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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en"><italic>Alternaria</italic> section <italic>Alternaria</italic>: Species, <italic>formae speciales</italic> or pathotypes?</title><author><name sortKey="Woudenberg, J H C" sort="Woudenberg, J H C" uniqKey="Woudenberg J" first="J. H. C." last="Woudenberg">J. H. C. Woudenberg</name><affiliation><nlm:aff id="aff1">CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Seidl, M F" sort="Seidl, M F" uniqKey="Seidl M" first="M. F." last="Seidl">M. F. Seidl</name><affiliation><nlm:aff id="aff2">Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Groenewald, J Z" sort="Groenewald, J Z" uniqKey="Groenewald J" first="J. Z." last="Groenewald">J. Z. Groenewald</name><affiliation><nlm:aff id="aff1">CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="De Vries, M" sort="De Vries, M" uniqKey="De Vries M" first="M." last="De Vries">M. De Vries</name><affiliation><nlm:aff id="aff1">CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Stielow, J B" sort="Stielow, J B" uniqKey="Stielow J" first="J. B." last="Stielow">J. B. Stielow</name><affiliation><nlm:aff id="aff1">CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Thomma, B P H J" sort="Thomma, B P H J" uniqKey="Thomma B" first="B. P. H. J." last="Thomma">B. P. H. J. Thomma</name><affiliation><nlm:aff id="aff2">Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Crous, P W" sort="Crous, P W" uniqKey="Crous P" first="P. W." last="Crous">P. W. Crous</name><affiliation><nlm:aff id="aff1">CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26951037</idno><idno type="pmc">4774270</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4774270</idno><idno type="RBID">PMC:4774270</idno><idno type="doi">10.1016/j.simyco.2015.07.001</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">001307</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>Alternaria</italic> section <italic>Alternaria</italic>: Species, <italic>formae speciales</italic> or pathotypes?</title><author><name sortKey="Woudenberg, J H C" sort="Woudenberg, J H C" uniqKey="Woudenberg J" first="J. H. C." last="Woudenberg">J. H. C. Woudenberg</name><affiliation><nlm:aff id="aff1">CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Seidl, M F" sort="Seidl, M F" uniqKey="Seidl M" first="M. F." last="Seidl">M. F. Seidl</name><affiliation><nlm:aff id="aff2">Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Groenewald, J Z" sort="Groenewald, J Z" uniqKey="Groenewald J" first="J. Z." last="Groenewald">J. Z. Groenewald</name><affiliation><nlm:aff id="aff1">CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="De Vries, M" sort="De Vries, M" uniqKey="De Vries M" first="M." last="De Vries">M. De Vries</name><affiliation><nlm:aff id="aff1">CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Stielow, J B" sort="Stielow, J B" uniqKey="Stielow J" first="J. B." last="Stielow">J. B. Stielow</name><affiliation><nlm:aff id="aff1">CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Thomma, B P H J" sort="Thomma, B P H J" uniqKey="Thomma B" first="B. P. H. J." last="Thomma">B. P. H. J. Thomma</name><affiliation><nlm:aff id="aff2">Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands</nlm:aff></affiliation></author><author><name sortKey="Crous, P W" sort="Crous, P W" uniqKey="Crous P" first="P. W." last="Crous">P. W. Crous</name><affiliation><nlm:aff id="aff1">CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa</nlm:aff></affiliation></author></analytic><series><title level="j">Studies in Mycology</title><idno type="ISSN">0166-0616</idno><idno type="eISSN">1872-9797</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The cosmopolitan fungal genus <italic>Alternaria</italic> consists of multiple saprophytic and pathogenic species. Based on phylogenetic and morphological studies, the genus is currently divided into 26 sections. <italic>Alternaria</italic> sect. <italic>Alternaria</italic> contains most of the small-spored <italic>Alternaria</italic> species with concatenated conidia, including important plant, human and postharvest pathogens. Species within sect. <italic>Alternaria</italic> have been mostly described based on morphology and / or host-specificity, yet molecular variation between them is minimal. To investigate whether the described morphospecies within sect. <italic>Alternaria</italic> are supported by