D. citri</italic>, <italic>D. cytosporella</italic>, <italic>D. foeniculina</italic> and <italic>D. rudis</italic></title><author><name sortKey="Udayanga, D" sort="Udayanga, D" uniqKey="Udayanga D" first="D." last="Udayanga">D. Udayanga</name><affiliation><nlm:aff id="A1"><xref ref-type="author-notes" rid="fn1">*</xref>Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705 USA;</nlm:aff></affiliation><affiliation><nlm:aff id="A2"> Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand.</nlm:aff></affiliation><affiliation><nlm:aff id="A3"> School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.</nlm:aff></affiliation></author><author><name sortKey="Castlebury, L A" sort="Castlebury, L A" uniqKey="Castlebury L" first="L. A." last="Castlebury">L. A. Castlebury</name><affiliation><nlm:aff id="A1"><xref ref-type="author-notes" rid="fn1">*</xref>Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705 USA;</nlm:aff></affiliation></author><author><name sortKey="Rossman, A Y" sort="Rossman, A Y" uniqKey="Rossman A" first="A. Y." last="Rossman">A. Y. Rossman</name><affiliation><nlm:aff id="A1"><xref ref-type="author-notes" rid="fn1">*</xref>Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705 USA;</nlm:aff></affiliation></author><author><name sortKey="Hyde, K D" sort="Hyde, K D" uniqKey="Hyde K" first="K. D." last="Hyde">K. D. Hyde</name><affiliation><nlm:aff id="A2"> Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand.</nlm:aff></affiliation><affiliation><nlm:aff id="A3"> School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.</nlm:aff></affiliation></author></analytic><series><title level="j">Persoonia : Molecular Phylogeny and Evolution of Fungi</title><idno type="ISSN">0031-5850</idno><idno type="eISSN">1878-9080</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Species of <italic>Diaporthe</italic> are important plant pathogens of a wide range of hosts worldwide. In the present study the species causing melanose and stem end rot diseases of <italic>Citrus</italic> spp. are revised. Three species of <italic>Diaporthe</italic> occurring on <italic>Citrus</italic> are characterised, including <italic>D. citri</italic>, <italic>D. cytosporella</italic> and <italic>D. foeniculina.</italic> Morphology and phylogenetic analyses of the complete nuclear ribosomal internal transcribed spacer regions and partial sequences of actin, beta-tubulin, calmodulin and translation elongation factor 1-α were used to resolve species on <italic>Citrus</italic> and related <italic>Diaporthe</italic> species. <italic>Diaporthe citri</italic> occurs on <italic>Citrus</italic> throughout the <italic>Citrus</italic>-growing regions of the world. <italic>Diaporthe cytosporella</italic> is found on <italic>Citrus</italic> in Europe and California (USA). <italic>Diaporthe foeniculina</italic>, including the synonym <italic>D. neotheicola</italic>, is recognised as a species with an extensive host range including <italic>Citrus</italic>. <italic>Diaporthe medusaea</italic>, a name widely used for <italic>D. citri</italic>, was determined to be a synonym of <italic>D. rudis</italic>, a species with a broad host range. <italic>Diaporthe citri</italic> is delimited based on molecular phylogenetic analysis with the inclusion of the conserved ex-type and additional collections from different geographic locations worldwide. <italic>Diaporthe cytosporella</italic>, <italic>D. foeniculina</italic> and <italic>D. rudis</italic> are epitypified, fully described and illustrated with a review of all synonyms based on molecular data and morphological studies<italic>.</italic> Newly designed primers are introduced to optimise the amplification and sequencing of calmodulin and actin genes in <italic>Diaporthe</italic>. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Persoonia</journal-id><journal-id journal-id-type="iso-abbrev">Persoonia</journal-id><journal-id journal-id-type="publisher-id">Persoonia</journal-id><journal-title-group><journal-title>Persoonia : Molecular Phylogeny and Evolution of Fungi</journal-title></journal-title-group><issn pub-type="ppub">0031-5850</issn><issn pub-type="epub">1878-9080</issn><publisher><publisher-name>Naturalis Biodiversity Center & Centraallbureau voor Schimmelcultures</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25264384</article-id><article-id pub-id-type="pmc">4150081</article-id><article-id pub-id-type="doi">10.3767/003158514X679984</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Species limits in <italic>Diaporthe</italic>: molecular re-assessment of <italic>D. citri</italic>, <italic>D. cytosporella</italic>, <italic>D. foeniculina</italic> and <italic>D. rudis</italic></article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Udayanga</surname><given-names>D.</given-names></name><xref ref-type="aff" rid="A1"><sup>1</sup></xref><xref ref-type="aff" rid="A2"><sup>2</sup></xref><xref ref-type="aff" rid="A3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Castlebury</surname><given-names>L.A.</given-names></name><xref ref-type="aff" rid="A1"><sup>1</sup></xref><xref ref-type="corresp" rid="COR1"></xref></contrib><contrib contrib-type="author"><name><surname>Rossman</surname><given-names>A.Y.</given-names></name><xref ref-type="aff" rid="A1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hyde</surname><given-names>K.D.</given-names></name><xref ref-type="aff" rid="A2"><sup>2</sup></xref><xref ref-type="aff" rid="A3"><sup>3</sup></xref></contrib></contrib-group><aff id="A1"><label>1</label><xref ref-type="author-notes" rid="fn1">*</xref>Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705 USA;</aff><aff id="A2"><label>2</label> Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand.</aff><aff id="A3"><label>3</label> School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.</aff><author-notes><corresp id="COR1">corresponding author e-mail: <email>Lisa.Castlebury@ars.usda.gov</email>.</corresp><fn id="fn1"><p>* Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the United States Department of Agriculture. USDA is an equal opportunity provider and employer.</p></fn></author-notes><pub-date pub-type="epub"><day>25</day><month>2</month><year>2014</year></pub-date><pub-date pub-type="ppub"><month>6</month><year>2014</year></pub-date><volume>32</volume><fpage>83</fpage><lpage>101</lpage><history><date date-type="received"><day>15</day><month>4</month><year>2013</year></date><date date-type="accepted"><day>9</day><month>8</month><year>2013</year></date></history><permissions><copyright-statement>© 2014 Naturalis Biodiversity Center & Centraalbureau voor Schimmelcultures</copyright-statement><copyright-year>2014</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode"><license-p>You are free to share - to copy, distribute and transmit the work, under the following conditions:</license-p><license-p>Attribution: You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work).</license-p><license-p>Non-commercial: You may not use this work for commercial purposes.</license-p><license-p>No derivative works: You may not alter, transform, or build upon this work.</license-p><license-p>For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode">http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode</ext-link>. Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights.</license-p></license></permissions><abstract abstract-type="executive-summary"><p>Species of <italic>Diaporthe</italic> are important plant pathogens of a wide range of hosts worldwide. In the present study the species causing melanose and stem end rot diseases of <italic>Citrus</italic> spp. are revised. Three species of <italic>Diaporthe</italic> occurring on <italic>Citrus</italic> are characterised, including <italic>D. citri</italic>, <italic>D. cytosporella</italic> and <italic>D. foeniculina.</italic> Morphology and phylogenetic analyses of the complete nuclear ribosomal internal transcribed spacer regions and partial sequences of actin, beta-tubulin, calmodulin and translation elongation factor 1-α were used to resolve species on <italic>Citrus</italic> and related <italic>Diaporthe</italic> species. <italic>Diaporthe citri</italic> occurs on <italic>Citrus</italic> throughout the <italic>Citrus</italic>-growing regions of the world. <italic>Diaporthe cytosporella</italic> is found on <italic>Citrus</italic> in Europe and California (USA). <italic>Diaporthe foeniculina</italic>, including the synonym <italic>D. neotheicola</italic>, is recognised as a species with an extensive host range including <italic>Citrus</italic>. <italic>Diaporthe medusaea</italic>, a name widely used for <italic>D. citri</italic>, was determined to be a synonym of <italic>D. rudis</italic>, a species with a broad host range. <italic>Diaporthe citri</italic> is delimited based on molecular phylogenetic analysis with the inclusion of the conserved ex-type and additional collections from different geographic locations worldwide. <italic>Diaporthe cytosporella</italic>, <italic>D. foeniculina</italic> and <italic>D. rudis</italic> are epitypified, fully described and illustrated with a review of all synonyms based on molecular data and morphological studies<italic>.</italic> Newly designed primers are introduced to optimise the amplification and sequencing of calmodulin and actin genes in <italic>Diaporthe</italic>. A discussion is provided of the utility of genes and the need for multi-gene phylogenies when distinguishing species of <italic>Diaporthe</italic> or describing new species.</p></abstract><kwd-group><kwd>epitypification</kwd><kwd>genealogical sorting index</kwd><kwd>melanose</kwd><kwd>multi-gene phylogeny</kwd><kwd>new primers</kwd><kwd><italic>Phomopsis</italic></kwd><kwd>species recognition</kwd><kwd>stem end rot</kwd><kwd>systematics</kwd></kwd-group></article-meta></front><body><sec id="s1"><title>INTRODUCTION</title><p>The genus <italic>Diaporthe</italic> is an economically important group of plant pathogenic fungi causing diseases on a wide range of crops, ornamentals and forest trees (<xref rid="R18" ref-type="bibr">Farr et al. 2002a</xref>, <xref rid="R19" ref-type="bibr">b</xref>, <xref rid="R11" ref-type="bibr">Crous 2005</xref>, <xref rid="R86" ref-type="bibr">Udayanga et al. 2011</xref>). Accurate species identification is vital for controlling the diseases caused by these fungi as well as for implementing quarantine regulations (<xref rid="R66" ref-type="bibr">Rossman & Palm-Hernández 2008</xref>, <xref rid="R7" ref-type="bibr">Cai et al. 2011</xref>, <xref rid="R73" ref-type="bibr">Shivas & Cai 2012</xref>). Until recently, species of <italic>Diaporthe</italic> have been defined based on morphology and host association. However, patterns of host association and speciation have yet to be fully understood within <italic>Diaporthe</italic>. Multiple species of <italic>Diaporthe</italic> can often be found on a single host and a single species of <italic>Diaporthe</italic> can be associated with many different hosts (<xref rid="R11" ref-type="bibr">Crous 2005</xref>, <xref rid="R54" ref-type="bibr">van Niekerk et al. 2005</xref>, <xref rid="R70" ref-type="bibr">Santos & Phillips 2009</xref>, <xref rid="R16" ref-type="bibr">Diogo et al. 2010</xref>, <xref rid="R30" ref-type="bibr">Gomes et al. 2013</xref>). Using molecular data, much progress has been made towards identifying and characterising emerging pathogens, prevalent endophytes and saprobes in the genus <italic>Diaporthe</italic> (<xref rid="R70" ref-type="bibr">Santos & Phillips 2009</xref>, <xref rid="R16" ref-type="bibr">Diogo et al. 2010</xref>, <xref rid="R45" ref-type="bibr">Luongo et al. 2011</xref>, <xref rid="R85" ref-type="bibr">Udayanga et al. 2012a</xref>, <xref rid="R87" ref-type="bibr">b</xref>, <xref rid="R80" ref-type="bibr">Thomidis et al. 2013</xref>).</p><p>Modern systematic accounts of <italic>Diaporthe</italic> have used DNA sequence data as the most accurate means to circumscribe species within this genus (<xref rid="R64" ref-type="bibr">Rehner & Uecker 1994</xref>, <xref rid="R10" ref-type="bibr">Castlebury et al. 2003</xref>, <xref rid="R65" ref-type="bibr">van Rensburg et al. 2006</xref>). Markers used in contemporary phylogenetic revisions include the complete nuclear ribosomal internal transcribed spacer regions (ITS) and more recently partial sequences of actin (ACT), beta-tubulin (TUB), calmodulin (CAL), histone H3 (HIS), mating type genes (MAT 1-1-1 and MAT 1-2-1) and translation elongation factor 1-alpha (EF1-α) (<xref rid="R54" ref-type="bibr">van Niekerk et al. 2005</xref>, <xref rid="R16" ref-type="bibr">Diogo et al. 2010</xref>, <xref rid="R69" ref-type="bibr">Santos et al. 2010</xref>, <xref rid="R85" ref-type="bibr">Udayanga et al. 2012a</xref>, <xref rid="R87" ref-type="bibr">b</xref>, <xref rid="R30" ref-type="bibr">Gomes et al. 2013</xref>). Multi-gene phylogenetic species delineation has become the most effective tool for taxonomic studies of fungi compared to traditional mating experiments and morphology (<xref rid="R79" ref-type="bibr">Taylor et al. 2000</xref>, <xref rid="R15" ref-type="bibr">Dettman et al. 2003</xref>). Although the ITS region is often useful for identification of <italic>Diaporthe</italic> species, multi-gene phylogenetic analyses are required for accurate reconstruction of species boundaries and relationships (<xref rid="R85" ref-type="bibr">Udayanga et al. 2012a</xref>, <xref rid="R30" ref-type="bibr">Gomes et al. 2013</xref>). Intraspecific variation observed in ITS sequences in several species of <italic>Diaporthe</italic> can cause confusion in species recognition when used alone (<xref rid="R18" ref-type="bibr">Farr et al. 2002a</xref>, <xref rid="R19" ref-type="bibr">b</xref>, <xref rid="R69" ref-type="bibr">Santos et al. 2010</xref>).</p><p><italic>Diaporthe citri</italic> is a pathogen that causes melanose and stem end rot disease of <italic>Citrus</italic> spp. throughout the world (<xref rid="R92" ref-type="bibr">Whiteside & Timmer 2000a</xref>, <xref rid="R51" ref-type="bibr">Mondal et al. 2007</xref>). Melanose disease can affect young leaves and fruits of different species and varieties of <italic>Citrus</italic> causing black blemishes on fruit rind and small, black, raised lesions often surrounded by yellow necrotic halos (<xref rid="R83" ref-type="bibr">Timmer & Kucharek 2001</xref>). Symptoms of the disease may vary with host variety, geographic location, seasonal occurrence, ecophysiological factors and severity of infection (<xref rid="R82" ref-type="bibr">Timmer & Fucik 1976</xref>, <xref rid="R91" ref-type="bibr">Whiteside 1977</xref>, <xref rid="R41" ref-type="bibr">Kucharek et al. 1983</xref>). The range of symptoms varies from small spots, scab lesions and mudcake to star melanose on different tissues of <italic>Citrus</italic> spp. (<xref rid="R81" ref-type="bibr">Timmer 2000</xref>, <xref rid="R92" ref-type="bibr">Whiteside & Timmer 2000a</xref>, <xref rid="R1" ref-type="bibr">Agostini et al. 2003</xref>). Perithecia and pycnidia are only produced on dead and dying twigs and on fruit affected by stem end rot. Because perithecia are rarely formed, conidia produced by pycnidia are the primary source of inoculum (<xref rid="R3" ref-type="bibr">Bach & Wolf 1928</xref>, <xref rid="R42" ref-type="bibr">Kuhara 1999</xref>).</p><p>Although the biology and epidemiology of melanose are well studied, the phylogenetic relationships of the causal organisms, genetic variability and population structure have not been investigated (<xref rid="R6" ref-type="bibr">Burnett 1962</xref>, <xref rid="R49" ref-type="bibr">Moherek 1970</xref>, <xref rid="R50" ref-type="bibr">Mondal et al. 2004</xref>, <xref rid="R51" ref-type="bibr">2007</xref>). <italic>Diaporthe</italic> pathogens of <italic>Citrus</italic> are usually identified as <italic>D. citri</italic> in taxonomic and plant pathological studies and regional checklists (<xref rid="R83" ref-type="bibr">Timmer & Kucharek 2001</xref>, <xref rid="R86" ref-type="bibr">Udayanga et al. 2011</xref>). In addition to <italic>D. citri</italic>, several other species of <italic>Diaporthe</italic> have been reported from <italic>Citrus</italic>, often as <italic>Phomopsis.</italic> These include <italic>D. citrincola</italic> described from the Philippines, <italic>Phomopsis californica</italic> from California, <italic>P. caribaea</italic> from Cuba and <italic>P. cytosporella</italic> (as <italic>Phoma cytosporella</italic>) from Italy, which have all previously been considered synonyms of <italic>D. citri</italic> (<xref rid="R63" ref-type="bibr">Rehm 1914</xref>, <xref rid="R21" ref-type="bibr">Fawcett 1922</xref>, <xref rid="R23" ref-type="bibr">1936</xref>, <xref rid="R31" ref-type="bibr">Horne 1922</xref>). <xref rid="R96" ref-type="bibr">Yamato (1976)</xref> recognised four unidentified morphological species on <italic>Citrus</italic> spp. in Japan. <italic>Diaporthe citri</italic> was also considered a synonym of <italic>D. medusaea</italic> by <xref rid="R89" ref-type="bibr">Wehmeyer (1933)</xref> who also listed <italic>D. californica</italic>, <italic>P. citri</italic> and <italic>P. citrincola</italic> as host or ecological forms of <italic>D. medusaea</italic>. Others followed this synonymy including <xref rid="R60" ref-type="bibr">Punithalingam & Holliday (1973)</xref> and <xref rid="R92" ref-type="bibr">Whiteside & Timmer (2000a)</xref>. The name <italic>D. medusaea</italic> is used in several articles and checklists for the fungus causing melanose and stem end rot, therefore, the true host range and geographic distribution of <italic>D. citri</italic> are difficult to determine (<xref rid="R39" ref-type="bibr">Kobayashi 1970</xref>, <xref rid="R58" ref-type="bibr">Pantidou 1973</xref>, <xref rid="R26" ref-type="bibr">French 1987</xref>).</p><p>Given the vague species concept of <italic>D. citri</italic> and its broad application, a modern taxonomic and phylogenetic reappraisal of <italic>D. citri</italic> and other <italic>Diaporthe</italic> species on <italic>Citrus</italic> is necessary<italic>.</italic> In this study, we analyse DNA sequence data from recent collections of <italic>Diaporthe</italic> isolated from <italic>Citrus</italic> and other hosts in Asia, Europe and the United States to accurately identify the taxa associated with <italic>Citrus</italic>. The objectives of this study are: 1) to define the species of <italic>Diaporthe</italic> on <italic>Citrus</italic> worldwide based on phylogenetic analysis of multi-gene sequence data, the genealogical sorting index and morphological characters; 2) to resolve taxonomic and nomenclatural uncertainty by providing modern descriptions for <italic>D. citri</italic> and designating epitypes for <italic>D. cytosporella</italic>, <italic>D. foeniculina</italic> and <italic>D. rudis</italic> and their synonyms; 3) to evaluate their host range and geographic distribution; and 4) to assess the utility of individual genes for accurate circumscription of these species.</p></sec><sec sec-type="materials|methods" id="s2"><title>MATERIALS AND METHODS</title><sec id="s2a"><title>Isolates and morphology</title><p>Strains of <italic>Diaporthe</italic> from <italic>Citrus</italic> hosts were obtained from China, Korea, New Zealand, Spain and the United States (California, Florida and Texas). These strains have been isolated from specimens with typical symptoms of <italic>Citrus</italic> melanose and stem end rot as well as saprobes on twigs and branches. Isolates from other hosts were obtained from culture collections including CBS (The Netherlands), Fawcett Laboratory, University of California, Riverside (CA, USA), ICMP (New Zealand), MFLUCC (Thailand) and the SMML, USDA-ARS (MD, USA) and various contributors listed in <xref ref-type="table" rid="T1">Table 1</xref>. Morphological descriptions are based on sporulating pycnidia from inoculated alfalfa stems placed on 1.5 % water agar (WA) for living cultures as well as type and other specimens. Digital images of fruiting bodies were captured using a Discovery V20 stereomicroscope and AxioCam digital camera (Carl Zeiss Microscopy, Thornwood, NY, USA) imaging system. Whenever possible, 20–30 measurements were made of the structures mounted in 5 % KOH using a Carl Zeiss Axioplan2 compound light microscope using the 40× or 100× objectives. The extreme measurements are given in parentheses with mean and standard deviation. Three sets of duplicate cultures of each isolate were used for determining colony characters on potato-dextrose agar (PDA, Becton, Dickinson and Company, Franklin Lakes, NJ, USA) at 25 °C in the dark following the methods of <xref rid="R4" ref-type="bibr">Brayford (1990)</xref>. Colony diameters on PDA were recorded at intervals of 24 h for 1 wk and used to calculate the growth rate of eight replicates per isolate. After 1 wk, colony size and colour of the colonies (<xref rid="R62" ref-type="bibr">Rayner 1970</xref>) and zonation were recorded.</p></sec><sec id="s2b"><title>DNA extraction, PCR and sequencing</title><p>Mycelial scrapings (50–60 mg) from the leading edge of cultures on PDA, incubated for 4–5 d at 25 °C were harvested and lysed in tubes containing 500 μm garnet media and a 6 mm zirconium bead (OPS Diagnostics, Lebanon, NJ, USA) with the Fast Prep FP120 (Fischer Scientific Inc, Waltham, MA, USA) for 20 s. Genomic DNA was extracted with the DNeasy Plant Mini Kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer’s instructions. The ACT, CAL, EF1-α, ITS and TUB gene regions were amplified following the conditions outlined in <xref ref-type="table" rid="T2">Table 2</xref> on a Bio-Rad Dyad Peltier thermal cycler in a 25 μL reaction volume: 10–15 ng genomic DNA, 12.5 μL Quick load Taq 2x Master Mix (New England BioLabs, Ipswich, MA, USA), 1 μL 10 mM of each primer and 1 % DMSO with volumes adjusted to 25 μL with nuclease-free water.</p><p>PCR products were visualised by electrophoresis in 1 % agarose gels stained with SYBR Safe DNA Gel Stain (Invitrogen, Eugene, OR, USA). Excess primers and dNTPs were removed from PCR amplification mixtures with ExoSAP-IT (USB Corp., Cleveland, OH, USA) according to the manufacturer’s instructions. Amplicons were sequenced using the BigDye Terminator v. 3.1 cycle sequencing kit (Life Technologies, Grand Island, NY, USA) on an Applied Biosystems 3130xl Genetic Analyzer using the primers used to amplify each of the gene regions (<xref ref-type="table" rid="T2">Table 2</xref>).</p></sec><sec id="s2c"><title>New primer design and PCR optimisation</title><p>Complete failure of amplification of the isolates in the <italic>D. foeniculina</italic> clade (<xref ref-type="fig" rid="F1">Fig. 1</xref>) and evidence of non-specific priming in the sequences of the CAL gene region was observed when using the CAL-228F/CAL-737R (<xref rid="R8" ref-type="bibr">Carbone & Kohn 1999</xref>) or CL1/CL2A (<xref rid="R56" ref-type="bibr">O’Donnell et al. 2000</xref>) primer sets. Additionally frequent failures of sequencing when using ACT-512F/ACT-783R (<xref rid="R8" ref-type="bibr">Carbone & Kohn 1999</xref>) were encountered in this clade. On closer inspection of ACT and CAL multiple sequence alignments for <italic>Diaporthe</italic>, non-specific binding sites were observed for both ACT-783R and CAL-228F primers (<xref rid="R8" ref-type="bibr">Carbone & Kohn 1999</xref>).</p><p>A sequence alignment consisting of both complete and partial sequences of CAL from <italic>Neurospora crassa</italic> (L02964), <italic>Pyricularia grisea</italic> (AF089808), <italic>Apiognomonia errabunda</italic> (DQ313615, DQ313596), <italic>Ophiognomonia clavigignenti-juglandacearum</italic> (GU993756), <italic>Diaporthe lusitanicae</italic> (JX197416), <italic>D. melonis</italic> (JX197417), <italic>D. ampelina</italic> (as <italic>Phomopsis viticola</italic> in GenBank) (AY745032), <italic>D. phaseolorum</italic> (JX197418, JX197419), <italic>D. rudis</italic> (JX197447), <italic>D. sclerotiodes</italic> (JX197420) and <italic>D. eres</italic> (as <italic>Phomopsis</italic> sp. OH-48 in GenBank, AY745025) was generated to design a new internal forward primer (CAL563F) located in the region corresponding to exon 4 in the <italic>N. crassa</italic> calmodulin gene (<xref ref-type="table" rid="T2">Table 2</xref>).</p><p>A sequence alignment of both complete and partial sequences of the actin gene from <italic>Neurospora crassa</italic> (U78026), <italic>Gaeumannomyces graminis</italic> (AY424309), <italic>Hypocrea orientalis</italic> (JQ238613), <italic>Magnaporthe oryzae</italic> (XM003719823), <italic>Fusarium oxysporum</italic> f. <italic>cubense</italic> (JQ965663), <italic>Thielavia terrestris</italic> (XM003649706), <italic>Nectria haematococca</italic> (XM003050001), <italic>Colletotrichum gloeosporioides</italic> f. sp. <italic>malvae</italic> (AF112537), <italic>Cleistogenes songorica</italic> (FJ972820), <italic>Verticillium alboatrum</italic> (XM003008431), <italic>Phaeosphaeria nodorum</italic> (XM001791742), <italic>Pyrenophora teres</italic> f. <italic>teres</italic> (XM003298028), <italic>Gibberella zeae</italic> (XM387511), <italic>Diaporthe neotheicola</italic> (JQ807344), <italic>D. vaccinii</italic> (JQ807322) and <italic>D. ampelina</italic> (as <italic>Phomopsis viticola</italic> in GenBank, JN230390) revealed that non-specific binding sites for the ACT-783R (<xref rid="R8" ref-type="bibr">Carbone & Kohn 1999</xref>) primer exist in <italic>Diaporthe</italic> resulting in the frequent failures of amplification and sequencing. To eliminate these problems a new reverse primer (ACT-878R) was designed. The primer combination of ACT-512F/ACT-878R was used for amplification with isolates in which amplification failed with the primer combination ACT-512F/783R in this study (<xref ref-type="table" rid="T1">Table 1</xref>).</p><p>Gradient PCR and reagent optimisations were used to develop the standard protocols for amplification of ACT and CAL genes (<xref ref-type="table" rid="T2">Table 2</xref>). Twelve reactions across an annealing temperature gradient of 50–65 °C for each of the test isolates were performed in three replicates. Optimal annealing temperatures were determined by the intensity of the amplicons visualized by agarose gel electrophoresis. Also the addition of 1 % DMSO to the PCR mix was used to enhance the reaction. Existing and newly designed primers used to amplify ACT and CAL were evaluated for thermal properties, hairpin formation and self-complementarities using the online platforms of OligoCalc (<ext-link ext-link-type="uri" xlink:href="http://www.basic.northwestern.edu/biotools/oligocalc.html">http://www.basic.northwestern.edu/biotools/oligocalc.html</ext-link>) and the Sequence Manipulation Suite (<ext-link ext-link-type="uri" xlink:href="http://www.bioinformatics.org/sms2/pcr_primer_stats.html">http://www.bioinformatics.org/sms2/pcr_primer_stats.html</ext-link>).</p></sec><sec id="s2d"><title>Sequence alignment and phylogenetic analysis</title><p>Raw sequences were assembled with Sequencer v. 4.9 for Windows (Gene Codes Corp., Ann Arbor, MI, USA). The assembled consensus sequences were initially aligned with Clustal W and optimised with MAFFT v. 7 using default settings (<ext-link ext-link-type="uri" xlink:href="http://mafft.cbrc.jp/alignment/server/">http://mafft.cbrc.jp/alignment/server/</ext-link>) and adjusted manually where necessary (<xref rid="R37" ref-type="bibr">Katoh & Standley 2013</xref>). Newly generated ITS sequences were analysed with all available type-derived sequences listed in <xref rid="R86" ref-type="bibr">Udayanga et al. (2011</xref>, <xref rid="R85" ref-type="bibr">2012a)</xref> to determine the preliminary identifications of the isolates. Sequences from isolates recognised as <italic>D. citri</italic>, <italic>D. cytosporella</italic>, <italic>D. foeniculina</italic> and <italic>D. rudis</italic> were analysed with a selected set of additional ITS sequences available in GenBank identified using the NCBIs BLAST search and authenticated by the publications where sequences were reported. To more fully resolve closely related species, single gene phylogenies were inferred for ACT, CAL, EF1-α, ITS and TUB and a selected set of isolates were subjected to a multi-gene combined analysis. Trees were rooted with <italic>D. helianthi</italic> (CBS 592.81), which was determined to fall outside of the clades included in this study (trees not shown).</p><p>PAUP v. 4.0b10 (<xref rid="R77" ref-type="bibr">Swofford 2002</xref>) was used to perform maximum parsimony analyses. Trees were inferred using the heuristic search option with 1 000 random sequence additions. Maxtrees were unlimited, branches of zero length were collapsed and all multiple equally parsimonious trees were saved. Descriptive tree statistics for parsimony (Tree Length (TL), Consistency Index (CI), Retention Index (RI), Related Consistency Index (RC) and Homoplasy Index (HI)) were calculated for trees generated in a parsimony analysis. Evolutionary models for phylogenetic analyses were selected independently for each locus using MrModeltest v. 2.3 (<xref rid="R55" ref-type="bibr">Nylander 2004</xref>) under the Akaike Information Criterion (AIC) implemented in both PAUP v. 4.0b10 and MrBayes v. 3. Phylogenetic reconstructions of concatenated and individual gene-trees were performed using both Bayesian Inference (BI) Markov Chain Monte Carlo and Maximum Likelihood (ML) criteria. Bayesian reconstructions were performed using MrBayes v. 3.1.2 (<xref rid="R33" ref-type="bibr">Huelsenbeck & Ronquist 2001</xref>). Two simultaneous analyses, each consisting of six Markov chains, were run for 1 000 000 generations with trees sampled every 100 generations resulting in 20 000 total trees. The first 2 000 trees, representing the burn-in phase of the analyses were discarded from each run and the 16 000 remaining trees were used for calculating posterior probabilities (PP).</p><p>Maximum likelihood trees were generated using the software RAxML v 7.4.2 Black Box (<xref rid="R75" ref-type="bibr">Stamatakis 2006</xref>, <xref rid="R76" ref-type="bibr">Stamatakis et al. 2008</xref>) in the CIPRES Science Gateway platform (<xref rid="R48" ref-type="bibr">Miller et al. 2010</xref>). For the combined dataset all free modal parameters were estimated by RAxML with ML estimate of 25 per site rate categories. The combined five-gene dataset was partitioned by gene region. The RAxML software accommodated the GTR model of nucleotide substitution with the additional options of modelling rate heterogeneity (Γ) and proportion invariable sites (I). These analyses utilised the rapid bootstrapping algorithm in RAxML in XSEDE high performance online computing service. Phylogenetic trees and data files were viewed in MEGA v. 5 (<xref rid="R78" ref-type="bibr">Tamura et al. 2011</xref>), TreeView v. 1.6.6 (<xref rid="R57" ref-type="bibr">Page 1996</xref>) and FigTree v. 1.4 (<xref rid="R61" ref-type="bibr">Rambaut & Drummond 2008</xref>).</p></sec><sec id="s2e"><title>Genealogical sorting index</title><p>The rooted gene genealogies resulting from each of the single gene analyses of ACT, CAL, EF1-α, ITS and TUB were submitted to the genealogical sorting index (<italic>gsi</italic>) parallel computing resource (<ext-link ext-link-type="uri" xlink:href="http://www.genealogicalsorting.org/">http://www.genealogicalsorting.org/</ext-link>) for analysis. The <italic>gsi</italic> estimates the degree of exclusive ancestry of individuals in labelled predefined groups in a rooted tree (<xref rid="R13" ref-type="bibr">Cummings et al. 2008</xref>). Values range from 0 to 1 with 0 corresponding to a lack of genealogical divergence from other groups and 1 corresponding to monophyly for the predetermined clade (or species). Each isolate was assigned to a predetermined species based on Genealogical Concordance Phylogenetic Species Recognition (GCPSR) and the <italic>gsi</italic> was calculated for the best tree selected in parsimony analysis and for all trees using 10 000 permutations (<xref rid="R13" ref-type="bibr">Cummings et al. 2008</xref>). The assignment of each tip to groups representing the recognised species was identical for the EF1-α and combined phylogenetic trees (<xref ref-type="fig" rid="F2">Fig. 2</xref>, <xref ref-type="fig" rid="F3">3</xref>). Taxa in the ITS tree that were not present in EF1-α and combined trees were not included in the calculation of <italic>gsi</italic>. The <italic>gsi</italic> and each of the probability values (P) corresponding to the species represented by more than one isolate were tabulated (<xref ref-type="table" rid="T3">Table 3</xref>). Species with one representative isolate including the outgroup were not subjected to <italic>gsi</italic> analysis. The ensemble genealogical sorting index (<italic>gsi</italic><sub>T</sub>) is the sum of the <italic>gsi</italic> values calculated for all individual gene trees (<xref ref-type="table" rid="T3">Table 3</xref>).</p><p>All the novel sequences were deposited in GenBank and the sequence alignments were submitted to TreeBASE (<ext-link ext-link-type="uri" xlink:href="http://www.treebase.org">www.treebase.org</ext-link>) as S14141 (ITS), S14146 (EF1) and S14147 (combined alignment). Taxonomic novelties (MB) and typifications (<ext-link ext-link-type="uri" xlink:href="http://www.studiesinmycology.org/cgi/external_ref?access_num=MBT175959&link_type=mb">MBT175959</ext-link>–<ext-link ext-link-type="uri" xlink:href="http://www.studiesinmycology.org/cgi/external_ref?access_num=MBT175968&link_type=mb">MBT175968</ext-link>) were registered in MycoBank (<ext-link ext-link-type="uri" xlink:href="http://www.mycobank.org">www.mycobank.org</ext-link>) (<xref rid="R12" ref-type="bibr">Crous et al. 2004</xref>).</p></sec></sec><sec id="s3"><title>RESULTS</title><sec id="s3a"><title>Phylogenetic analysis</title><p>Three hundred new sequences were generated in this study from 77 cultures (<xref ref-type="table" rid="T1">Table 1</xref>)<italic>.</italic> Other available sequences were obtained from GenBank. Six alignments were analysed corresponding to single gene analyses of ACT, CAL, EF1-α, ITS and TUB and a combined alignment of the five genes. Comparison of the alignment properties and nucleotide substitution models are provided in <xref ref-type="table" rid="T3">Table 3</xref>. Phylogenetic trees inferred from EF1-α and ITS to show the phylogenetic placement of species and a combined alignment of five genes are presented with annotations for species, host and geographic origin (<xref ref-type="fig" rid="F1">Fig. 1</xref>, <xref ref-type="fig" rid="F2">2</xref>, <xref ref-type="fig" rid="F3">3</xref>). Individual gene trees for ACT, CAL and TUB did not markedly differ from the EF1-α and ITS gene trees and are not shown.</p></sec><sec id="s3b"><title>ITS phylogenetic analysis</title><p>The ITS sequence alignment contained 126 sequences including the outgroup taxon (<xref ref-type="table" rid="T3">Table 3</xref>). Maximum parsimony analysis resulted in 45 equally most parsimonious trees (TL = 209, CI = 0.684, RI = 0.977, RC = 0.668, HI = 0.316). BI and ML trees were identical to the MP tree presented in <xref ref-type="fig" rid="F1">Fig. 1</xref>. A total of 12 clades were resolved corresponding to the species recognised as <italic>D. alleghaniensis</italic>, <italic>D. australafricana</italic>, <italic>D. canthii</italic>, <italic>D. citri</italic>, <italic>D. cotoneastri</italic>, <italic>D. cytosporella</italic>, <italic>D. foeniculina</italic>, <italic>D. pterocarpi</italic>, <italic>D. pterocarpicola</italic>, <italic>D. rudis</italic>, <italic>D. thunbergii</italic> and <italic>D. vaccinii</italic>. <italic>Diaporthe cynaroidis</italic> was not resolved as distinct from <italic>D. rudis</italic>. Among the major clades of interest in this study, the <italic>D. foeniculina</italic> clade consists of 48 isolates derived from 21 different hosts in ten countries representing the geographic regions of Australia, Europe, New Zealand, northern South America and South Africa. The isolates from <italic>Citrus</italic> in this clade originated from California (USA), Spain and New Zealand. The ex-type of <italic>D. rhusicola</italic> is also placed within the <italic>D. foeniculina</italic> clade. <italic>Diaporthe cytosporella</italic> is represented by four isolates from <italic>Citrus</italic> in Spain and <italic>Citrus</italic> and <italic>Vitis</italic> in California (USA). <italic>Diaporthe rudis</italic> comprises 34 isolates derived from 18 different hosts from 13 countries representing the geographic regions of Canada, Europe, New Zealand, South America and South Africa, including the epitype culture of <italic>D. viticola</italic>. No isolates of <italic>D. rudis</italic> were reported from <italic>Citrus</italic>. Isolates identified here as <italic>D. citri</italic> include 19 from various <italic>Citrus</italic> spp. in China, Korea, New Zealand and the United States (Florida and Texas).</p></sec><sec id="s3c"><title>EF1-α phylogenetic analysis</title><p>The EF1-α data matrix contained 77 sequences including the outgroup and consisted of 429 characters including gaps (<xref ref-type="table" rid="T3">Table 3</xref>). Maximum parsimony analysis yielded a single most parsimonious tree and is presented here as <xref ref-type="fig" rid="F2">Fig. 2</xref> (TL = 442, CI = 0.742, RI = 0.964, RC = 0.715, HI = 0.258). The MP, BI and ML trees generated were identical. The closely related taxa <italic>D. foeniculina</italic> and <italic>D. cytosporella</italic> were clearly distinguished and <italic>D. rhusicola</italic> was placed within <italic>D. foeniculina</italic>. Isolates of <italic>D. australafricana</italic> including the ex-type isolate were placed within the <italic>D. rudis</italic> clade, whereas <italic>D. cynaroidis</italic>, represented by the ex-type isolate, formed a distinct branch. Inspection of EF1-α sequences of <italic>D. australafricana</italic> vs <italic>D. rudis</italic> isolates revealed two base changes including one insertion and one transversion between the two taxa.</p></sec><sec id="s3d"><title>Combined analysis of five genes</title><p>The combined data matrix consisted of 74 isolates including the outgroup with 2 033 characters included in the maximum parsimony analysis (<xref ref-type="table" rid="T3">Table 3</xref>). The maximum parsimony analysis of the alignment yielded a single most parsimonious tree presented here as <xref ref-type="fig" rid="F3">Fig. 3</xref> (TL = 1302, CI = 0.720, RI = 0.961, RC = 0.692, HI = 0.280). The MP, BI and ML trees generated were identical. A total of 13 clades were resolved in the combined phylogenetic tree. <italic>Diaporthe citri</italic> forms a sister clade to a clade containing <italic>D. cotoneastri</italic> and <italic>D. vaccinii. Diaporthe citri</italic> occurs only on <italic>Citrus</italic> in the United States and elsewhere while <italic>D. vaccinii</italic> occurs only on <italic>Vaccinium</italic> in North America. The <italic>D. rudis</italic> clade includes the taxon previously known as <italic>D. viticola</italic> represented by an ex-epitype culture (CBS 113201) and several authentic isolates previously known as <italic>D. medusaea. Diaporthe australafricana</italic> forms a well-supported clade closely related to <italic>D. rudis</italic>. The multi-gene phylogenetic tree resolves the closely related taxa <italic>D. canthii</italic>, <italic>D. cytosporella</italic>, <italic>D. foeniculina</italic> and <italic>D. pterocarpi</italic>. The ex-type of <italic>D. rhusicola</italic> is placed within the <italic>D. foeniculina</italic> clade. <italic>Diaporthe cytosporella</italic>, <italic>D. foeniculina</italic> and <italic>D. pterocarpi</italic> are all found to occur on multiple, unrelated hosts. <italic>Diaporthe canthii</italic>, represented by a single isolate, is known only from its type host.</p></sec><sec id="s3e"><title>Analysis of gsi data</title><p>All <italic>gsi</italic> values were in range of 0.5–1.0 with the exception of TUB (0.4482) for <italic>D. cytosporella</italic> and TUB (0.4051), CAL (0.2712) and ACT (0.1187) for <italic>D. australafricana</italic> (<xref ref-type="table" rid="T4">Table 4</xref>). Despite minor variation within the ITS1 region in both <italic>D. foeniculina</italic> and <italic>D. rudis</italic>, the <italic>gsi</italic> recognised each as monophyletic for each of the genes, confirming the placement of the ex-type culture of <italic>D. rhusicola</italic> with <italic>D. foeniculina</italic>. Therefore, the observed variation in the ITS regions of these two species is not considered meaningful in terms of species distinction and does not conflict with the other gene regions. Individually, the ITS and EF1-α genes estimated significant measures of exclusive ancestry for all the species including <italic>D. australafricana</italic> and <italic>D. cytosporella</italic>. The ACT gene resolved all species as monophyletic except <italic>D. australafricana.</italic> The ensemble <italic>gsi</italic> value (<italic>gsi</italic><sub>T</sub>) for all species included indicated significant genealogical divergence from all other species in spite of the conflict observed among genes for <italic>D. australafricana</italic> and <italic>D. cytosporella</italic>. All other species resolved in the combined phylogeny were supported without conflict.</p></sec><sec id="s3f"><title>New primers for Diaporthe and protocols for amplification</title><p>The evaluation of the thermal properties of the primers by OligoCalc and Sequence Manipulation Suite revealed that the forward CAL primers, CAL-228F (<xref rid="R8" ref-type="bibr">Carbone & Kohn 1999</xref>) and CL1 (<xref rid="R56" ref-type="bibr">O’Donnell et al. 2000</xref>), showed potential for self-annealing in each of the tests in addition to issues with non-specific binding sites in the targeted gene region. The newly designed CAL-563F primer and the existing CL2A reverse primer (<xref rid="R56" ref-type="bibr">O’Donnell et al. 2000</xref>) were determined to be a suitable primer pair under the criteria given including percentage GC, self-annealing, GC clamp, hairpin formation and length. They were used to eliminate the problems in amplification and sequencing encountered in this study. Use of this primer pair resulted in an amplicon overlapping c. 300 bp of the 500-bp CAL-228F/CAL-737R fragment. However, two additional introns, each c. 60–100 bp in length, are found in the extended sequence obtained using the primers CAL-563F/CL2A. One of these informative introns in <italic>Diaporthe</italic> is not found in either of the <italic>N. crassa</italic> or <italic>P. grisea</italic> reference sequences used as references for primer design.</p><p>The newly designed reverse primer for actin (ACT-878R) worked well in combination with ACT-512F for isolates that failed with the ACT-512F/ACT-783R primer combination and resulted in an amplicon of c. 350 bp in length. The extended 3’ region of the newly generated amplicons was not included in the analyses as the majority of the sequences were generated with primer pairs ACT-512F/ACT-783R and it consisted entirely of exon sequence with little variation among isolates.</p></sec><sec id="s3g"><title>TAXONOMY</title><p>In this section we provide modern descriptions and illustrations of the species resolved here based on multi-gene phylogenetic analyses and morphological characters. <italic>Diaporthe citri</italic> occurs only on <italic>Citrus</italic> while <italic>D. cytosporella</italic> and <italic>D. foeniculina</italic> occur on <italic>Citrus</italic> and other woody and herbaceous hosts including high value crops. <italic>Diaporthe rudis</italic> is not known from <italic>Citrus</italic> but was previously confused with those species especially as <italic>D. medusaea</italic> and has a broad host range. Each species is described based on type and other specimens as well as ex-epitype cultures. Synonymous names of <italic>Diaporthe</italic> or <italic>Phomopsis</italic> are reviewed based on protologues, type and other specimens and cultures. When specimens with cultures from similar substrates and localities are available, epitype specimens with ex-epitype cultures are designated for both accepted and synonymous names.</p><p><bold><italic>Diaporthe citri</italic></bold> (H.S. Fawc.) F.A. Wolf, J. Agric. Res. 33: 625. 1926. — <xref ref-type="fig" rid="F4">Fig. 4</xref></p><p><italic>Basionym</italic>. <italic>Phomopsis citri</italic> H.S. Fawc., Phytopathology 2: 109. 1912 nom. conserv. prop. non <italic>Phomopsis citri</italic> (Sacc.) <xref rid="R84" ref-type="bibr">Traverso & Spessa 1910</xref>.</p><p>= <italic>Diaporthe citrincola</italic> Rehm, Leafl. Philipp. Bot. 6: 2269. 1914.</p><p>= <italic>Phomopsis caribaea</italic> W.T. Horne, Phytopathology 12: 417. 1922.</p><p><italic>Perithecia</italic> on decaying twigs, black, globose to conical, 130–200 μm diam, scattered, solitary or in groups, immersed deep in bark with tapering perithecial necks 190–700 μm long. <italic>Asci</italic> unitunicate, 8-spored, sessile, elongate to clavate, (37.3–)40.5–50.5(–55) × (9–)10.5–12(–12.2) μm. <italic>Ascospores</italic> hyaline, 2-celled, often 4-guttulate, with larger guttules at centre and smaller one at ends, elongated to elliptical, (12–)12.4–14(–14.2) × 3.2–3.6(–3.8) μm (av. ± SD = 13.2 ± 0.8 × 3.3 ± 0.2, n = 30). <italic>Pycnidia</italic> on alfalfa twigs on WA: globose, 200–250 μm diam, later conical, embedded in tissue, erumpent at maturity, up to 450 μm diam, 65–100 μm high, with an elongated black neck, often with a yellowish, spiral conidial cirrus extruding from ostiole; walls parenchymatous, consisting of 3–4 layers of medium brown <italic>textura angularis</italic>. <italic>Conidiophores</italic> hyaline, smooth, unbranched, ampulliform, straight to sinuous, 10–15 × 1–2 μm. <italic>Conidiogenous cells</italic> phialidic, cylindrical, terminal, slight tapering towards apex, 0.5–1 μm diam. <italic>Paraphyses</italic> abundant among conidiophores, 20–40 × 1–2 μm. <italic>Alpha conidia</italic> aseptate, hyaline, smooth, ovate to ellipsoidal, mono- to biguttulate, rarely 3-guttulate, base subtruncate, (7.6–)8–9(–10.2) × 3–4.2 μm (av. ± SD = 8.5 ± 0.8 × 3.7 ± 0.2 , n = 30). <italic>Beta</italic> and <italic>gamma conidia</italic> not observed on alfalfa twigs or in culture.</p><p>Culture characteristics — In dark at 25 °C for 1 wk, colonies on PDA slow growing, 4.2 ± 0.2 mm/day (n = 8), white, fluffy aerial mycelium, reverse centre greenish yellow pigmentation developing in centre.</p><p>Host range — Causing melanose and stem end rot disease, associated with dying or dead twigs of <italic>Citrus</italic> spp. and closely related hosts including <italic>C. aurantiifolia</italic>, <italic>C. aurantium</italic>, <italic>C. maxima</italic> (<italic>= C. grandis</italic>), <italic>C. nobilis</italic>, <italic>C. paradisi</italic>, <italic>C. reticulata</italic>, <italic>C. sinensis</italic>, <italic>C. sudachi</italic>, <italic>C. unshiu</italic>, × <italic>Citrofortunella microcarpa</italic> (= × <italic>C. mitis</italic>), <italic>Fortunella japonica</italic> (<xref rid="R40" ref-type="bibr">Kobayashi 2007</xref>), <italic>F. margarita</italic>, <italic>Poncirus trifoliata</italic>.</p><p>Distribution — Probably throughout <italic>Citrus</italic>-growing regions of the world. Reported from Brazil, China, Cuba, Japan, Korea, New Zealand, The Philippines, Puerto Rico and the United States (Florida, Texas).</p><p><italic>Type specimens examined.</italic> USA, Florida, Lake Alfred, Ana, on twigs of <italic>Citrus</italic> sp, 26 Apr. 2000, <italic>L.W. Timmer</italic>, dried specimen from culture sporulating on alfalfa stem (type of <italic>Phomopsis citri</italic> proposed for conservation in <xref rid="R67" ref-type="bibr">Rossman et al. (2013)</xref> (BPI 892456, ex-type culture AR 3405 = CBS 135422). – P<sc>HILIPPINES</sc>, Los Baños, on dead twigs of <italic>Citrus nobilis</italic>, Oct. 1913, coll. <italic>M.B. Raimundo</italic>, comm. C.F. Baker, no. 1875 (holotype of <italic>Diaporthe citrincola</italic> S-F52860). – C<sc>UBA</sc>, Isle of Pines, on <italic>Citrus paradisi</italic>, 30 Oct. 1917, <italic>Fredrick Maskew</italic>, intercepted in San Francisco, derived culture sporulating on <italic>Citrus</italic> twig (lectotype of <italic>Phomopsis caribaea</italic> designated here BPI 358328, isolectotype NY01097305; <ext-link ext-link-type="uri" xlink:href="http://www.studiesinmycology.org/cgi/external_ref?access_num=MBT175959&link_type=mb">MBT175959</ext-link>).</p><p><italic>Additional materials examined.</italic> B<sc>RAZIL</sc>, Escola Agr., Vicosa, Minas Gerais, on peel of <italic>Citrus</italic> sp., 17 May 1932, <italic>P.H. Rolfs</italic> (BPI 615855); intercepted New York #pi 7163, on fruit of <italic>Citrus sinensis</italic>, 22 June 1924, <italic>A.C. Hill</italic>, det. A.J. Bruman (BPI 358408). – J<sc>APAN</sc>, Yokohama, intercepted Seattle Washington #pi 4780, on fruit of <italic>Citrus sinensis</italic>, 14 Jan. 1940, <italic>A.G. Webb</italic>, det. J.A. Stevenson (BPI 358405). – M<sc>EXICO</sc>, intercepted Brownsville Texas #692229, on leaves of <italic>Citrus</italic> sp., 30 Jan. 1930, <italic>Mueller</italic>, det. D.J. Smith, A.E. Jenkins, J.A. Watson (BPI 615856); intercepted Laredo Texas #50818, on leaves of <italic>Citrus</italic> sp., 23 Jan. 1951, <italic>Trotter</italic>, det. A.H. Lewis, J.A. Watson (BPI 615857). – P<sc>UERTO</sc> R<sc>ICO</sc>, Bayamon, on leaves of <italic>Citrus grandis</italic>, 22 Aug. 1933, <italic>C.G. Anderson</italic> (BPI 358392). – USA, Florida, Orlando, on dead stems of <italic>Citrus aurantifolia</italic>, July 1925, <italic>F.A. Wolf</italic> (BPI 615860); Florida, Orlando, on dead stems of <italic>Citrus</italic> sp., Jan. 1926, <italic>F.A. Wolf</italic> (BPI 615959); Florida, Orlando, on leaves of <italic>Citrus sinensis</italic>, Mar. 1922, <italic>J.R. Winston</italic> (BPI358409); Florida, Eustis, on leaves of <italic>Citrus grandis</italic>, 8 Jan. 1932, <italic>H.S. Fawcett</italic> (BPI 358391); Florida, St. Nicholas, on stem of <italic>Citrus sinensis</italic>, 28 Nov. 1895, det. F. Albert, W.W. Diehl (BPI 358404); Florida, Fort Myers, on stems of <italic>Citrus sinensis</italic>, 16 Feb. 1924, <italic>J.A. Stevenson</italic> (BPI 358407); Florida, Gainesville, Florida Agricultural Experiment Station, on stems of <italic>Citrus sinensis</italic>, 16 Mar. 1910, <italic>H.S. Fawcett</italic> (BPI 358406); Florida, Winter Park, on stems of <italic>Citrus grandis</italic>, 21 Feb. 1923, <italic>C.L. Shear</italic> (BPI 615868); Florida, Winter Park, on stems of <italic>Citrus grandis</italic>, 20 Jan. 1925, <italic>H.E. Stevens</italic>, det. C.L. Shear (BPI 615869); Florida, on dead stem of <italic>Citrus</italic> sp., 1913, <italic>J.G. Grossenbacker</italic>, det. C.L. Shear (BPI 615858); Florida, on dead stem of <italic>Citrus</italic> sp., 8 July 1929, <italic>F.A. Wolf</italic>, det. C.L. Shear (BPI 615854); Florida, on leaves of <italic>Citrus grandis</italic>, 6 Jan. 1932, <italic>H.S. Fawcett</italic> (BPI 358393).</p><p>Notes — The name <italic>D. citri</italic> is based on <italic>Phomopsis citri</italic> H.S. Fawc. 1912, a later homonym of <italic>Phomopsis citri</italic> (Sacc.) <xref rid="R84" ref-type="bibr">Traverso & Spessa 1910</xref>. A conservation proposal has been published to continue the use of the widely used name for the species associated with melanose or stem end rot of <italic>Citrus</italic> as <italic>D. citri</italic> (<xref rid="R67" ref-type="bibr">Rossman et al. 2013</xref>). <italic>Diaporthe citri</italic> based on the basionym <italic>Phomopsis citri</italic> H.S. Fawc. has priority over the later synonyms <italic>D. citrincola</italic> and <italic>P. caribaea</italic>. This is also in accordance with the change to unit nomenclature with the older genus <italic>Diaporthe</italic> serving as the correct name for all species in <italic>Diaporthe-Phomopsis</italic> (<xref rid="R46" ref-type="bibr">McNeill et al. 2012</xref>). No type specimen for <italic>P. citri</italic> could be located at BPI or FLAS, leaving only an illustration (<xref rid="R20" ref-type="bibr">Fawcett 1912</xref>) as a potential, but unsatisfactory, iconotype, thus <italic>P. citri</italic> is proposed for conservation with a new type specimen (<xref rid="R67" ref-type="bibr">Rossman et al. 2013</xref>). The type specimens of <italic>D. citrincola</italic> and <italic>P. caribaea</italic> were examined and contributed to the conclusions that these names are synonyms of <italic>D. citri</italic>. A lectotype of <italic>P. caribaea</italic> is designated.</p><p>The fruiting structures of <italic>D. citri</italic> are found on dead twigs, stems and fruits of <italic>Citrus</italic> affected by melanose and stem end rot (<xref rid="R95" ref-type="bibr">Wolf 1926</xref>, <xref rid="R22" ref-type="bibr">Fawcett 1932</xref>, <xref rid="R93" ref-type="bibr">Whiteside & Timmer 2000b</xref>). The fungus generally propagates itself on dead twigs of <italic>Citrus</italic>. A few days after infecting leaf tissue or fruit, the melanose symptoms appear as small, brown, discrete or confluent, sunken spots. A few epidermal cell layers on infected tissue are killed and become impregnated with reddish brown gum that later become raised black pustules (<xref rid="R81" ref-type="bibr">Timmer 2000</xref>). Although pustules on leaves are initially surrounded by yellow halos, they recover and become green again and corky pustules are often the only symptoms (<xref rid="R3" ref-type="bibr">Bach & Wolf 1928</xref>, <xref rid="R53" ref-type="bibr">Nelson 2008</xref>). Fungal structures such as pycnidia or perithecia are never visible in these melanose lesions, therefore, the fungus cannot be observed in the infected leaves or fruit. When the fruiting structures are present on dead twigs or bark of the stems, the pycnidia or ascomata are abundant deep in the tissue.</p><p><bold><italic>Diaporthe cytosporella</italic></bold> (Penz. & Sacc.) Udayanga & Castl., <italic>comb. nov.</italic> — MycoBank <ext-link ext-link-type="uri" xlink:href="http://www.studiesinmycology.org/cgi/external_ref?access_num=MB803986&link_type=mb">MB803986</ext-link>; <xref ref-type="fig" rid="F5">Fig. 5</xref>, <xref ref-type="fig" rid="F6">6</xref></p><p><italic>Basionym</italic>. <italic>Phoma cytosporella</italic> Penz. & Sacc., Fung. Agron.: 361. 1887.</p><p>≡ <italic>Phomopsis cytosporella</italic> (Penz. & Sacc.) H.S. Fawc. & H.A. Lee, Citrus diseases and their control, Ed. 1: 407. 1926.</p><p><italic>Perithecia</italic> unknown. <italic>Pycnidia</italic> on alfalfa twigs on WA: globose, 150–200 μm diam, mostly embedded in tissue and erumpent at maturity, up to 450 μm diam, 65–100 μm high, with an elongated black neck, often with a yellowish conidial cirrus extruding from ostiole; walls parenchymatous consisting of 3–4 layers of medium brown <italic>textura angularis</italic>. <italic>Paraphyses</italic> lacking. <italic>Conidiophores</italic> 7–18 × 1–2 μm, hyaline, smooth, branched or unbranched, ampulliform, cylindrical, wider at base, occurring in dense clusters. <italic>Conidiogenous cells</italic> phialidic, cylindrical, terminal, with slight tapering towards apex, 0.5–1 μm diam. <italic>Alpha conidia</italic> (6.9–)8–9(–12.6) × (2.3–)2.6–3.2 μm (av. ± SD = 8.8 ± 0.9 × 3.0 ± 0.3, n = 30), aseptate, hyaline, smooth, ovate to ellipsoidal, biguttulate or multi-guttulate, base subtruncate, occasionally larger alpha conidia present in culture and on alfalfa stems. <italic>Beta</italic> and <italic>gamma conidia</italic> not observed on alfalfa twigs or in culture.</p><p>Culture characteristics — In dark at 25 °C for 1 wk, colonies on PDA relatively slow growing, 4.0 ± 0.2 mm/day (n = 8). On PDA white, fluffy aerial mycelium, reverse with ash colour pigmentation developing in centre. In a 2-wk-old culture, clusters of black, branched stromata occurring in concentric rings with sporulating pycnidia.</p><p>Host range — <italic>Citrus limon</italic>, <italic>C. sinensis</italic> and <italic>Vitis vinifera</italic>.</p><p>Distribution — Europe (Spain, Italy), United States (California).</p><p><italic>Type specimens examined</italic>. I<sc>TALY</sc>, Rome, Modena, on <italic>Citrus limonia</italic>, Jan. 1886 (holotype of <italic>Phoma cytosporella</italic> BPI 798526). – S<sc>PAIN</sc>, on <italic>Citrus limon</italic>, <italic>M.E. Palm</italic>, dried culture (epitype of <italic>Phoma cytosporella</italic> designated here: BPI 892459, living culture FAU461 = CBS 137020; <ext-link ext-link-type="uri" xlink:href="http://www.studiesinmycology.org/cgi/external_ref?access_num=MBT175960&link_type=mb">MBT 175960</ext-link>).</p><p><italic>Additional material examined</italic>. USA, California, on twigs of <italic>Citrus sinensis</italic>, 4 Oct. 2011, <italic>A. Eskalen</italic> UCR1751, dried culture with pycnidia sporulating on alfalfa stems (BPI 892457, living culture AR5149); ibid., UCR1750, dried culture with pycnidia sporulating on alfalfa stems (BPI 892458, living culture AR5148).</p><p>Notes — <italic>Diaporthe cytosporella</italic> is phylogenetically closely related to <italic>D. foeniculina</italic> but clearly distinguished based on ITS and EF1-α sequences (<xref ref-type="fig" rid="F1">Fig. 1</xref>, <xref ref-type="fig" rid="F2">2</xref>). The species was first described from Italy and later synonymised under <italic>D. citri.</italic> Although in this study this species is primarily recognized using isolates from <italic>Citrus limon</italic> in Europe (Spain) and the United States (California), two ITS sequences (FJ94470, AY745085) from GenBank are 100 % identical suggesting that this species may also occur on <italic>Vitis</italic> and other host species in California (retrieved on 1 Feb. 2013). At maturity cultures of <italic>D. cytosporella</italic> (AR5148 and AR5149) on PDA produce distinctive black, branched stromata. Perithecia were not observed in culture. Morphological characters were highly similar among the type specimen (<xref ref-type="fig" rid="F6">Fig. 6</xref>) and the isolates used in epitype and genetically similar additional materials examined.</p><p><bold><italic>Diaporthe foeniculina</italic></bold> (Sacc.) Udayanga & Castl., <italic>comb. nov</italic>. — MycoBank <ext-link ext-link-type="uri" xlink:href="http://www.studiesinmycology.org/cgi/external_ref?access_num=MB803929&link_type=mb">MB803929</ext-link>; <xref ref-type="fig" rid="F7">Fig. 7</xref></p><p><italic>Basionym</italic>. <italic>Phoma foeniculina</italic> Sacc., Michelia 2: 95. 1880.</p><p>≡ <italic>Phomopsis foeniculina</italic> (Sacc.) Sousa da Câmara, Agron. Lusit. 9: 104. 1947.</p><p>= <italic>Diaporthe theicola</italic> Curzi, Atti Ist. Bot. Lab. Crittog. Univ. Pavia 3 Sér. 3: 60. 1927.</p><p>= <italic>Phomopsis theicola</italic> Curzi, Atti Ist. Bot. Lab. Crittog. Univ. Pavia 3 Sér. 3: 64. 1927.</p><p>= <italic>Phomopsis californica</italic> H.S. Fawc., Phytopathology 12: 419. 1922.</p><p>= <italic>Diaporthe neotheicola</italic> A.J.L. Phillips & J.M. Santos, Fung. Diversity 34: 120. 2009.</p><p>= <italic>Diaporthe rhusicola</italic> Crous, Persoonia 26: 135. 2011.</p><p><italic>Perithecia</italic> on decaying twigs black, globose to subglobose (200–)360 × 200 μm, scattered, solitary or in groups, with tapering perithecial necks barely protruding through epidermis. <italic>Asci</italic> unitunicate, 8-spored, sessile, cylindrical to clavate, (40–)50.5–60.5(–65) × 8–10(–12.2) μm. <italic>Ascospores</italic> hyaline, 2-celled, often with four guttules, larger guttules near centre and smaller ones at ends, elongated to elliptical, (9.0–)12.4–14(–15.2) × (3.2–)3.4–3.6(–5.2) μm (av. ± SD = 13.2 ± 0.8 × 3.5 ± 0.1, n = 30). <italic>Pycnidia</italic> on alfalfa twigs on WA: globose to subglobose 400–700 μm diam, erumpent at maturity, (300–)500–800(–930) μm high, with an elongated, black neck, mostly embedded in tissue, often with a yellowish, drop-like conidial cirrus extruding from ostiole; walls parenchymatous, consisting of 2–3 layers of medium brown <italic>textura angularis</italic>. <italic>Paraphyses</italic> lacking. <italic>Conidiophores</italic> hyaline, smooth, unbranched, cylindrical, straight to sinuous, 9–15(–18) × 1–2 μm. <italic>Conidiogenous cells</italic> phialidic, cylindrical, terminal, with slight taper towards apex, 0.5–1 μm diam. <italic>Alpha conidia</italic> aseptate, hyaline, smooth, ellipsoidal or fusiform, with none, two or many guttules, rarely with subtruncate base, (7.5–)8.5–9(–9.2) × (2–)2.3–2.5(–2.7) μm (av. ± SD = 8.8 ± 0.3 × 2.4 ± 0.1 μm, n = 30). <italic>Beta conidia</italic> hyaline, aseptate, eguttulate, hamate or slightly curved, abundant, base subtruncate, acute apex, (20–)22–28(–29) × (1.1–)1.4–1.6(–2) μm (av. ± SD = 25.1 ± 3.3 × 1.5 ± 0.1 μm, n = 30).</p><p>Culture characteristics — In dark at 25 °C for 1 wk, colonies on PDA slow growing, 5.2 ± 0.2 mm/day (n = 8), white, sparse aerial mycelium, greenish yellow pigmentation developing in reverse centre.</p><p>Host range — <italic>Acacia</italic>, <italic>Acer</italic>, <italic>Actinidia deliciosa</italic>, <italic>Aspalathus linearis</italic>, <italic>Bougainvillea spectabilis</italic>, <italic>Camellia sinensis</italic>, <italic>Castanea</italic>, <italic>Citrus limon</italic>, <italic>C. limonia</italic>, <italic>Crataegus</italic>, <italic>Diospyros</italic>, <italic>Foeniculum vulgare</italic>, <italic>Fuchsia</italic>, <italic>Hydrangea</italic>, <italic>Juglans</italic>, <italic>Malus</italic>, <italic>Olea</italic>, <italic>Prunus</italic>, <italic>Pyrus</italic>, <italic>Quercus</italic>, <italic>Rhus</italic>, <italic>Ribes</italic>, <italic>Vitis vinifera</italic> and <italic>Wisteria sinensis.</italic> In addition to the hosts on the specimens listed below, these hosts are represented in <xref ref-type="fig" rid="F1">Fig. 1</xref> based on the ITS phylogeny and <xref rid="R30" ref-type="bibr">Gomes et al. (2013)</xref> as <italic>D. foeniculacea</italic>.</p><p>Distribution — Argentina, Australia, Europe (Greece, Portugal, Spain, Italy), New Zealand, South Africa and USA (California).</p><p><italic>Type specimens examined</italic>. F<sc>RANCE</sc>, on stems of <italic>Foeniculum ‘arvensis’</italic>, <italic>Brunaud</italic>, cited in <xref rid="R59" ref-type="bibr">Phillips (2003)</xref> with illustration (holotype of <italic>Phoma foeniculina</italic> PAD 281 – unavailable, not examined). – P<sc>ORTUGAL</sc>, Madeira, Serra da Agua, at base of 2-yr-old stem of <italic>Foeniculum vulgare</italic>, Aug. 2001, <italic>A.J.L. Phillips</italic> (epitype of <italic>Phoma foeniculina</italic> designated here LISE 94791, ex-epitype culture from single ascospores CBS 111553 = DP0391; <ext-link ext-link-type="uri" xlink:href="http://www.studiesinmycology.org/cgi/external_ref?access_num=MBT175961&link_type=mb">MBT175961</ext-link>). – USA, California, Santa Barbara County, on dead outer bark and decaying fruit of <italic>Citrus limonia</italic>, 3 Mar. 1922, <italic>H.S. Fawcett</italic> (holotype of <italic>Phomopsis californica</italic> BPI0358313); California, San Diego, on branch of <italic>Citrus limonia</italic>, 16 Nov. 2012, <italic>Akif Eskalen</italic> (epitype of <italic>Phomopsis californica</italic> designated here BPI 892460, ex-epitype culture AR5142 = CBS135430; <ext-link ext-link-type="uri" xlink:href="http://www.studiesinmycology.org/cgi/external_ref?access_num=MBT175962&link_type=mb">MBT 175962</ext-link>). – I<sc>TALY</sc>, on <italic>Camellia sinensis</italic>, <italic>Curzi</italic>, dried culture specimen (epitype of <italic>Diaporthe theicola</italic> designated here BPI 892462, ex-epitype culture CBS 187.27, same as ex-isotype culture of <italic>Phomopsis theicola</italic>; <ext-link ext-link-type="uri" xlink:href="http://www.studiesinmycology.org/cgi/external_ref?access_num=MBT175963&link_type=mb">MBT175963</ext-link>); Illustration in Atti dell’Istituto Botanica della Universita e Laboratoria Crittogamico di Pavia 3 Sér. 3: 60 (1926) [1927] (lectotype of <italic>Phomopsis theicola</italic> designated here; <ext-link ext-link-type="uri" xlink:href="http://www.studiesinmycology.org/cgi/external_ref?access_num=MBT175964&link_type=mb">MBT175964</ext-link>). – P<sc>ORTUGAL</sc>, Évora, on <italic>Foeniculum vulgare</italic>, Nov. 2007, <italic>A.J.L. Phillips</italic> (holotype of <italic>Diaporthe neotheicola</italic> CBS-H 20131, ex-holotype culture (Di-C004/5 = CBS 123208).</p><p><italic>Additional specimens examined</italic>. P<sc>ORTUGAL</sc>, Madeira, Serra da Agua, at base of 2-yr-old stem of <italic>Foeniculum vulgarae</italic>, Aug. 2001, <italic>A.J.L. Phillips</italic> (LISE 94792 as <italic>Diaporthe foeniculacea</italic>, culture from single ascospores DP0392 = CBS 111554. – S<sc>PAIN</sc>, on fruit of <italic>Citrus limon</italic>, intercepted at Elizabeth, New Jersey, 20 Mar. 1987, <italic>C. Markham</italic> 001514, <italic>M.E. Palm</italic> (BPI 1107900, living culture MEP1289); ibid. (BPI 747926); ibid. (BPI 747927); on peel of <italic>Citrus limonia</italic>, intercepted New York #87452, 13 Nov. 1940, <italic>Hodson</italic>, <italic>E.A. Jenkins</italic> (BPI 615878); ibid., on fruit of <italic>Citrus limon</italic>, <italic>M.E. Palm</italic> (BPI 892461, culture FAU460 = CBS).</p><p>Notes — <italic>Diaporthe foeniculina</italic> is known to occur on <italic>Citrus</italic> and many other woody plants hosts in temperate and tropical regions. This species causes a stem end rot of lemandarin (<italic>Citrus limonia</italic>) in Europe and the United States (California) and was observed as a saprobe on branches of this host. As <italic>D. neotheicola</italic>, this species has been reported to cause diseases of temperate and tropical fruits from Australia, Europe and South Africa. Our results indicate that isolates from <italic>Citrus</italic> in Spain are conspecific with the type isolate of the recently described <italic>D. neotheicola</italic> from <italic>Foeniculum</italic> as well as isolates from other hosts now considered to be <italic>D. foeniculina</italic>. We reviewed the possible synonyms of this species based on available molecular data, living cultures and type specimens. The specimen deposited in LISE 94792 corresponding to the living culture CBS 111554 was selected as the epitype specimen for <italic>Phoma foeniculina</italic>, now recognised as <italic>D. foeniculina.</italic> Molecular data derived from the epitype of <italic>Phoma foeniculina</italic>, now <italic>D. foeniculina</italic>, and additional isolates show that this taxon is conspecific with the ex-type isolates of <italic>D. neotheicola</italic> and <italic>P. theicola</italic> (<xref rid="R59" ref-type="bibr">Phillips 2003</xref>, <xref rid="R70" ref-type="bibr">Santos & Phillips 2009</xref>, <xref rid="R30" ref-type="bibr">Gomes et al. 2013</xref>) as well as isolates from <italic>Citrus</italic> in Spain. The name <italic>D. neotheicola</italic> has been widely used for this taxon (<xref rid="R70" ref-type="bibr">Santos & Phillips 2009</xref>, <xref rid="R85" ref-type="bibr">Udayanga et al. 2012a</xref>, <xref rid="R80" ref-type="bibr">Thomidis et al. 2013</xref>).</p><p><italic>Phomopsis foeniculina</italic> (syn. <italic>Phoma foeniculina</italic>) was considered a synonym of <italic>D. foeniculacea</italic> (syn. <italic>Sphaeria foeniculacea</italic>) by <xref rid="R59" ref-type="bibr">Phillips (2003)</xref>. We examined the type specimen of <italic>Sphaeria foeniculacea</italic> and agree with <xref rid="R2" ref-type="bibr">von Arx & Müller (1954)</xref> who recognised this species as <italic>Guignardia foeniculacea</italic> (Mont.) Arx & E. Müll. (as <italic>G. foeniculata</italic>). <xref rid="R30" ref-type="bibr">Gomes et al. (2013)</xref> used the name <italic>D. foeniculacea</italic> to refer to this species based on <xref rid="R59" ref-type="bibr">Phillips (2003)</xref>. However, observation of type specimens of <italic>Sphaeria foeniculacea</italic> confirmed that this name cannot be applied to a species of <italic>Diaporthe</italic>. This is further explained under the excluded species.</p><p>Although type specimens of <italic>Phomopsis theicola</italic> and <italic>D. theicola</italic> could not be located, an ex-type culture of <italic>P. theicola</italic> exists as mentioned by <xref rid="R70" ref-type="bibr">Santos & Phillips (2009)</xref>. They stated that <italic>P. theicola</italic> was not the same as <italic>D. theicola</italic> based on the illustrations in the protologues of these taxa and described the name <italic>D. neotheicola</italic> for the sexual state of <italic>P. theicola</italic>, with an ex-holotype culture from <italic>Foeniculum</italic>. However, measurements of asci and ascospores in <xref rid="R14" ref-type="bibr">Curzi’s (1927)</xref> original description of <italic>D. theicola</italic> are consistent with those of <italic>D. foeniculina</italic> specimens examined in this study. We agree with the opinion of <xref rid="R14" ref-type="bibr">Curzi (1927)</xref> that <italic>D. theicola</italic> and <italic>P. theicola</italic> are known sexual and asexual states of the same fungus, simultaneously described from the same specimen and therefore here we epitypify the name <italic>D. theicola</italic> with Curzi’s ex-type culture of <italic>P. theicola</italic>.</p><p><bold><italic>Diaporthe rudis</italic></bold> (Fr.) Nitschke, Pyrenomycetes Germanici 2: 282. 1870. — <xref ref-type="fig" rid="F8">Fig. 8</xref></p><p><italic>Basionym</italic>. <italic>Sphaeria rudis</italic> Fr., Elench. Fung. (Griefswald) 2: 98. 1828.</p><p>≡ <italic>Rabenhorstia rudis</italic> (Fr.) Fr., Summa Veg. Scand., Section Post. (Stockholm): 410. 1849.</p><p>≡ <italic>Aglaospora rudis</italic> (Fr.) Tul. & C. Tul., Select. Fung. Carpol. (Paris) 2: 165. 1863.</p><p>= <italic>Phoma rudis</italic> Sacc., Michelia 1: 257. 1878.</p><p>≡<bold></bold><italic>Phomopsis rudis</italic> (Sacc.) Höhn<bold>.</bold>, Sitzungsber. Kaiserl. Akad. Wiss., Math.-Naturwiss. Cl., Abt. 1, 115: 680. 1906.</p><p>= <italic>Diaporthe faginea</italic> Sacc., Syll. Fung. 1: 619. 1882.</p><p>= <italic>Diaporthe macrostoma</italic> Nitschke, Pyrenomycetes Germanici 2: 284. 1870.</p><p>= <italic>Diaporthe medusaea</italic> Nitschke, Pyrenomycetes Germanici 2: 251. 1870.</p><p>= <italic>Diaporthe viticola</italic> Nitschke, Pyrenomycetes Germanici 2: 264. 1870.</p><p>=<italic>Diaporthe silvestris</italic> Sacc. & Berl., Atti Rev. Instit. Venet. Ser. II, 6: 737. 1885.</p><p><italic>Perithecia</italic> black, clustered, globose, 300–350 μm, with tapering perithecial necks, 200–700 μm long. Asci unitunicate, sessile, elongate to clavate, (50.3–)53.5–58.5(–59.6) × (8.9–)10.6–12(–12.3) μm. <italic>Ascospores</italic> hyaline, 2-celled, often tetra-guttulate, with larger guttules at centre and smaller at ends, elongated to clavate, (11.6–)12–14.2(–15) × (2.8–)3.5–3.7(–3.8) μm (av. ± SD = 13.2 ± 1.1 × 3.6 ± 0.1, n = 30). <italic>Pycnidia</italic> on alfalfa twigs on WA: globose 200–250 μm diam, erumpent at maturity, up to 400–500 μm diam; walls 60–150 μm diam, parenchymatous, consisting of 3–4 layers of medium brown <italic>textura angularis</italic>. <italic>Conidiophores</italic> cylindrical, hyaline, smooth, branched, ampulliform, straight to sinuous, 20–45 × 2–2.4 μm. <italic>Conidiogenous cells</italic> phialidic, cylindrical, terminal, with slight tapering towards apex, 0.5–1 μm diam. <italic>Paraphyses</italic> abundant among conidiophores 20–40 × 1–2 μm. <italic>Alpha conidia</italic> aseptate, hyaline, smooth, ovate to ellipsoidal, biguttulate, base subtruncate (6.3–)7–8(8.7) × 2–2.5 μm (av. ± SD = 7.5 ± 0.4 × 2.2 ± 0.2, n = 30). <italic>Beta conidia</italic> aseptate, hyaline, smooth, fusiform or hooked, base subtruncate, 27–31(–35.2) × (3–)3.4–3.8(–4.2) μm (av. ± SD = 29.5 ± 2 ×3.6 ± 2, n = 30). <italic>Gamma conidia</italic> aseptate, hyaline, smooth, fusiform, mostly biguttulate, base subtruncate (10–)14–15 × 1–2 μm (av. ± SD = 14.4 ± 0.2 × 1.7 ± 0.24, n = 30).</p><p>Culture characteristics — In dark at 25 °C for 1 wk, colonies on PDA relatively slow growing, 4.2 mm/day, white, fluffy aerial mycelium, reverse with yellow pigmentation developing in centre.</p><p>Host range — <italic>Acer</italic>, <italic>Asphodelus albus</italic>, <italic>Aucuba japonica</italic>, <italic>Brugmansia</italic>, <italic>Castanea</italic>, <italic>Corylus</italic>, <italic>Dipsacus fullonum</italic>, <italic>Epilobium</italic>, <italic>Eucalyptus</italic>, <italic>Fagus</italic>, <italic>Fraxinus</italic>, <italic>Holcus</italic>, <italic>Hydrangea</italic>, <italic>Ileostylis</italic>, <italic>Laburnum</italic>, <italic>Lupinus</italic>, <italic>Malus</italic>, <italic>Protea</italic>, <italic>Pyrus</italic>, <italic>Rosa</italic>, <italic>Sambucus</italic>, <italic>Salix</italic>, <italic>Vaccinium</italic> and <italic>Vitis vinifera.</italic> In addition to the hosts on the specimens listed below, these hosts are represented in <xref ref-type="fig" rid="F1">Fig. 1</xref> based on ITS phylogeny and <xref rid="R30" ref-type="bibr">Gomes et al. (2013)</xref> as <italic>D. viticola</italic>.</p><p>Distribution — Australia, Canada, Chile, Europe (Austria, Germany, Italy, Latvia, Portugal, Spain, Sweden, Switzerland), New Zealand and South Africa.</p><p><italic>Type specimens examined</italic>. F<sc>RANCE</sc>, on a dead branch of <italic>Laburnum anagyroides</italic> (as <italic>Cytisus laburnum)</italic>, ex herb. Guépin no. 163 (holotype of <italic>Sphaeria rudis</italic> UPS F-004948). <italic>–</italic> A<sc>USTRIA</sc>, Vienna, 19. 7763/2, Reisenbergbach-Weg, on stem of <italic>Laburnum anagyroides</italic>, 8 Apr. 2000, <italic>W. Jaklitsch</italic> (epitype of <italic>Sphaeria rudis</italic> designated here BPI 748231, ex-epitype culture AR 3422 = CBS 109292; <ext-link ext-link-type="uri" xlink:href="http://www.studiesinmycology.org/cgi/external_ref?access_num=MBT175965&link_type=mb">MBT175965</ext-link>). – G<sc>ERMANY</sc>, Nordrhein-Westfalen, Landkreis Unna, Cappenberg, Schloßgarten zu Cappenberg, on twigs of <italic>Laburnum anagyroides</italic> (syn. <italic>Cytisus laburnum</italic>), 18 Aug. 1866, <italic>T. Nitschke</italic> (holotype of <italic>Diaporthe medusaea</italic> B 70 0009168). – A<sc>USTRIA</sc>, Vienna, 19. 7763/2, Reisenbergbach-Weg, on stem of <italic>Laburnum anagyroides</italic>, 8 Apr. 2000, <italic>W. Jaklitsch</italic> (epitype of <italic>Diaporthe medusaea</italic> designated here BPI 748231, ex epitype culture AR3422 = CBS 109292; <ext-link ext-link-type="uri" xlink:href="http://www.studiesinmycology.org/cgi/external_ref?access_num=MBT175966&link_type=mb">MBT175966</ext-link>). – G<sc>ERMANY</sc>, Nordrhein-Westfalen, Munsterland, Munster Botanischer Garten, on thin branch of <italic>Fagus sylvatica</italic>, 18 May 1866, <italic>T. Nitschke</italic> (holotype of <italic>Diaporthe macrostoma</italic> B 70 0009167). – G<sc>ERMANY</sc>, Westfalen, Munster, bei der Wienburg, on <italic>Vitis vinifera</italic>, Feb. 1866, <italic>Nitschke</italic> (holotype of <italic>Diaporthe viticola</italic> B: not seen), ibid. (isotype BPI 797316). – P<sc>ORTUGAL</sc>, Santo Tirso, Burgaes, on <italic>Vitis vinifera</italic>,16 Feb. 1998, <italic>A.J.L. Phillips</italic> (epitype of <italic>D. viticola</italic> designated in <xref rid="R54" ref-type="bibr">van Niekerk et al. (2005)</xref> CBS-H 7950 not seen, ex-epitype culture STE-U 5683 = CBS 113201). – I<sc>TALY</sc>, “In sarmentis <italic>Vitis viniferae silvestris</italic>, <italic>Cervarese</italic>” (holotype of <italic>Diaporthe silvestris</italic>: PAD 228 not seen). The synonymy of this name is based on <xref rid="R54" ref-type="bibr">van Niekerk et al. (2005)</xref> in which the holotype specimen was observed and considered to be <italic>D. viticola.</italic></p><p><italic>Additional specimens examined</italic>. A<sc>USTRIA</sc>, Vienna, stem of <italic>Rosa canina</italic>, 13 May 2001, <italic>W. Jaklitsch</italic> (BPI 840948, living culture AR3654); Vienna, stem of <italic>Acer pseudoplatanus</italic>, 31 Mar. 2001, <italic>W. Jaklitsch</italic> (BPI840940, living culture AR3634). – G<sc>ERMANY</sc>, urban residential area, container plant, dead stem of <italic>Brugmansia</italic> sp., 31 Oct. 2012, <italic>R. Schumacher</italic> (BPI 892463, living culture DA243 = CBS135435). – I<sc>TALY</sc>, on dead stem of <italic>Acer opalus</italic>, 2 May 2012, <italic>E. Camporesi</italic> ER285 (BPI 892464, living culture ER285A = CBS 135437); ibid., (ER 286, BPI 892465, living culture ER286D).</p><p>Notes — The name <italic>D. rudis</italic> is based on the oldest epithet of the many synonyms for this species including <italic>D. medusaea</italic>. <italic>Diaporthe medusaea</italic>, originally described from <italic>Laburnum anagyroides</italic> in Germany, has been used as the name for the fungus causing melanose and stem end rot of <italic>Citrus</italic> in North America. We observed holotype material as well as isolates on the same host from Austria in order to recognise the similarities or differences as discussed herein. <xref rid="R89" ref-type="bibr">Wehmeyer (1933)</xref> listed a number of synonyms for <italic>D. medusaea</italic> including <italic>D. citri</italic>, <italic>D. citrincola</italic>, <italic>D. faginea</italic>, <italic>D. rudis</italic> and <italic>D. viticola</italic>. <italic>Diaporthe citrincola</italic> is here recognised as a synonym of <italic>D. citri. Diaporthe faginea</italic> was established as a legitimate name for <italic>Sphaeria faginea</italic> Curr., Trans. Linn. Soc. London 22: 281. 1859 nom. illeg. non <italic>S. faginea</italic> Pers. 1794. No specimen as <italic>D. faginea</italic> exists in PAD. Based on an ITS sequence (EF155490) of the isolate from <italic>Fagus</italic> in Germany and a morphological comparison of the protologue, this name is accepted as a synonym of <italic>D. rudis</italic>. Although <italic>D. viticola</italic> was recognised as a distinct taxon and characterised and epitypified using a specimen on <italic>Vitis</italic> by <xref rid="R54" ref-type="bibr">van Niekerk et al. (2005)</xref>, it is here determined to be a synonym of <italic>D. rudis</italic>.</p></sec></sec><sec id="s4"><title>EXCLUDED SPECIES</title><p><bold><italic>Phoma citri</italic></bold> Sacc., Nuovo Giorn. Bot. Ital. 8: 200. 1876.</p><p>≡ <italic>Phomopsis citri</italic> (Sacc.) Traverso & Spessa, Bol. Soc. Brot. 25: 100. 1910.</p><p>I<sc>TALY</sc>, Traviso, a Vittorio, on branches of <italic>Citrus limon</italic>, Oct. 1873 (lectotype specimen of <italic>Phoma citri</italic> designated here, Mycotheca Veneto no. 332, FH labelled <italic>Diplodia citri</italic>; <ext-link ext-link-type="uri" xlink:href="http://www.studiesinmycology.org/cgi/external_ref?access_num=MBT175967&link_type=mb">MBT175967</ext-link>).</p><p>Notes — <italic>Phoma citri</italic> has been confused with <italic>Phomopsis citri</italic>, now regarded as <italic>Diaporthe citri</italic>. Examination of type material of <italic>Phoma citri</italic> confirms that this taxon is not a <italic>Phomopsis</italic> and should be treated as a distinct taxon in the genus <italic>Phoma</italic>.</p><p><bold><italic>Diaporthe foeniculacea</italic></bold> (Mont.) Niessl, in Thüm., Inst. Rev. Sci. Litt. Coimbra 27: 250. 1879.</p><p><italic>Basionym</italic>. <italic>Sphaeria foeniculacea</italic> Mont., Ann. Sci. Nat., Bot., sér. 3, 11: 40. 1849.</p><p>≡ <italic>Physalospora foeniculacea</italic> (Mont.) Sacc. (as ‘<italic>foeniculata</italic>’), Syll. Fung. (Abellini) 1: 445. 1882.</p><p>≡ <italic>Sphaerella foeniculacea</italic> (Mont.) Cooke (as ‘<italic>foeniculata</italic>’), J. Bot. London 21: 70. 1883.</p><p>≡ <italic>Guignardia foeniculacea</italic> (Mont.) Arx & E. Müll. (as ‘<italic>foeniculata</italic>’), Beitr. Kryptogamenfl. Schweiz 11 (no. 1): 48. 1954.</p><p>P<sc>ORTUGAL</sc>, Coimbra, on stem of <italic>Foeniculum officinalis</italic>, June 1881, (lectotype specimen of <italic>Sphaeria foeniculacea</italic> designated here: in Thümen, Mycotheca Universalis 2260, bound collection in BPI; <ext-link ext-link-type="uri" xlink:href="http://www.studiesinmycology.org/cgi/external_ref?access_num=MBT175968&link_type=mb">MBT175968</ext-link>). Isolectotypes: ibid<italic>.</italic> (BPI 616247, BPI 797288 Shear Types and Rarities).</p><p>Notes — One of the names mentioned in <xref rid="R59" ref-type="bibr">Phillips (2003)</xref> is <italic>Diaporthe foeniculacea</italic> (Mont.) Niessl (basionym <italic>Sphaeria foeniculacea</italic> Mont.), a name that has been confused with <italic>Phomopsis foeniculina</italic> (basionym <italic>Phoma foeniculina</italic>). We observed three isotype specimens of <italic>D. foeniculacea</italic> in BPI and confirmed the status of this species as a <italic>Guignardia</italic> (sexual morph of <italic>Phyllosticta</italic>) as suggested by <xref rid="R2" ref-type="bibr">von Arx & Müller (1954)</xref>, unrelated to <italic>Diaporthe</italic>. One of these specimens is here designated the lectotype.</p></sec><sec id="s5"><title>DISCUSSION</title><p>Melanose and stem end rot of <italic>Citrus</italic> have been reported from the United States since the late 18th century killing twigs and causing a minor form of gummosis by latent infection (<xref rid="R25" ref-type="bibr">Floyd & Stevens 1912</xref>, <xref rid="R23" ref-type="bibr">Fawcett 1936</xref>). A disease of <italic>Citrus</italic> to which the common name melanose is applied was first recognised near Citra, Florida, by Swingle & Webber in 1892 (<xref rid="R25" ref-type="bibr">Floyd & Stevens 1912</xref>). The stem end rot disease was investigated in Florida by <xref rid="R5" ref-type="bibr">Burger (1923)</xref> and <xref rid="R94" ref-type="bibr">Winston et al. (1923)</xref>. <italic>Phomopsis citri</italic> was first described from the United States (Florida) as a pycnidial fungus on dead branches and decayed fruits of <italic>Citrus aurantium</italic>, <italic>C. decumana</italic> and <italic>C. nobilis</italic> (<xref rid="R20" ref-type="bibr">Fawcett 1912</xref>). This name is a later homonym of <italic>Phomopsis citri</italic> (Sacc.) <xref rid="R84" ref-type="bibr">Traverso & Spessa (1910)</xref> based on <italic>Phoma citri</italic> Sacc. (1876) originally described from <italic>Citrus limonia</italic> in Italy and now considered to belong in <italic>Phoma</italic>. <italic>Diaporthe citri</italic> (H.S. Fawc.) F.A. Wolf, described as sexual morph of <italic>Phomopsis citri</italic> H.S. Fawc., was originally collected from the United States (Florida) and has since been reported as saprobic or parasitic on leaves, stems and fruits of <italic>Citrus</italic> spp. throughout the world. <xref rid="R24" ref-type="bibr">Fisher (1972)</xref> used the concept of <xref rid="R89" ref-type="bibr">Wehmeyer (1933)</xref> and considered <italic>Phomopsis cytosporella</italic> as the valid name for <italic>D. citri</italic> based on the chronology of names. However, this interpretation was not adopted by plant pathologists or taxonomists. In our study <italic>P. cytosporella</italic> is determined to be a distinct taxon in <italic>Diaporthe</italic>, <italic>D. cytosporella</italic>, and epitypified based on fresh collections from Europe.</p><p>In addition to the association with <italic>Citrus</italic> in the United States, <italic>Diaporthe citri</italic> is confirmed here in Brazil, China, Korea and New Zealand and appears to be widespread in Asia, Australasia and South America. Based on sampling in this study, we did not find <italic>D. citri</italic> to occur in Europe or any sequences in public databases corresponding to <italic>D. citri</italic> from Europe. However, our results suggest that this species may be pantropical. The genetic similarities of the isolates of <italic>D. citri</italic> from Asia where <italic>Citrus</italic> originated with those found worldwide suggest a long standing co-existence and the probable widespread movement of the pathogen with its host. <italic>Diaporthe citri</italic> was the dominant species causing melanose and stem end rot symptoms among the recent collections from <italic>Citrus</italic> spp. throughout China (<xref rid="R32" ref-type="bibr">Huang et al. 2013</xref>). Two newly described species discovered in north central China (Shaanxi Province) in the same study, <italic>Diaporthe citiasiana</italic> and <italic>D. citrichinensis</italic>, were primarily associated with dead wood of <italic>Citrus unshiu</italic> (satsuma mandarin) and not with melanose and stem end rot diseases. <xref rid="R30" ref-type="bibr">Gomes et al. (2013)</xref> included two species from <italic>Citrus</italic> from Suriname in their analysis, <italic>Diaporthe arecae</italic> and an unidentified species. None of these species were encountered in this study. This indicates that numerous species are associated with <italic>Citrus</italic> worldwide and it is likely that more will be discovered.</p><p><italic>Diaporthe foeniculina</italic> (referred to as <italic>D. foeniculacea</italic> in <xref rid="R30" ref-type="bibr">Gomes et al. 2013</xref>, see taxonomy section) is found to be a pathogen of diverse hosts ranging from crops to temperate woody plants and fruit trees. The recent reports of <italic>D. foeniculina</italic> (as <italic>D. neotheicola</italic>) causing diseases of temperate cultivated fruit trees including shoot blight of persimmon in Australia and kiwifruit disease in Greece suggest potential for this species to infect a wide range of fruits as an opportunistic pathogen (<xref rid="R29" ref-type="bibr">Golzar et al. 2012</xref>, <xref rid="R80" ref-type="bibr">Thomidis et al. 2013</xref>). Although a number of isolates from <italic>Citrus</italic> in California are identified in this study as <italic>D. foeniculina</italic>, its pathogenicity on <italic>Citrus</italic> in California is unknown. Herbarium specimens previously identified as <italic>D. citri</italic> intercepted at ports in the United States on the fruits of <italic>Citrus limonia</italic> from Spain were identified morphologically as <italic>D. foeniculina</italic> (BPI 615878: intercepted in New York, 1940; BPI 747926, BPI 747927, BPI 1107900: intercepted in New Jersey, 1987). A living culture (MEP1289-1) from BPI 1107900 was used in the phylogenetic analyses in this study and is confirmed as <italic>D. foeniculina</italic>.</p><p>Phylogenetic analysis of ITS sequence data was able to resolve the closely related species <italic>D. canthii</italic>, <italic>D. cytosporella</italic>, <italic>D. foeniculina</italic> and <italic>D. pterocarpi</italic>. Although the ITS sequence analysis resolved a clade corresponding to the recently described <italic>D. rhusicola</italic>, this clade was not supported by the ACT, CAL, EF1-α or TUB gene regions, individually or in the multi-gene phylogeny. Inspection of the ITS sequences for this group of isolates (<italic>D. foeniculina</italic> and <italic>D. rhusicola</italic>) indicated that the ITS differences consisted of two deletions and one transition in the ITS1 and two transitions in the ITS2 region. Alternatively, in the case of <italic>D. cynaroidis</italic> and <italic>D. rudis</italic>, ITS sequences do not definitively distinguish the two species although EF1-α, CAL, HIS and TUB do distinguish the two species.</p><p>In the case of <italic>D. rudis</italic> (referred to as <italic>D. viticola</italic> in <xref rid="R54" ref-type="bibr">van Niekerk et al. 2005</xref> and <xref rid="R30" ref-type="bibr">Gomes et al. 2013</xref>) and <italic>D. australafricana</italic>, the ITS1 region differs by a single transition while the ITS2 region shows minor differences over a span of c. 7 bp consisting of three transitions, one transversion and one deletion. The CAL gene differs by one transition and isolates of <italic>D. rudis</italic> share a 9 bp insertion in ACT not found in <italic>D. australafricana</italic>. Data from <xref rid="R30" ref-type="bibr">Gomes et al. (2013)</xref> show a 3 bp insertion in isolates of <italic>D. australafricana</italic> not shared by <italic>D. rudis</italic> in HIS. Isolates with ITS sequences matching that of <italic>D. australafricana</italic> were previously only known from Africa and Australia on <italic>Vitis</italic> but have recently been found on <italic>Vaccinium</italic> and <italic>Corylus</italic> in Chile and <italic>Persea</italic> from California in the United States (<xref rid="R43" ref-type="bibr">Latorre et al. 2012</xref>, <xref rid="R17" ref-type="bibr">Elfar et al. 2013</xref>). Although closely related, the low but consistent variation found in the sampled genes is considered sufficient to recognise <italic>D. australafricana</italic> as a distinct phylogenetic species in agreement with <xref rid="R54" ref-type="bibr">van Niekerk et al. (2005)</xref>, <xref rid="R85" ref-type="bibr">Udayanga et al. (2012a)</xref> and <xref rid="R30" ref-type="bibr">Gomes et al. (2013)</xref>. However, additional isolates of both taxa would be desirable in order to further investigate population structure and species boundaries.</p><p>Much confusion in the literature exists in how to interpret the ITS sequences of closely related species in <italic>Diaporthe</italic> and authors treat observed variation in ITS sequences in different ways (<xref rid="R18" ref-type="bibr">Farr et al. 2002a</xref>, <xref rid="R19" ref-type="bibr">b</xref>, <xref rid="R52" ref-type="bibr">Murali et al. 2006</xref>, <xref rid="R69" ref-type="bibr">Santos et al. 2010</xref>). This can result in superfluous, multiple terminal branches in combined gene analyses, even when other gene regions do not support these distinctions. Additionally <xref rid="R69" ref-type="bibr">Santos et al. (2010)</xref> showed the occurrence of two phylogenetically distinct ITS populations within an unidentified species of <italic>Diaporthe</italic> based on the sequencing of single ascospore-derived isolates from the same perithecium. Sequence differences were confined to the ITS1 region over a span of c. 40 bp and are more extensive than those differences noted among isolates of a single species in this study. Sequence differences were not noted in the EF1-α and mating type genes in their analyses and the isolates were fully reproductively compatible (<xref rid="R69" ref-type="bibr">Santos et al. 2010</xref>).</p><p>While we consider ITS rDNA sequences to be useful as barcodes for identification of known, circumscribed <italic>Diaporthe</italic> species, we suggest that caution is warranted when differences are noted in the absence of other data and that at the minimum EF1-α should be used to confirm identities of <italic>Diaporthe</italic> species. The EF1-α gene region amplified by primers EF1-728F/EF1-986R has given the most consistent results when analysing available ex-type sequences of reliably identified and vouchered species (<xref rid="R9" ref-type="bibr">Castlebury 2005</xref>, <xref rid="R69" ref-type="bibr">Santos et al. 2010</xref>, <xref rid="R71" ref-type="bibr">2011</xref>, <xref rid="R85" ref-type="bibr">Udayanga et al. 2012a</xref>). Phylogenetic signals observed in protein coding genes are generally considered superior to rRNA genes, although there is less standardisation in terms of universal primers, genes or even regions of genes sequenced for fungi (<xref rid="R72" ref-type="bibr">Schoch et al. 2012</xref>). However, results from this study suggest that use of CAL and TUB genes can be problematic with the potential for incorrect species identification in <italic>Diaporthe</italic> due to non-specific priming and the resulting poor sequence quality (CAL) or potential paralogy (TUB), necessitating critical evaluation of sources of conflict in gene trees.</p><p>Epitypification is recognised as the best approach to resolve long standing taxonomic and phylogenetic issues of known taxa that are poorly circumscribed, thus providing a modern interpretive type (<xref rid="R36" ref-type="bibr">Hyde & Zhang 2008</xref>). There is an unprecedented need for mycologists to return to the field to recollect species, fully characterise taxa with DNA sequences and morphological descriptions and epitypify species in <italic>Diaporthe</italic>, which includes a large number of names not linked to DNA sequence data or ex-type cultures (<xref rid="R34" ref-type="bibr">Hyde et al. 2010a</xref>, <xref rid="R35" ref-type="bibr">b</xref>, <xref rid="R38" ref-type="bibr">Ko-Ko et al. 2011</xref>, <xref rid="R86" ref-type="bibr">Udayanga et al. 2011</xref>). Several modern studies aimed at epitypification of important pathogens in <italic>Diaporthe</italic> provide clarification and knowledge of the phylogeny and species boundaries within the genus (<xref rid="R10" ref-type="bibr">Castlebury et al. 2003</xref>, <xref rid="R54" ref-type="bibr">van Niekerk et al. 2005</xref>, <xref rid="R65" ref-type="bibr">Rensburg et al. 2006</xref>, <xref rid="R16" ref-type="bibr">Diogo et al. 2010</xref>, <xref rid="R87" ref-type="bibr">Udayanga et al. 2012b</xref>, <xref rid="R30" ref-type="bibr">Gomes et al. 2013</xref>). Application of genealogical concordance and/or <italic>gsi</italic> in combination with epitypification can provide critical insights into speciation processes, ecology and host associations (<xref rid="R68" ref-type="bibr">Sakalidis et al. 2011</xref>, <xref rid="R27" ref-type="bibr">Gazis et al. 2011</xref>, <xref rid="R47" ref-type="bibr">Mejia et al. 2011</xref>, <xref rid="R74" ref-type="bibr">Silva et al. 2012</xref>, <xref rid="R88" ref-type="bibr">Walker et al. 2012</xref>).</p><p>Species circumscription should only be undertaken in conjunction with rigorous application of multi-gene analyses and genealogical concordance. In addition best practices for introduction of new names should require a thorough investigation of existing names and type specimens. This is particularly important to prevent additional superfluous names in a genus such as <italic>Diaporthe</italic> with an abundance of existing names including those in <italic>Phomopsis.</italic> A total of 2 453 results are returned when searching for <italic>Diaporthe</italic> and <italic>Phomopsis</italic> ITS sequences in the NCBI GenBank databases. A search using the terms ‘Phomopsis sp.’ (Organism) AND ‘internal transcribed’ (All Fields) returned 922 sequences; substituting ‘Diaporthe sp.’ returned 341 sequences (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov">http://www.ncbi.nlm.nih.gov</ext-link>, retrieved 3 April 2013), which suggests that c. 51 % of all <italic>Diaporthe</italic> and <italic>Phomopsis</italic> ITS sequences in GenBank are unidentified. Of the 49 % that do have species names, many do not include culture or specimen vouchers and it is likely that the majority are misidentified or named without a proper taxonomic revision. As sequence data accumulate in public databases, the need for correctly identifying and vouchering sequences, particularly from ex-type or epitype cultures, becomes pressing as these data are being used for identification of pathogens by plant pathologists and in public health and quarantine situations.</p></sec></body><back><ack><p>The following individuals are thanked for sharing cultures, specimens and unpublished sequence data: Aaron Kennedy, John McKemy and Mary Palm (USDA-APHIS); Akif Eskalen and Joey Mayorquin (Fawcett Laboratory of University of California Riverside, CA); Peter Johnston and Bevan Weir (Landcare Research, New Zealand); Erio Camporesi (Italy, Asco-France); Sung Kee Hong (Korea); Rene Schumacher (Germany); and Walter Jaklitsch (University of Vienna, Austria). Herbarium curators and managers of B, BPI, FH, LISE, NY and S are gratefully acknowledged for loan of specimens. 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MP/RAxML bootstrap values/Bayesian posterior probabilities ≥ 70 % are displayed above or below each branch. Ex-type and ex-epitype culture numbers are in <bold>bold</bold>. GenBank accessions are given for downloaded sequences and isolate codes for the newly generated sequences annotated with host and location. Isolates from <italic>Citrus</italic> are indicated in green. ITS sequences obtained from GenBank verified as <italic>D. cytosporella</italic>, <italic>D. foeniculina</italic> and <italic>D. rudis</italic> are indicated with an asterisk. The tree is rooted with <italic>D. helianthi</italic> (CBS 592.81).</p></caption><graphic xlink:href="per-32-83-g001"></graphic></fig><fig id="F2" orientation="portrait" position="float"><label>Fig. 2</label><caption><p>The single most parsimonious tree generated from the analysis of the EF1-α sequence alignment. MP/RAxML bootstrap values/Bayesian posterior probabilities ≥ 70 % are displayed above or below each branch. Ex-type and ex-epitype culture numbers are in <bold>bold</bold>. GenBank accessions are given for downloaded sequences and isolate codes for the newly generated sequences annotated with host and location. Isolates from <italic>Citrus</italic> are indicated in green. The tree is rooted with <italic>D. helianthi</italic> (CBS 592.81)</p></caption><graphic xlink:href="per-32-83-g002"></graphic></fig><fig id="F3" orientation="portrait" position="float"><label>Fig. 3</label><caption><p>The single most parsimonious tree generated from the analysis of the combined ACT, CAL, EF1-α, ITS and TUB sequence alignment. MP/RAxML bootstrap values/Bayesian posterior probabilities ≥ 70 % are displayed above or below each branch. Ex-type and ex-epitype culture numbers are in <bold>bold</bold>. GenBank accessions are given for the downloaded sequences and isolate codes for the newly generated sequences annotated with host and location. Isolates from <italic>Citrus</italic> are indicated in green. Red squares indicate the epitypes designated in this study including the conserved ex-type of <italic>Diaporthe citri</italic> in <xref rid="R67" ref-type="bibr">Rossman et al. (2013)</xref>. The tree is rooted with <italic>D. helianthi</italic> (CBS 592.81)</p></caption><graphic xlink:href="per-32-83-g003"></graphic></fig><fig id="F4" orientation="portrait" position="float"><label>Fig. 4</label><caption><p><italic>Diaporthe citri</italic> (ex-epitype culture AR3405 = CBS 135422). a. Sporulation on alfalfa stem in WA; b. culture on PDA (25 °C, dark, 7 d); c. pycnidial walls lined with paraphyses and conidiophores; d. section through conidiomata; e. conidiophores; f. alpha conidia; g. germinating conidia on a slide. — Scale bars: a = 500 μm; c = 20 μm; d–g = 10 μm.</p></caption><graphic xlink:href="per-32-83-g004"></graphic></fig><fig id="F5" orientation="portrait" position="float"><label>Fig. 5</label><caption><p><italic>Diaporthe cytosporella</italic> (AR5149). a. Sporulating pycnidia on alfalfa stem; b. culture on PDA (25 °C, dark, 7 d); c. concentric pycnidial in rings on culture; d. pycnidia on culture; e. conidiophores; f. alpha conidia. — Scale bars: a, c = 2 000 μm; d = 3 000 μm; e, f = 20 μm.</p></caption><graphic xlink:href="per-32-83-g005"></graphic></fig><fig id="F6" orientation="portrait" position="float"><label>Fig. 6</label><caption><p>Holotype specimen of <italic>Diaporthe cytosporella</italic> (BPI 798526). a. Pycnidia-bearing bark of <italic>Citrus</italic> sp.; b. branched stroma and sporulating pycnidia; c. section through pycnidia with pycnidial wall and conidiophores; d. alpha conidia. — Scale bars: a = 1 000 μm; b = 50 μm; c, d = 15 μm.</p></caption><graphic xlink:href="per-32-83-g006"></graphic></fig><fig id="F7" orientation="portrait" position="float"><label>Fig. 7</label><caption><p><italic>Diaporthe foeniculina</italic> (ex-epitype culture DP0391 = CBS 111553). a. Sporulation on alfalfa stem in WA; b. culture on PDA (25 °C, dark, 7 d); c. conidiophores; d. alpha conidia; e. beta conidia. — Scale bars: a = 2 000 μm; all others = 10 μm.</p></caption><graphic xlink:href="per-32-83-g007"></graphic></fig><fig id="F8" orientation="portrait" position="float"><label>Fig. 8</label><caption><p><italic>Diaporthe rudis</italic>. a, b. Ectostroma and perithecia on <italic>Laburnum anagyroides</italic>; c. perithecia in transverse section; d. perithecial wall in longitudinal section; e, f. perithecia in longitudinal section; g–j. asci; k. ascospores; l. conidiophores developing on alfalfa stem in culture; m. alpha and beta conidia developing on alfalfa stem in culture (a–k. Epitype specimen BPI 748231; l–n. ex-epitype culture AR3422 = CBS 109292). — Scale bars: a = 2 000 μm; b, c = 1 000 μm; d = 50 μm; e, f = 100 μm; g–k = 25 μm; l–n = 15 μm.</p></caption><graphic xlink:href="per-32-83-g008"></graphic></fig><table-wrap id="T1" orientation="portrait" position="float"><label>Table 1</label><caption><p>Isolates used and genes sequenced in this study.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">Species</th><th align="left" rowspan="1" colspan="1">Isolate no.<xref ref-type="table-fn" rid="tfn1"><sup>1</sup></xref></th><th align="left" rowspan="1" colspan="1">Host</th><th align="left" rowspan="1" colspan="1">Origin</th><th align="left" rowspan="1" colspan="1">Collector/contributor</th><th align="center" colspan="5" rowspan="1">GenBank accession no.<hr></hr></th></tr><tr><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1">ITS</th><th align="left" rowspan="1" colspan="1">EF 1-α</th><th align="left" rowspan="1" colspan="1">TUB</th><th align="left" rowspan="1" colspan="1">ACT</th><th align="left" rowspan="1" colspan="1">CAL</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"><italic>D. alleghaniensis</italic></td><td align="left" rowspan="1" colspan="1">CBS 495.72<xref ref-type="table-fn" rid="tfn2">*</xref></td><td align="left" rowspan="1" colspan="1"><italic>Betula alleghaniensis</italic></td><td align="left" rowspan="1" colspan="1">Canada: Ontario</td><td align="left" rowspan="1" colspan="1">R. Arnold</td><td align="left" rowspan="1" colspan="1">FJ889444</td><td align="left" rowspan="1" colspan="1">GQ250298</td><td align="left" rowspan="1" colspan="1">KC843228</td><td align="left" rowspan="1" colspan="1">JQ807299</td><td align="left" rowspan="1" colspan="1">KC343249</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. australafricana</italic></td><td align="left" rowspan="1" colspan="1">CBS 113487<xref ref-type="table-fn" rid="tfn2">*</xref></td><td align="left" rowspan="1" colspan="1"><italic>Vitis vinifera</italic></td><td align="left" rowspan="1" colspan="1">South Africa</td><td align="left" rowspan="1" colspan="1">L. Mostert</td><td align="left" rowspan="1" colspan="1">KC343039</td><td align="left" rowspan="1" colspan="1">KC843099</td><td align="left" rowspan="1" colspan="1">JX275457</td><td align="left" rowspan="1" colspan="1">KC843265</td><td align="left" rowspan="1" colspan="1">JX197448</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">CBS 111886</td><td align="left" rowspan="1" colspan="1"><italic>Vitis vinifera</italic></td><td align="left" rowspan="1" colspan="1">Australia</td><td align="left" rowspan="1" colspan="1">R.W.A. Schepers</td><td align="left" rowspan="1" colspan="1">KC343038</td><td align="left" rowspan="1" colspan="1">KC343764</td><td align="left" rowspan="1" colspan="1">KC344006</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">KC343280</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR5209 = CBS 135771</td><td align="left" rowspan="1" colspan="1"><italic>Persea americana</italic></td><td align="left" rowspan="1" colspan="1">USA: California</td><td align="left" rowspan="1" colspan="1">Akif Eskalen</td><td align="left" rowspan="1" colspan="1">KF199875</td><td align="left" rowspan="1" colspan="1">KF199877</td><td align="left" rowspan="1" colspan="1">KF199879</td><td align="left" rowspan="1" colspan="1">KF199883</td><td align="left" rowspan="1" colspan="1">KF199881</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR5210 = CBS 135772</td><td align="left" rowspan="1" colspan="1"><italic>Persea americana</italic></td><td align="left" rowspan="1" colspan="1">USA: California</td><td align="left" rowspan="1" colspan="1">Akif Eskalen</td><td align="left" rowspan="1" colspan="1">KF199876</td><td align="left" rowspan="1" colspan="1">KF199878</td><td align="left" rowspan="1" colspan="1">KF199880</td><td align="left" rowspan="1" colspan="1">KF199884</td><td align="left" rowspan="1" colspan="1">KF199882</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. canthii</italic></td><td align="left" rowspan="1" colspan="1">CBS 132533<xref ref-type="table-fn" rid="tfn2">*</xref></td><td align="left" rowspan="1" colspan="1"><italic>Canthium inerme</italic></td><td align="left" rowspan="1" colspan="1">South Africa</td><td align="left" rowspan="1" colspan="1">P.W. Crous</td><td align="left" rowspan="1" colspan="1">JX069864</td><td align="left" rowspan="1" colspan="1">KC843120</td><td align="left" rowspan="1" colspan="1">KC843230</td><td align="left" rowspan="1" colspan="1">KC843291</td><td align="left" rowspan="1" colspan="1">KC843174</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. citri</italic></td><td align="left" rowspan="1" colspan="1">AR3405<xref ref-type="table-fn" rid="tfn2">*</xref> = CBS 135422</td><td align="left" rowspan="1" colspan="1"><italic>Citrus</italic> sp.</td><td align="left" rowspan="1" colspan="1">USA: Florida</td><td align="left" rowspan="1" colspan="1">L.W. Timmer</td><td align="left" rowspan="1" colspan="1">KC843311</td><td align="left" rowspan="1" colspan="1">KC843071</td><td align="left" rowspan="1" colspan="1">KC843187</td><td align="left" rowspan="1" colspan="1">KC843234</td><td align="left" rowspan="1" colspan="1">KC843157</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR3404</td><td align="left" rowspan="1" colspan="1"><italic>Citrus</italic> sp.</td><td align="left" rowspan="1" colspan="1">USA: Florida</td><td align="left" rowspan="1" colspan="1">L.W. Timmer</td><td align="left" rowspan="1" colspan="1">KC843316</td><td align="left" rowspan="1" colspan="1">KC843076</td><td align="left" rowspan="1" colspan="1">KC843192</td><td align="left" rowspan="1" colspan="1">KC843239</td><td align="left" rowspan="1" colspan="1">KC843162</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR3406</td><td align="left" rowspan="1" colspan="1"><italic>Citrus</italic> sp.</td><td align="left" rowspan="1" colspan="1">USA: Florida</td><td align="left" rowspan="1" colspan="1">L.W. Timmer</td><td align="left" rowspan="1" colspan="1">KC843320</td><td align="left" rowspan="1" colspan="1">KC843080</td><td align="left" rowspan="1" colspan="1">KC843196</td><td align="left" rowspan="1" colspan="1">KC843243</td><td align="left" rowspan="1" colspan="1">KC843166</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR4469 = CBS 135423</td><td align="left" rowspan="1" colspan="1"><italic>Citrus</italic> sp.</td><td align="left" rowspan="1" colspan="1">USA: Florida</td><td align="left" rowspan="1" colspan="1">L.W. Timmer</td><td align="left" rowspan="1" colspan="1">KC843321</td><td align="left" rowspan="1" colspan="1">KC843081</td><td align="left" rowspan="1" colspan="1">KC843197</td><td align="left" rowspan="1" colspan="1">KC843244</td><td align="left" rowspan="1" colspan="1">KC843167</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR4470</td><td align="left" rowspan="1" colspan="1"><italic>Citrus</italic> sp.</td><td align="left" rowspan="1" colspan="1">USA: Florida</td><td align="left" rowspan="1" colspan="1">L.W. Timmer</td><td align="left" rowspan="1" colspan="1">KC843318</td><td align="left" rowspan="1" colspan="1">KC843078</td><td align="left" rowspan="1" colspan="1">KC843194</td><td align="left" rowspan="1" colspan="1">KC843241</td><td align="left" rowspan="1" colspan="1">KC843164</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR4471</td><td align="left" rowspan="1" colspan="1"><italic>Citrus</italic> sp.</td><td align="left" rowspan="1" colspan="1">USA: Florida</td><td align="left" rowspan="1" colspan="1">L.W. Timmer</td><td align="left" rowspan="1" colspan="1">KC843317</td><td align="left" rowspan="1" colspan="1">KC843077</td><td align="left" rowspan="1" colspan="1">KC843193</td><td align="left" rowspan="1" colspan="1">KC843240</td><td align="left" rowspan="1" colspan="1">KC843163</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">FAU583 = CBS 135424</td><td align="left" rowspan="1" colspan="1"><italic>Citrus paradisi</italic></td><td align="left" rowspan="1" colspan="1">USA: Florida</td><td align="left" rowspan="1" colspan="1">F.A. Uecker</td><td align="left" rowspan="1" colspan="1">KC843327</td><td align="left" rowspan="1" colspan="1">KC843087</td><td align="left" rowspan="1" colspan="1">KC843203</td><td align="left" rowspan="1" colspan="1">KC843250</td><td align="left" rowspan="1" colspan="1">KC843173</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR3403</td><td align="left" rowspan="1" colspan="1"><italic>Citrus</italic> sp.</td><td align="left" rowspan="1" colspan="1">USA: Florida</td><td align="left" rowspan="1" colspan="1">L.W. Timmer</td><td align="left" rowspan="1" colspan="1">KC843310</td><td align="left" rowspan="1" colspan="1">KC843070</td><td align="left" rowspan="1" colspan="1">KC843186</td><td align="left" rowspan="1" colspan="1">KC843233</td><td align="left" rowspan="1" colspan="1">KC843156</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR4473</td><td align="left" rowspan="1" colspan="1"><italic>Citrus</italic> sp.</td><td align="left" rowspan="1" colspan="1">USA: Florida</td><td align="left" rowspan="1" colspan="1">L.W. Timmer</td><td align="left" rowspan="1" colspan="1">KC843319</td><td align="left" rowspan="1" colspan="1">KC843079</td><td align="left" rowspan="1" colspan="1">KC843195</td><td align="left" rowspan="1" colspan="1">KC843242</td><td align="left" rowspan="1" colspan="1">KC843165</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR3407</td><td align="left" rowspan="1" colspan="1"><italic>Citrus</italic> sp.</td><td align="left" rowspan="1" colspan="1">USA: Florida</td><td align="left" rowspan="1" colspan="1">L.W. Timmer</td><td align="left" rowspan="1" colspan="1">KC843313</td><td align="left" rowspan="1" colspan="1">KC843073</td><td align="left" rowspan="1" colspan="1">KC843189</td><td align="left" rowspan="1" colspan="1">KC843236</td><td align="left" rowspan="1" colspan="1">KC843159</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR4472</td><td align="left" rowspan="1" colspan="1"><italic>Citrus</italic> sp.</td><td align="left" rowspan="1" colspan="1">USA: Florida</td><td align="left" rowspan="1" colspan="1">L.W. Timmer</td><td align="left" rowspan="1" colspan="1">KC843312</td><td align="left" rowspan="1" colspan="1">KC843072</td><td align="left" rowspan="1" colspan="1">KC843188</td><td align="left" rowspan="1" colspan="1">KC843235</td><td align="left" rowspan="1" colspan="1">KC843158</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR4364 = CBS 135425</td><td align="left" rowspan="1" colspan="1"><italic>Citrus</italic> unshiu cv. juwadeun</td><td align="left" rowspan="1" colspan="1">Korea: Odeung-dong</td><td align="left" rowspan="1" colspan="1">S.K. Hong</td><td align="left" rowspan="1" colspan="1">KC843326</td><td align="left" rowspan="1" colspan="1">KC843086</td><td align="left" rowspan="1" colspan="1">KC843202</td><td align="left" rowspan="1" colspan="1">KC843249</td><td align="left" rowspan="1" colspan="1">KC843172</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR4370 = CBS 135426</td><td align="left" rowspan="1" colspan="1"><italic>Citrus</italic> unshiu cv. juwadeun</td><td align="left" rowspan="1" colspan="1">Korea: Odeung-dong</td><td align="left" rowspan="1" colspan="1">S.K. Hong</td><td align="left" rowspan="1" colspan="1">KC843324</td><td align="left" rowspan="1" colspan="1">KC843084</td><td align="left" rowspan="1" colspan="1">KC843200</td><td align="left" rowspan="1" colspan="1">KC843247</td><td align="left" rowspan="1" colspan="1">KC843170</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR4350</td><td align="left" rowspan="1" colspan="1"><italic>Citrus</italic> unshiu cv. juwadeun</td><td align="left" rowspan="1" colspan="1">Korea: Odeung-dong</td><td align="left" rowspan="1" colspan="1">S.K. Hong</td><td align="left" rowspan="1" colspan="1">KC843325</td><td align="left" rowspan="1" colspan="1">KC843085</td><td align="left" rowspan="1" colspan="1">KC843201</td><td align="left" rowspan="1" colspan="1">KC843248</td><td align="left" rowspan="1" colspan="1">KC843171</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">CBS 135767</td><td align="left" rowspan="1" colspan="1"><italic>Citrus reticulata</italic></td><td align="left" rowspan="1" colspan="1">China</td><td align="left" rowspan="1" colspan="1">D. Udayanga</td><td align="left" rowspan="1" colspan="1">KC843322</td><td align="left" rowspan="1" colspan="1">KC843082</td><td align="left" rowspan="1" colspan="1">KC843198</td><td align="left" rowspan="1" colspan="1">KC843245</td><td align="left" rowspan="1" colspan="1">KC843168</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">DA103 = CBS 135427</td><td align="left" rowspan="1" colspan="1"><italic>Citrus reticulata</italic></td><td align="left" rowspan="1" colspan="1">China</td><td align="left" rowspan="1" colspan="1">D. Udayanga</td><td align="left" rowspan="1" colspan="1">KC843323</td><td align="left" rowspan="1" colspan="1">KC843083</td><td align="left" rowspan="1" colspan="1">KC843199</td><td align="left" rowspan="1" colspan="1">KC843246</td><td align="left" rowspan="1" colspan="1">KC843169</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ICMP 10355</td><td align="left" rowspan="1" colspan="1"><italic>Citrus reticulata</italic></td><td align="left" rowspan="1" colspan="1">New Zealand: Kerikeri</td><td align="left" rowspan="1" colspan="1">G.J. Samuels</td><td align="left" rowspan="1" colspan="1">KC843314</td><td align="left" rowspan="1" colspan="1">KC843074</td><td align="left" rowspan="1" colspan="1">KC843190</td><td align="left" rowspan="1" colspan="1">KC843237</td><td align="left" rowspan="1" colspan="1">KC843160</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ICMP 6981</td><td align="left" rowspan="1" colspan="1"><italic>Citrus</italic> sp.</td><td align="left" rowspan="1" colspan="1">USA: Texas</td><td align="left" rowspan="1" colspan="1">G.J. Samuels</td><td align="left" rowspan="1" colspan="1">KC843315</td><td align="left" rowspan="1" colspan="1">KC843075</td><td align="left" rowspan="1" colspan="1">KC843191</td><td align="left" rowspan="1" colspan="1">KC843238</td><td align="left" rowspan="1" colspan="1">KC843161</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. cotoneastri</italic></td><td align="left" rowspan="1" colspan="1">CBS 439.82<xref ref-type="table-fn" rid="tfn2">*</xref></td><td align="left" rowspan="1" colspan="1"><italic>Cotoneaster</italic> sp.</td><td align="left" rowspan="1" colspan="1">UK: Scotland</td><td align="left" rowspan="1" colspan="1">H. Butin</td><td align="left" rowspan="1" colspan="1">FJ889450</td><td align="left" rowspan="1" colspan="1">GQ250341</td><td align="left" rowspan="1" colspan="1">JX275437</td><td align="left" rowspan="1" colspan="1">KC843231</td><td align="left" rowspan="1" colspan="1">JX197429</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">DP0667 = CBS 135428</td><td align="left" rowspan="1" colspan="1"><italic>Juglans cinerea</italic></td><td align="left" rowspan="1" colspan="1">USA: North Carolina</td><td align="left" rowspan="1" colspan="1">S. Anagnostakis</td><td align="left" rowspan="1" colspan="1">KC843328</td><td align="left" rowspan="1" colspan="1">KC843121</td><td align="left" rowspan="1" colspan="1">KC843229</td><td align="left" rowspan="1" colspan="1">KC843232</td><td align="left" rowspan="1" colspan="1">KC843155</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. cynaroidis</italic></td><td align="left" rowspan="1" colspan="1">CBS 122676<xref ref-type="table-fn" rid="tfn2">*</xref></td><td align="left" rowspan="1" colspan="1"><italic>Protea cynaroidis</italic></td><td align="left" rowspan="1" colspan="1">South Africa</td><td align="left" rowspan="1" colspan="1">P.W. Crous</td><td align="left" rowspan="1" colspan="1">EU552122</td><td align="left" rowspan="1" colspan="1">EU552093</td><td align="left" rowspan="1" colspan="1">KC344026</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">KC343300</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. cytosporella</italic></td><td align="left" rowspan="1" colspan="1">FAU461 = CBS 137020</td><td align="left" rowspan="1" colspan="1"><italic>Citrus limon</italic></td><td align="left" rowspan="1" colspan="1">Spain</td><td align="left" rowspan="1" colspan="1">M. Palm</td><td align="left" rowspan="1" colspan="1">KC843307</td><td align="left" rowspan="1" colspan="1">KC843116</td><td align="left" rowspan="1" colspan="1">KC843221</td><td align="left" rowspan="1" colspan="1">KC843285</td><td align="left" rowspan="1" colspan="1">KC843141</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR5148</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">USA: California</td><td align="left" rowspan="1" colspan="1">A. Eskalen</td><td align="left" rowspan="1" colspan="1">KC843308</td><td align="left" rowspan="1" colspan="1">KC843117</td><td align="left" rowspan="1" colspan="1">KC843222</td><td align="left" rowspan="1" colspan="1">KC843286</td><td align="left" rowspan="1" colspan="1">KC843142</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR5149<xref ref-type="table-fn" rid="tfn2">*</xref></td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">USA: California</td><td align="left" rowspan="1" colspan="1">A. Eskalen</td><td align="left" rowspan="1" colspan="1">KC843309</td><td align="left" rowspan="1" colspan="1">KC843118</td><td align="left" rowspan="1" colspan="1">KC843222</td><td align="left" rowspan="1" colspan="1">KC843287</td><td align="left" rowspan="1" colspan="1">KC843143</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. foeniculina</italic></td><td align="left" rowspan="1" colspan="1">FAU460</td><td align="left" rowspan="1" colspan="1"><italic>Citrus limon</italic></td><td align="left" rowspan="1" colspan="1">Spain</td><td align="left" rowspan="1" colspan="1">M. Palm</td><td align="left" rowspan="1" colspan="1">KC843304</td><td align="left" rowspan="1" colspan="1">KC843113</td><td align="left" rowspan="1" colspan="1">KC843218</td><td align="left" rowspan="1" colspan="1">KC843282</td><td align="left" rowspan="1" colspan="1">KC843138</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">MEP1289-1</td><td align="left" rowspan="1" colspan="1"><italic>Citrus limon</italic></td><td align="left" rowspan="1" colspan="1">Spain</td><td align="left" rowspan="1" colspan="1">D. Grenier</td><td align="left" rowspan="1" colspan="1">KC843305</td><td align="left" rowspan="1" colspan="1">KC843114</td><td align="left" rowspan="1" colspan="1">KC843219</td><td align="left" rowspan="1" colspan="1">KC843283</td><td align="left" rowspan="1" colspan="1">KC843139</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">FAU462 = CBS 135429</td><td align="left" rowspan="1" colspan="1"><italic>Citrus limon</italic></td><td align="left" rowspan="1" colspan="1">Spain</td><td align="left" rowspan="1" colspan="1">M. Palm</td><td align="left" rowspan="1" colspan="1">KC843292</td><td align="left" rowspan="1" colspan="1">KC843101</td><td align="left" rowspan="1" colspan="1">KC843206</td><td align="left" rowspan="1" colspan="1">KC843270</td><td align="left" rowspan="1" colspan="1">KC843126</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ICMP 6986</td><td align="left" rowspan="1" colspan="1"><italic>Citrus limon</italic></td><td align="left" rowspan="1" colspan="1">New Zealand: Hope</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">KC145897</td><td align="left" rowspan="1" colspan="1">KC145989</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ICMP 6970</td><td align="left" rowspan="1" colspan="1"><italic>Acacia</italic> sp.</td><td align="left" rowspan="1" colspan="1">New Zealand: Auckland</td><td align="left" rowspan="1" colspan="1">G.J. Samuels</td><td align="left" rowspan="1" colspan="1">KC145896</td><td align="left" rowspan="1" colspan="1">KC145984</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ICMP 12285</td><td align="left" rowspan="1" colspan="1"><italic>Juglans regia</italic></td><td align="left" rowspan="1" colspan="1">New Zealand</td><td align="left" rowspan="1" colspan="1">K. Knight</td><td align="left" rowspan="1" colspan="1">KC145853</td><td align="left" rowspan="1" colspan="1">KC145937</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ICMP 6987</td><td align="left" rowspan="1" colspan="1"><italic>Malus domestica</italic></td><td align="left" rowspan="1" colspan="1">New Zealand: Nelson</td><td align="left" rowspan="1" colspan="1">G.J. Samuels</td><td align="left" rowspan="1" colspan="1">KC145894</td><td align="left" rowspan="1" colspan="1">KC145990</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ICMP 17058</td><td align="left" rowspan="1" colspan="1"><italic>Paraserianthes lophantha</italic></td><td align="left" rowspan="1" colspan="1">New Zealand: Auckland</td><td align="left" rowspan="1" colspan="1">C.F. Hill</td><td align="left" rowspan="1" colspan="1">KC145842</td><td align="left" rowspan="1" colspan="1">KC145977</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ICMP 11892</td><td align="left" rowspan="1" colspan="1"><italic>Fuchsia excorticata</italic></td><td align="left" rowspan="1" colspan="1">New Zealand: Taupo</td><td align="left" rowspan="1" colspan="1">J.M. Young</td><td align="left" rowspan="1" colspan="1">KC145898</td><td align="left" rowspan="1" colspan="1">KC145931</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">DP0454</td><td align="left" rowspan="1" colspan="1"><italic>Ribes nigrum</italic></td><td align="left" rowspan="1" colspan="1">New Zealand: Nelson</td><td align="left" rowspan="1" colspan="1">C.F. Hill</td><td align="left" rowspan="1" colspan="1">KC843297</td><td align="left" rowspan="1" colspan="1">KC843106</td><td align="left" rowspan="1" colspan="1">KC843211</td><td align="left" rowspan="1" colspan="1">KC843275</td><td align="left" rowspan="1" colspan="1">KC843131</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR3607 = STE-U2654</td><td align="left" rowspan="1" colspan="1"><italic>Vitis vinifera</italic></td><td align="left" rowspan="1" colspan="1">South Africa</td><td align="left" rowspan="1" colspan="1">L. Mostert</td><td align="left" rowspan="1" colspan="1">AF230743</td><td align="left" rowspan="1" colspan="1">JQ807419</td><td align="left" rowspan="1" colspan="1">KC843204</td><td align="left" rowspan="1" colspan="1">JQ807344</td><td align="left" rowspan="1" colspan="1">KC843123</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">DP0392 = CBS 111554</td><td align="left" rowspan="1" colspan="1"><italic>Foeniculum vulgare</italic></td><td align="left" rowspan="1" colspan="1">Portugal: Marcos</td><td align="left" rowspan="1" colspan="1">A.J.L. Phillips</td><td align="left" rowspan="1" colspan="1">KC843296</td><td align="left" rowspan="1" colspan="1">KC843105</td><td align="left" rowspan="1" colspan="1">KC843210</td><td align="left" rowspan="1" colspan="1">KC843274</td><td align="left" rowspan="1" colspan="1">KC843130</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">DP0391 = CBS 111553<xref ref-type="table-fn" rid="tfn2">*</xref></td><td align="left" rowspan="1" colspan="1"><italic>Foeniculum vulgare</italic></td><td align="left" rowspan="1" colspan="1">Portugal: Marcos</td><td align="left" rowspan="1" colspan="1">A.J.L. Phillips</td><td align="left" rowspan="1" colspan="1">KC843295</td><td align="left" rowspan="1" colspan="1">KC843104</td><td align="left" rowspan="1" colspan="1">KC843209</td><td align="left" rowspan="1" colspan="1">KC843273</td><td align="left" rowspan="1" colspan="1">KC843129</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR5151</td><td align="left" rowspan="1" colspan="1"><italic>Citrus latifolia</italic></td><td align="left" rowspan="1" colspan="1">USA: California</td><td align="left" rowspan="1" colspan="1">A. Eskalen</td><td align="left" rowspan="1" colspan="1">KC843303</td><td align="left" rowspan="1" colspan="1">KC843112</td><td align="left" rowspan="1" colspan="1">KC843217</td><td align="left" rowspan="1" colspan="1">KC843281</td><td align="left" rowspan="1" colspan="1">KC843137</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. foeniculina</italic> (cont.)</td><td align="left" rowspan="1" colspan="1">AR5142 = CBS 135430</td><td align="left" rowspan="1" colspan="1"><italic>Citrus limon</italic></td><td align="left" rowspan="1" colspan="1">USA: California</td><td align="left" rowspan="1" colspan="1">A. Eskalen</td><td align="left" rowspan="1" colspan="1">KC843301</td><td align="left" rowspan="1" colspan="1">KC843110</td><td align="left" rowspan="1" colspan="1">KC843215</td><td align="left" rowspan="1" colspan="1">KC843279</td><td align="left" rowspan="1" colspan="1">KC843135</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR5145</td><td align="left" rowspan="1" colspan="1"><italic>Citrus limon</italic></td><td align="left" rowspan="1" colspan="1">USA: California</td><td align="left" rowspan="1" colspan="1">A. Eskalen</td><td align="left" rowspan="1" colspan="1">KC843306</td><td align="left" rowspan="1" colspan="1">KC843115</td><td align="left" rowspan="1" colspan="1">KC843220</td><td align="left" rowspan="1" colspan="1">KC843284</td><td align="left" rowspan="1" colspan="1">KC843140</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR5147</td><td align="left" rowspan="1" colspan="1"><italic>Citrus limon</italic></td><td align="left" rowspan="1" colspan="1">USA: California</td><td align="left" rowspan="1" colspan="1">A. Eskalen</td><td align="left" rowspan="1" colspan="1">KC843299</td><td align="left" rowspan="1" colspan="1">KC843108</td><td align="left" rowspan="1" colspan="1">KC843213</td><td align="left" rowspan="1" colspan="1">KC843277</td><td align="left" rowspan="1" colspan="1">KC843133</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR5144</td><td align="left" rowspan="1" colspan="1"><italic>Citrus limon</italic></td><td align="left" rowspan="1" colspan="1">USA: California</td><td align="left" rowspan="1" colspan="1">A. Eskalen</td><td align="left" rowspan="1" colspan="1">KC843302</td><td align="left" rowspan="1" colspan="1">KC843111</td><td align="left" rowspan="1" colspan="1">KC843216</td><td align="left" rowspan="1" colspan="1">KC843280</td><td align="left" rowspan="1" colspan="1">KC843136</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR5143</td><td align="left" rowspan="1" colspan="1"><italic>Citrus limon</italic></td><td align="left" rowspan="1" colspan="1">USA: California</td><td align="left" rowspan="1" colspan="1">A. Eskalen</td><td align="left" rowspan="1" colspan="1">KC843294</td><td align="left" rowspan="1" colspan="1">KC843103</td><td align="left" rowspan="1" colspan="1">KC843208</td><td align="left" rowspan="1" colspan="1">KC843294</td><td align="left" rowspan="1" colspan="1">KC843128</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR5146</td><td align="left" rowspan="1" colspan="1"><italic>Citrus limon</italic></td><td align="left" rowspan="1" colspan="1">USA: California</td><td align="left" rowspan="1" colspan="1">A. Eskalen</td><td align="left" rowspan="1" colspan="1">KC843298</td><td align="left" rowspan="1" colspan="1">KC843107</td><td align="left" rowspan="1" colspan="1">KC843212</td><td align="left" rowspan="1" colspan="1">KC843298</td><td align="left" rowspan="1" colspan="1">KC843132</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR5150 = CBS 135431</td><td align="left" rowspan="1" colspan="1"><italic>Citrus latifolia</italic></td><td align="left" rowspan="1" colspan="1">USA: California</td><td align="left" rowspan="1" colspan="1">A. Eskalen</td><td align="left" rowspan="1" colspan="1">KC843293</td><td align="left" rowspan="1" colspan="1">KC843102</td><td align="left" rowspan="1" colspan="1">KC843207</td><td align="left" rowspan="1" colspan="1">KC843293</td><td align="left" rowspan="1" colspan="1">KC843127</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR5152</td><td align="left" rowspan="1" colspan="1"><italic>Citrus latifolia</italic></td><td align="left" rowspan="1" colspan="1">USA: California</td><td align="left" rowspan="1" colspan="1">A. Eskalen</td><td align="left" rowspan="1" colspan="1">KC843300</td><td align="left" rowspan="1" colspan="1">KC843109</td><td align="left" rowspan="1" colspan="1">KC843214</td><td align="left" rowspan="1" colspan="1">KC843300</td><td align="left" rowspan="1" colspan="1">KC843134</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. foeniculina</italic> (syn. <italic>P. theicola</italic>)</td><td align="left" rowspan="1" colspan="1">CBS 187.27<xref ref-type="table-fn" rid="tfn2">*</xref></td><td align="left" rowspan="1" colspan="1"><italic>Camellia sinesis</italic></td><td align="left" rowspan="1" colspan="1">Italy</td><td align="left" rowspan="1" colspan="1">M. Curzi</td><td align="left" rowspan="1" colspan="1">DQ286287</td><td align="left" rowspan="1" colspan="1">DQ286261</td><td align="left" rowspan="1" colspan="1">JX275463</td><td align="left" rowspan="1" colspan="1">JQ807298</td><td align="left" rowspan="1" colspan="1">KC843122</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. foeniculina</italic> (syn. <italic>D. neotheicola</italic>)</td><td align="left" rowspan="1" colspan="1">CBS 123208<xref ref-type="table-fn" rid="tfn2">*</xref></td><td align="left" rowspan="1" colspan="1"><italic>Foeniculum valgare</italic></td><td align="left" rowspan="1" colspan="1">Portugal</td><td align="left" rowspan="1" colspan="1">A.J.L. Phillips</td><td align="left" rowspan="1" colspan="1">EU814480</td><td align="left" rowspan="1" colspan="1">GQ250315</td><td align="left" rowspan="1" colspan="1">JX275464</td><td align="left" rowspan="1" colspan="1">KC843269</td><td align="left" rowspan="1" colspan="1">KC843125</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. foeniculina</italic> (syn<italic>. D. rhusicola</italic>)</td><td align="left" rowspan="1" colspan="1">CBS 129528<xref ref-type="table-fn" rid="tfn2">*</xref></td><td align="left" rowspan="1" colspan="1"><italic>Rhus pendulina</italic></td><td align="left" rowspan="1" colspan="1">South Africa</td><td align="left" rowspan="1" colspan="1">P.W. Crous</td><td align="left" rowspan="1" colspan="1">JF951146</td><td align="left" rowspan="1" colspan="1">KC843100</td><td align="left" rowspan="1" colspan="1">KC843205</td><td align="left" rowspan="1" colspan="1">KC843268</td><td align="left" rowspan="1" colspan="1">KC843124</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. helianthi</italic></td><td align="left" rowspan="1" colspan="1">CBS 592.81</td><td align="left" rowspan="1" colspan="1"><italic>Helianthus annuus</italic></td><td align="left" rowspan="1" colspan="1">Serbia</td><td align="left" rowspan="1" colspan="1">M Muntanola-Cvetkovic</td><td align="left" rowspan="1" colspan="1">AY705842</td><td align="left" rowspan="1" colspan="1">GQ250308</td><td align="left" rowspan="1" colspan="1">JX275465</td><td align="left" rowspan="1" colspan="1">KF199885</td><td align="left" rowspan="1" colspan="1">JX197454</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. pterocarpi</italic></td><td align="left" rowspan="1" colspan="1">MFLUCC10-588</td><td align="left" rowspan="1" colspan="1"><italic>Magnolia</italic> sp.</td><td align="left" rowspan="1" colspan="1">Thailand: Chiang Rai</td><td align="left" rowspan="1" colspan="1">D. Udayanga</td><td align="left" rowspan="1" colspan="1">JQ619900</td><td align="left" rowspan="1" colspan="1">JX275417</td><td align="left" rowspan="1" colspan="1">JX275461</td><td align="left" rowspan="1" colspan="1">KC843289</td><td align="left" rowspan="1" colspan="1">JX197452</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">MFLUCC10-575 = CBS 137021</td><td align="left" rowspan="1" colspan="1"><italic>Pterocarpus indicus</italic></td><td align="left" rowspan="1" colspan="1">Thailand: Chiang Rai</td><td align="left" rowspan="1" colspan="1">N.F. Wulandari</td><td align="left" rowspan="1" colspan="1">JQ619901</td><td align="left" rowspan="1" colspan="1">JX275418</td><td align="left" rowspan="1" colspan="1">JX275462</td><td align="left" rowspan="1" colspan="1">KC843288</td><td align="left" rowspan="1" colspan="1">JX197453</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">MFLUCC10-571<xref ref-type="table-fn" rid="tfn2">*</xref> = CBS 135768</td><td align="left" rowspan="1" colspan="1"><italic>Pterocarpus indicus</italic></td><td align="left" rowspan="1" colspan="1">Thailand: Chiang Rai</td><td align="left" rowspan="1" colspan="1">D. Udayanga</td><td align="left" rowspan="1" colspan="1">JQ619899</td><td align="left" rowspan="1" colspan="1">JX275416</td><td align="left" rowspan="1" colspan="1">JX275460</td><td align="left" rowspan="1" colspan="1">KC843290</td><td align="left" rowspan="1" colspan="1">JX197451</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. pterocarpicola</italic></td><td align="left" rowspan="1" colspan="1">MFLUCC10-580a<xref ref-type="table-fn" rid="tfn2">*</xref> = CBS 135432</td><td align="left" rowspan="1" colspan="1"><italic>Pterocarpus indicus</italic></td><td align="left" rowspan="1" colspan="1">Thailand: Chiang Rai</td><td align="left" rowspan="1" colspan="1">D. Udayanga</td><td align="left" rowspan="1" colspan="1">JQ619887</td><td align="left" rowspan="1" colspan="1">JX275403</td><td align="left" rowspan="1" colspan="1">JX275441</td><td align="left" rowspan="1" colspan="1">KF214779</td><td align="left" rowspan="1" colspan="1">JX197433</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">MFLUCC10-580b</td><td align="left" rowspan="1" colspan="1"><italic>Pterocarpus indicus</italic></td><td align="left" rowspan="1" colspan="1">Thailand: Chiang Rai</td><td align="left" rowspan="1" colspan="1">N.F. Wulandari</td><td align="left" rowspan="1" colspan="1">JQ619889</td><td align="left" rowspan="1" colspan="1">JX275405</td><td align="left" rowspan="1" colspan="1">JX275443</td><td align="left" rowspan="1" colspan="1">KF214780</td><td align="left" rowspan="1" colspan="1">JX197435</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. rudis</italic></td><td align="left" rowspan="1" colspan="1">AR3654 = CBS 135433</td><td align="left" rowspan="1" colspan="1"><italic>Rosa canina</italic></td><td align="left" rowspan="1" colspan="1">Austria</td><td align="left" rowspan="1" colspan="1">W. Jaklitsch</td><td align="left" rowspan="1" colspan="1">KC843338</td><td align="left" rowspan="1" colspan="1">KC843097</td><td align="left" rowspan="1" colspan="1">KC843184</td><td align="left" rowspan="1" colspan="1">KC843262</td><td align="left" rowspan="1" colspan="1">KC843153</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">DP0423</td><td align="left" rowspan="1" colspan="1"><italic>Pyrus</italic> sp.</td><td align="left" rowspan="1" colspan="1">New Zealand</td><td align="left" rowspan="1" colspan="1">W. Kandula</td><td align="left" rowspan="1" colspan="1">KC843335</td><td align="left" rowspan="1" colspan="1">KC843094</td><td align="left" rowspan="1" colspan="1">KC843181</td><td align="left" rowspan="1" colspan="1">KC843258</td><td align="left" rowspan="1" colspan="1">KC843150</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">DP0350 = CBS 135434</td><td align="left" rowspan="1" colspan="1"><italic>Castanea</italic> sp. </td><td align="left" rowspan="1" colspan="1">New Zealand: Churchill</td><td align="left" rowspan="1" colspan="1">H. Smith</td><td align="left" rowspan="1" colspan="1">KC843338</td><td align="left" rowspan="1" colspan="1">KC843098</td><td align="left" rowspan="1" colspan="1">KC843185</td><td align="left" rowspan="1" colspan="1">KC843264</td><td align="left" rowspan="1" colspan="1">KC843154</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ICMP 12522</td><td align="left" rowspan="1" colspan="1"><italic>Ileostylis micranthus</italic></td><td align="left" rowspan="1" colspan="1">New Zealand: Central Otago</td><td align="left" rowspan="1" colspan="1">P.R. Johnston</td><td align="left" rowspan="1" colspan="1">KC145906</td><td align="left" rowspan="1" colspan="1">KC145940</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ICMP 15267</td><td align="left" rowspan="1" colspan="1"><italic>Alnus</italic> sp.</td><td align="left" rowspan="1" colspan="1">New Zealand: Mid Canterbury</td><td align="left" rowspan="1" colspan="1">K. Eade</td><td align="left" rowspan="1" colspan="1">KC145839</td><td align="left" rowspan="1" colspan="1">KC145998</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ICMP 16419</td><td align="left" rowspan="1" colspan="1"><italic>Castanea sativa</italic></td><td align="left" rowspan="1" colspan="1">New Zealand: Mid Canterbury</td><td align="left" rowspan="1" colspan="1">H.C. Smith</td><td align="left" rowspan="1" colspan="1">KC145904</td><td align="left" rowspan="1" colspan="1">KC145976</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ICMP 7025</td><td align="left" rowspan="1" colspan="1"><italic>Vaccinium corymbosum</italic></td><td align="left" rowspan="1" colspan="1">New Zealand: Waikato</td><td align="left" rowspan="1" colspan="1">P.R. Johnston</td><td align="left" rowspan="1" colspan="1">KC145885</td><td align="left" rowspan="1" colspan="1">KC145995</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR3422 = CBS 109292<xref ref-type="table-fn" rid="tfn2">*</xref></td><td align="left" rowspan="1" colspan="1"><italic>Laburnum anagyroides</italic></td><td align="left" rowspan="1" colspan="1">Austria</td><td align="left" rowspan="1" colspan="1">W. Jaklitsch</td><td align="left" rowspan="1" colspan="1">KC843331</td><td align="left" rowspan="1" colspan="1">KC843090</td><td align="left" rowspan="1" colspan="1">KC843177</td><td align="left" rowspan="1" colspan="1">KC843254</td><td align="left" rowspan="1" colspan="1">KC843146</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR3646</td><td align="left" rowspan="1" colspan="1"><italic>Epilobium angustifolium</italic></td><td align="left" rowspan="1" colspan="1">Canada: British Columbia</td><td align="left" rowspan="1" colspan="1">M. Barr</td><td align="left" rowspan="1" colspan="1">KC843330</td><td align="left" rowspan="1" colspan="1">KC843089</td><td align="left" rowspan="1" colspan="1">KC843176</td><td align="left" rowspan="1" colspan="1">KC843253</td><td align="left" rowspan="1" colspan="1">KC843145</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">AR3478 = CBS 109768</td><td align="left" rowspan="1" colspan="1"><italic>Epilobium angustifolium</italic></td><td align="left" rowspan="1" colspan="1">Canada: British Columbia</td><td align="left" rowspan="1" colspan="1">M. Barr</td><td align="left" rowspan="1" colspan="1">KC843329</td><td align="left" rowspan="1" colspan="1">KC843088</td><td align="left" rowspan="1" colspan="1">KC843175</td><td align="left" rowspan="1" colspan="1">KC843252</td><td align="left" rowspan="1" colspan="1">KC843144</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">DA243 = CBS 135435</td><td align="left" rowspan="1" colspan="1"><italic>Brugmansia</italic> sp.</td><td align="left" rowspan="1" colspan="1">Germany</td><td align="left" rowspan="1" colspan="1">R. Schumacher</td><td align="left" rowspan="1" colspan="1">KC843332</td><td align="left" rowspan="1" colspan="1">KC843091</td><td align="left" rowspan="1" colspan="1">KC843178</td><td align="left" rowspan="1" colspan="1">KC843255</td><td align="left" rowspan="1" colspan="1">KC843147</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">DA244</td><td align="left" rowspan="1" colspan="1"><italic>Brugmansia</italic> sp.</td><td align="left" rowspan="1" colspan="1">Germany</td><td align="left" rowspan="1" colspan="1">R. Schumacher</td><td align="left" rowspan="1" colspan="1">KC843334</td><td align="left" rowspan="1" colspan="1">KC843093</td><td align="left" rowspan="1" colspan="1">KC843180</td><td align="left" rowspan="1" colspan="1">KC843257</td><td align="left" rowspan="1" colspan="1">KC843149</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ER285A = CBS 135437</td><td align="left" rowspan="1" colspan="1"><italic>Acer opalus</italic></td><td align="left" rowspan="1" colspan="1">Italy</td><td align="left" rowspan="1" colspan="1">E. Camporesi</td><td align="left" rowspan="1" colspan="1">KC843336</td><td align="left" rowspan="1" colspan="1">KC843095</td><td align="left" rowspan="1" colspan="1">KC843182</td><td align="left" rowspan="1" colspan="1">KC843259</td><td align="left" rowspan="1" colspan="1">KC843151</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ER286C</td><td align="left" rowspan="1" colspan="1"><italic>Acer opalus</italic></td><td align="left" rowspan="1" colspan="1">Italy</td><td align="left" rowspan="1" colspan="1">E. Camporesi</td><td align="left" rowspan="1" colspan="1">KC843337</td><td align="left" rowspan="1" colspan="1">KC843096</td><td align="left" rowspan="1" colspan="1">KC843183</td><td align="left" rowspan="1" colspan="1">KC843260</td><td align="left" rowspan="1" colspan="1">KC843152</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ER286D</td><td align="left" rowspan="1" colspan="1"><italic>Acer opalus</italic></td><td align="left" rowspan="1" colspan="1">Italy</td><td align="left" rowspan="1" colspan="1">E. Camporesi</td><td align="left" rowspan="1" colspan="1">KC843333</td><td align="left" rowspan="1" colspan="1">KC843092</td><td align="left" rowspan="1" colspan="1">KC843179</td><td align="left" rowspan="1" colspan="1">KC843256</td><td align="left" rowspan="1" colspan="1">KC843148</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">DPG01</td><td align="left" rowspan="1" colspan="1"><italic>Vitis viniferra</italic></td><td align="left" rowspan="1" colspan="1">Italy</td><td align="left" rowspan="1" colspan="1">X.Z. Liu</td><td align="left" rowspan="1" colspan="1">JQ619896</td><td align="left" rowspan="1" colspan="1">JX275412</td><td align="left" rowspan="1" colspan="1">JX27545</td><td align="left" rowspan="1" colspan="1">KC843261</td><td align="left" rowspan="1" colspan="1">JX197446</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">DPG02</td><td align="left" rowspan="1" colspan="1"><italic>Vitis viniferra</italic></td><td align="left" rowspan="1" colspan="1">Italy</td><td align="left" rowspan="1" colspan="1">X.Z. Liu</td><td align="left" rowspan="1" colspan="1">JQ619897</td><td align="left" rowspan="1" colspan="1">JX275413</td><td align="left" rowspan="1" colspan="1">JX275456</td><td align="left" rowspan="1" colspan="1">KC843263</td><td align="left" rowspan="1" colspan="1">JX197447</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. rudis</italic> (syn. <italic>D. viticola</italic>)</td><td align="left" rowspan="1" colspan="1">CBS 113201<xref ref-type="table-fn" rid="tfn2">*</xref></td><td align="left" rowspan="1" colspan="1"><italic>Vitis vinifera</italic></td><td align="left" rowspan="1" colspan="1">Portugal</td><td align="left" rowspan="1" colspan="1">A.J.L. Phillips</td><td align="left" rowspan="1" colspan="1">AY485750</td><td align="left" rowspan="1" colspan="1">GQ250327</td><td align="left" rowspan="1" colspan="1">JX275454</td><td align="left" rowspan="1" colspan="1">KC843251</td><td align="left" rowspan="1" colspan="1">JX197445</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. thunbergii</italic></td><td align="left" rowspan="1" colspan="1">MFLUCC10-576a<xref ref-type="table-fn" rid="tfn2">*</xref> = CBS 135769</td><td align="left" rowspan="1" colspan="1"><italic>Thunbergia laurifolia</italic></td><td align="left" rowspan="1" colspan="1">Thailand: Chiang Mai</td><td align="left" rowspan="1" colspan="1">D.S. Manamgoda</td><td align="left" rowspan="1" colspan="1">JQ619893</td><td align="left" rowspan="1" colspan="1">JX275409</td><td align="left" rowspan="1" colspan="1">JX275449</td><td align="left" rowspan="1" colspan="1">KF199886</td><td align="left" rowspan="1" colspan="1">JX197440</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">MFLUCC10-576b</td><td align="left" rowspan="1" colspan="1"><italic>Thunbergia laurifolia</italic></td><td align="left" rowspan="1" colspan="1">Thailand: Chiang Mai</td><td align="left" rowspan="1" colspan="1">S.C. Karunaratne</td><td align="left" rowspan="1" colspan="1">JQ619894</td><td align="left" rowspan="1" colspan="1">JX275410</td><td align="left" rowspan="1" colspan="1">JX275450</td><td align="left" rowspan="1" colspan="1">KF199887</td><td align="left" rowspan="1" colspan="1">JX197441</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">MFLUCC10-576c</td><td align="left" rowspan="1" colspan="1"><italic>Thunbergia laurifolia</italic></td><td align="left" rowspan="1" colspan="1">Thailand: Chiang Mai</td><td align="left" rowspan="1" colspan="1">D. Udayanga</td><td align="left" rowspan="1" colspan="1">JQ619895</td><td align="left" rowspan="1" colspan="1">JX275411</td><td align="left" rowspan="1" colspan="1">JX275451</td><td align="left" rowspan="1" colspan="1">KF199888</td><td align="left" rowspan="1" colspan="1">JX197442</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. vaccinii</italic></td><td align="left" rowspan="1" colspan="1">CBS 160.32<xref ref-type="table-fn" rid="tfn2">*</xref></td><td align="left" rowspan="1" colspan="1"><italic>Vaccinium macrocarpon</italic></td><td align="left" rowspan="1" colspan="1">USA: Massachusetts</td><td align="left" rowspan="1" colspan="1">C. Shear</td><td align="left" rowspan="1" colspan="1">AF317578</td><td align="left" rowspan="1" colspan="1">GQ250326</td><td align="left" rowspan="1" colspan="1">JX275436</td><td align="left" rowspan="1" colspan="1">JQ807297</td><td align="left" rowspan="1" colspan="1">KC343470</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">(as <italic>Oxycoccus macrocarpos</italic>)</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">FAU446 = CBS 122113</td><td align="left" rowspan="1" colspan="1"><italic>Vaccinium macrocarpon</italic></td><td align="left" rowspan="1" colspan="1">USA: Massachusetts</td><td align="left" rowspan="1" colspan="1">F. Caruso</td><td align="left" rowspan="1" colspan="1">U11317,U11367</td><td align="left" rowspan="1" colspan="1">JQ807398</td><td align="left" rowspan="1" colspan="1">KC843224</td><td align="left" rowspan="1" colspan="1">JQ807322</td><td align="left" rowspan="1" colspan="1">KC849455</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">DF5032 = CBS 135436</td><td align="left" rowspan="1" colspan="1"><italic>Vaccinium corymbosum</italic></td><td align="left" rowspan="1" colspan="1">USA: North Carolina</td><td align="left" rowspan="1" colspan="1">D. Farr</td><td align="left" rowspan="1" colspan="1">AF317570</td><td align="left" rowspan="1" colspan="1">JQ807380</td><td align="left" rowspan="1" colspan="1">KC843225</td><td align="left" rowspan="1" colspan="1">JQ807303</td><td align="left" rowspan="1" colspan="1">KC849456</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">FAU633</td><td align="left" rowspan="1" colspan="1"><italic>Vaccinium</italic> sp.</td><td align="left" rowspan="1" colspan="1">USA: Michigan</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">U11360,U11414</td><td align="left" rowspan="1" colspan="1">JQ807413</td><td align="left" rowspan="1" colspan="1">KC843226</td><td align="left" rowspan="1" colspan="1">JQ807338</td><td align="left" rowspan="1" colspan="1">KC849457</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">FAU468</td><td align="left" rowspan="1" colspan="1"><italic>Vaccinium macrocarpon</italic></td><td align="left" rowspan="1" colspan="1">USA: New Jersey</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">U113327,U11377</td><td align="left" rowspan="1" colspan="1">JQ807399</td><td align="left" rowspan="1" colspan="1">KC843227</td><td align="left" rowspan="1" colspan="1">JQ807323</td><td align="left" rowspan="1" colspan="1">KC849458</td></tr></tbody></table><table-wrap-foot><fn id="tfn1"><p><sup>1</sup> AR, DA, DF, DLR, DP, DPG, ER, FAU, MEP: isolates in SMML culture collection, USDA-ARS, Beltsville, MD, USA; CBS: CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; ICMP: International Collection of Microorganisms from Plants, Landcare Research, New Zealand; MFLUCC: Mae Fah Luang University Culture Collection; STE-U: University of Stellenbosch culture collection, Stellenbosch, South Africa;</p></fn><fn id="tfn2"><p>* = ex-type cultures.</p></fn></table-wrap-foot></table-wrap><table-wrap id="T2" orientation="portrait" position="float"><label>Table 2</label><caption><p>Primers used and alternative new primers designed for current study and optimised PCR protocols.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">Locus</th><th align="left" rowspan="1" colspan="1">Primers</th><th align="left" rowspan="1" colspan="1">Optimised PCR protocols</th><th align="left" rowspan="1" colspan="1">Approximate sizes of the PCR amplicons obtained</th><th align="left" rowspan="1" colspan="1">References for primers<sup>a</sup> & protocols<sup>b</sup></th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">ACT</td><td align="left" rowspan="1" colspan="1">ACT-512F:</td><td align="left" rowspan="1" colspan="1">(95 °C: 30 s, 55 °C: 50 s, 72 °C: 1 min)</td><td align="left" rowspan="1" colspan="1">280bp (ACT512F/ACT783R)</td><td align="left" rowspan="1" colspan="1"><xref rid="R8" ref-type="bibr">Carbone & Kohn 1999</xref><sup>a</sup></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ATGTGCAAGGCCGGTTTCGC</td><td align="left" rowspan="1" colspan="1">×39 cycles for ACT512F/ACT783R</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ACT-783R</td><td align="left" rowspan="1" colspan="1">(95 °C: 30 s, 58 °C: 50 s, 72 °C: 1 min)</td><td align="left" rowspan="1" colspan="1">380bp (ACT512F/ACT878R)</td><td align="left" rowspan="1" colspan="1">This study<sup>a,</sup><sup>b</sup></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">(5’-TACGAGTCCTTCTGGCCCAT-3’)</td><td align="left" rowspan="1" colspan="1">×39 cycles for ACT512F/ACT878R</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ACT878R (new):</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ATCTTCTCC ATGTCGTCCCAG</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">TUB</td><td align="left" rowspan="1" colspan="1">Bt-2a:</td><td align="left" rowspan="1" colspan="1">(95 °C: 30 s, 58 °C: 50 s, 72 °C: 1 min)</td><td align="left" rowspan="1" colspan="1">500bp</td><td align="left" rowspan="1" colspan="1"><xref rid="R28" ref-type="bibr">Glass & Donaldson 1995</xref><sup>a</sup></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">GGTAACCAAATCGGTGCTGCTTTC</td><td align="left" rowspan="1" colspan="1">×39 cycles</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><xref rid="R85" ref-type="bibr">Udayanga et al. 2012a</xref><sup>b</sup></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">BT-2b:</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ACCCTCAGTGTAGTGACCCTTGGC</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">CAL</td><td align="left" rowspan="1" colspan="1">CAL-228F:</td><td align="left" rowspan="1" colspan="1">(95 °C: 30 s, 55 °C: 50 s, 72 °C: 1 min)</td><td align="left" rowspan="1" colspan="1">500bp (CAL228F.CAL737R)</td><td align="left" rowspan="1" colspan="1"><xref rid="R8" ref-type="bibr">Carbone & Kohn 1999</xref><sup>a</sup></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">GAGTTCAAGGAGGCCTTCTCCC</td><td align="left" rowspan="1" colspan="1">×39 cycles for CAL228F/CAL737R</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">CAL-737R:</td><td align="left" rowspan="1" colspan="1">(95 °C: 30 s, 52 °C: 50 s, 72 °C: 1 min)</td><td align="left" rowspan="1" colspan="1">800bp (CL1/CL2A)</td><td align="left" rowspan="1" colspan="1"><xref rid="R56" ref-type="bibr">O’Donnell et al. 2000</xref><sup>a</sup>;</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">CATCTTCTGGCCATCATGG</td><td align="left" rowspan="1" colspan="1">×39 cycles for CL1/CL2A</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><xref rid="R85" ref-type="bibr">Udayanga et al. 2012a</xref><sup>b</sup></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">CL1F:</td><td align="left" rowspan="1" colspan="1">(95 °C: 30 s, 51 °C: 50 s, 72 °C: 1 min)</td><td align="left" rowspan="1" colspan="1">570bp (CAL563F/CL2A)</td><td align="left" rowspan="1" colspan="1">This study<sup>a,</sup><sup>b</sup></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">GARTWCAAGGAGGCCTTCTC</td><td align="left" rowspan="1" colspan="1">×39 cycles for CAL563F/CL2A</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">CL2A :</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">TTTTTGCATCATGAGTTGGAC</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">CAL563F (new):</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">GACAAATCA CCACCAARGAGC</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">EF1-α</td><td align="left" rowspan="1" colspan="1">EF1-728F:</td><td align="left" rowspan="1" colspan="1">(95 °C: 30 s, 58 °C: 50 s, 72 °C: 1 min)</td><td align="left" rowspan="1" colspan="1">350bp</td><td align="left" rowspan="1" colspan="1"><xref rid="R8" ref-type="bibr">Carbone & Kohn 1999</xref><sup>a</sup></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">CATCGAGAAGTTCGAGAAGG</td><td align="left" rowspan="1" colspan="1">×39 cycles</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><xref rid="R85" ref-type="bibr">Udayanga et al. 2012a</xref><sup>b</sup></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">EF1-986R:</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">TACTTGAAGGAACCCTTACC</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">ITS</td><td align="left" rowspan="1" colspan="1">ITS1:</td><td align="left" rowspan="1" colspan="1">(95 °C: 30 s, 55 °C: 50 s, 72 °C: 1 min)</td><td align="left" rowspan="1" colspan="1">600bp</td><td align="left" rowspan="1" colspan="1"><xref rid="R90" ref-type="bibr">White et al. 1990</xref><sup>a</sup></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">TCCGTAGGTGAACCTGCGG</td><td align="left" rowspan="1" colspan="1">×39 cycles</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><xref rid="R85" ref-type="bibr">Udayanga et al. 2012a</xref><sup>b</sup></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">ITS4:</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">TCCTCCGCTTATTGATATGC</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr></tbody></table></table-wrap><table-wrap id="T3" orientation="portrait" position="float"><label>Table 3</label><caption><p>Comparison of alignment properties in parsimony analysis of genes and nucleotide substitution models used in phylogenetic analysis.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">Genes/loci</th><th align="left" rowspan="1" colspan="1">ITS</th><th align="left" rowspan="1" colspan="1">EF1-α</th><th align="left" rowspan="1" colspan="1">TUB<xref ref-type="table-fn" rid="tfn3">*</xref></th><th align="left" rowspan="1" colspan="1">ACT<xref ref-type="table-fn" rid="tfn3">*</xref></th><th align="left" rowspan="1" colspan="1">CAL<xref ref-type="table-fn" rid="tfn3">*</xref></th><th align="left" rowspan="1" colspan="1">Combined ITS / EF / ACT / CAL</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">Characters included (with gaps)</td><td align="center" rowspan="1" colspan="1">508</td><td align="center" rowspan="1" colspan="1">347</td><td align="center" rowspan="1" colspan="1">454</td><td align="center" rowspan="1" colspan="1">279</td><td align="center" rowspan="1" colspan="1">232</td><td align="center" rowspan="1" colspan="1">2033</td></tr><tr><td align="left" rowspan="1" colspan="1">Invariable characters</td><td align="center" rowspan="1" colspan="1">360</td><td align="center" rowspan="1" colspan="1">155</td><td align="center" rowspan="1" colspan="1">318</td><td align="center" rowspan="1" colspan="1">205</td><td align="center" rowspan="1" colspan="1">129</td><td align="center" rowspan="1" colspan="1">1337</td></tr><tr><td align="left" rowspan="1" colspan="1">Parsimony informative characters (%)</td><td align="center" rowspan="1" colspan="1">97 (20 %)</td><td align="center" rowspan="1" colspan="1">189 (55 %)</td><td align="center" rowspan="1" colspan="1">132 (29 %)</td><td align="center" rowspan="1" colspan="1">68 (24 %)</td><td align="center" rowspan="1" colspan="1">95 (40 %)</td><td align="center" rowspan="1" colspan="1">659 (32 %)</td></tr><tr><td align="left" rowspan="1" colspan="1">Uninformative polymorphic characters</td><td align="center" rowspan="1" colspan="1">14</td><td align="center" rowspan="1" colspan="1">3</td><td align="center" rowspan="1" colspan="1">4</td><td align="center" rowspan="1" colspan="1">6</td><td align="center" rowspan="1" colspan="1">8</td><td align="center" rowspan="1" colspan="1">37</td></tr><tr><td align="left" rowspan="1" colspan="1">Alignment strategy (MAFFT v6)</td><td align="center" rowspan="1" colspan="1">FFT-NS-I+manual</td><td align="center" rowspan="1" colspan="1">FFT-NS-I+manual</td><td align="center" rowspan="1" colspan="1">FFT-NS-I</td><td align="center" rowspan="1" colspan="1">FFT-NS-I</td><td align="center" rowspan="1" colspan="1">FFT-NS-I+manual</td><td align="center" rowspan="1" colspan="1">–</td></tr><tr><td align="left" rowspan="1" colspan="1">Number of branches > 70 % bootstrap MP/BI and ML analysis</td><td align="center" rowspan="1" colspan="1">18</td><td align="center" rowspan="1" colspan="1">17</td><td align="center" rowspan="1" colspan="1">15</td><td align="center" rowspan="1" colspan="1">11</td><td align="center" rowspan="1" colspan="1">11</td><td align="center" rowspan="1" colspan="1">20</td></tr><tr><td align="left" rowspan="1" colspan="1">Nucleotide substitution models for Bayesian analysis (determined by MrModeltest)</td><td align="center" rowspan="1" colspan="1">SYM+I+G</td><td align="center" rowspan="1" colspan="1">GTR+I+G</td><td align="center" rowspan="1" colspan="1">HKY+G</td><td align="center" rowspan="1" colspan="1">GTR+G</td><td align="center" rowspan="1" colspan="1">HKY+G</td><td align="center" rowspan="1" colspan="1">GTR+I+G</td></tr></tbody></table><table-wrap-foot><fn id="tfn3"><p>* Phylogenetic trees not shown.</p></fn></table-wrap-foot></table-wrap><table-wrap id="T4" orientation="portrait" position="float"><label>Table 4</label><caption><p>Genealogical Sorting Index (<italic>gsi</italic>) and probability values (P) for gene trees of species resolved in this study.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">Species</th><th align="left" rowspan="1" colspan="1">ITS gsi<xref ref-type="table-fn" rid="tfn4"><sup>1</sup></xref> P</th><th align="left" rowspan="1" colspan="1">EF1-α gsi<xref ref-type="table-fn" rid="tfn4"><sup>1</sup></xref> P</th><th align="left" rowspan="1" colspan="1">TUB gsi<xref ref-type="table-fn" rid="tfn4"><sup>1</sup></xref> P</th><th align="left" rowspan="1" colspan="1">CAL gsi<xref ref-type="table-fn" rid="tfn4"><sup>1</sup></xref> P</th><th align="left" rowspan="1" colspan="1">ACT gsi<xref ref-type="table-fn" rid="tfn4"><sup>1</sup></xref> P</th><th align="left" rowspan="1" colspan="1">ALL gsi<xref ref-type="table-fn" rid="tfn4"><sup>1</sup></xref><sub>T</sub> P<sub>T</sub></th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"><italic>D. australafricana</italic></td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">0.4051*</td><td align="left" rowspan="1" colspan="1">0.2712*</td><td align="left" rowspan="1" colspan="1">0.1187</td><td align="left" rowspan="1" colspan="1">0.7353*</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.0004</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.001</td><td align="left" rowspan="1" colspan="1">0.0078</td><td align="left" rowspan="1" colspan="1">0.0483</td><td align="left" rowspan="1" colspan="1">0.0001</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. citri</italic></td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.0004</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. cotoneastri</italic></td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.0005</td><td align="left" rowspan="1" colspan="1">0.0019</td><td align="left" rowspan="1" colspan="1">0.0008</td><td align="left" rowspan="1" colspan="1">0.0079</td><td align="left" rowspan="1" colspan="1">0.0007</td><td align="left" rowspan="1" colspan="1">0.0001</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. cytosporella</italic></td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">0.4492*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0002</td><td align="left" rowspan="1" colspan="1">0.0003</td><td align="left" rowspan="1" colspan="1">0.0003</td><td align="left" rowspan="1" colspan="1">0.0004</td><td align="left" rowspan="1" colspan="1">0.0001</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. foeniculina</italic></td><td align="left" rowspan="1" colspan="1">0.869*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">0.9476*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">0.9301</td><td align="left" rowspan="1" colspan="1">0.9598*</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. pterocarpi</italic></td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0002</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0003</td><td align="left" rowspan="1" colspan="1">0.0002</td><td align="left" rowspan="1" colspan="1">0.0001</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. pterocarpicola</italic></td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.0014</td><td align="left" rowspan="1" colspan="1">0.0020</td><td align="left" rowspan="1" colspan="1">0.0010</td><td align="left" rowspan="1" colspan="1">0.0088</td><td align="left" rowspan="1" colspan="1">0.0002</td><td align="left" rowspan="1" colspan="1">0.0001</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. rudis</italic></td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">0.9138*</td><td align="left" rowspan="1" colspan="1">0.8392</td><td align="left" rowspan="1" colspan="1">0.7719</td><td align="left" rowspan="1" colspan="1">0.9332*</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. thunbergii</italic></td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0002</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>D. vaccinii</italic></td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td><td align="left" rowspan="1" colspan="1">1*</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">0.0004</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td><td align="left" rowspan="1" colspan="1">0.0001</td></tr></tbody></table><table-wrap-foot><fn id="tfn4"><p><sup>1</sup> The <italic>gsi</italic> statistic is based on a continuum of 0–1, with 0 = lack of genealogical divergence from other groups and 1 = monophyly; (*) = statistically significant P-value ≤ 0.05. The <italic>gsi</italic> is calculated under the null hypothesis that the gene copies labeled as each species assigned are a single group of mixed genealogical ancestry. gsi<sub>T</sub> = ensemble <italic>gsi</italic> of 5 gene trees. Species represented by single isolate are excluded in calculation of <italic>gsi</italic>.</p></fn></table-wrap-foot></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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