molecular data, whole-genome sequencing of nine <italic>Alternaria</italic> morphospecies supplemented with transcriptome sequencing of 12 <italic>Alternaria</italic> morphospecies as well as multi-gene sequencing of 168 <italic>Alternaria</italic> isolates was performed. The assembled genomes ranged in size from 33.3–35.2 Mb within sect. <italic>Alternaria</italic> and from 32.0–39.1 Mb for all <italic>Alternaria</italic> genomes. The number of repetitive sequences differed significantly between the different <italic>Alternaria</italic> genomes; ranging from 1.4–16.5 %. The repeat content within sect. <italic>Alternaria</italic> was relatively low with only 1.4–2.7 % of repeats. Whole-genome alignments revealed 96.7–98.2 % genome identity between sect. <italic>Alternaria</italic> isolates, compared to 85.1–89.3 % genome identity for isolates from other sections to the <italic>A. alternata</italic> reference genome. Similarly, 1.4–2.8 % and 0.8–1.8 % single nucleotide polymorphisms (SNPs) were observed in genomic and transcriptomic sequences, respectively, between isolates from sect. <italic>Alternaria</italic>, while the percentage of SNPs found in isolates from different sections compared to the <italic>A. alternata</italic> reference genome was considerably higher; 8.0–10.3 % and 6.1–8.5 %. The topology of a phylogenetic tree based on the whole-genome and transcriptome reads was congruent with multi-gene phylogenies based on commonly used gene regions. Based on the genome and transcriptome data, a set of core proteins was extracted, and primers were designed on two gene regions with a relatively low degree of conservation within sect. <italic>Alternaria</italic> (96.8 and 97.3 % conservation). Their potential discriminatory power within sect. <italic>Alternaria</italic> was tested next to nine commonly used gene regions in sect. <italic>Alternaria</italic>, namely the SSU, LSU, ITS, <italic>gapdh</italic>, <italic>rpb2</italic>, <italic>tef1</italic>, <italic>Alt a 1</italic>, <italic>endoPG</italic> and OPA10-2 gene regions. The phylogenies from the two gene regions with a relatively low conservation, KOG1058 and KOG1077, could not distinguish the described morphospecies within sect. <italic>Alternaria</italic> more effectively than the phylogenies based on the commonly used gene regions for <italic>Alternaria</italic>. Based on genome and transcriptome comparisons and molecular phylogenies, <italic>Alternaria</italic> sect. <italic>Alternaria</italic> consists of only 11 phylogenetic species and one species complex. Thirty-five morphospecies, which cannot be distinguished based on the multi-gene phylogeny, are synonymised under <italic>A. alternata</italic>. By providing guidelines for the naming and identification of phylogenetic species in <italic>Alternaria</italic> sect. <italic>Alternaria</italic>, this manuscript provides a clear and stable species classification in this section.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Akagi, Y" uniqKey="Akagi Y">Y. Akagi</name></author><author><name sortKey="Akamatsu, H" uniqKey="Akamatsu H">H. Akamatsu</name></author><author><name sortKey="Otani, H" uniqKey="Otani H">H. Otani</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Akamatsu, H" uniqKey="Akamatsu H">H. Akamatsu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Akimitsu, K" uniqKey="Akimitsu K">K. Akimitsu</name></author><author><name sortKey="Tsuge, T" uniqKey="Tsuge T">T. Tsuge</name></author><author><name sortKey="Kodama, M" uniqKey="Kodama M">M. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Stud Mycol</journal-id><journal-id journal-id-type="iso-abbrev">Stud. Mycol</journal-id><journal-title-group><journal-title>Studies in Mycology</journal-title></journal-title-group><issn pub-type="ppub">0166-0616</issn><issn pub-type="epub">1872-9797</issn><publisher><publisher-name>CBS Fungal Biodiversity Centre</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26951037</article-id><article-id pub-id-type="pmc">4774270</article-id><article-id pub-id-type="publisher-id">S0166-0616(15)00012-3</article-id><article-id pub-id-type="doi">10.1016/j.simyco.2015.07.001</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Paper</subject></subj-group></article-categories><title-group><article-title><italic>Alternaria</italic> section <italic>Alternaria</italic>: Species, <italic>formae speciales</italic> or pathotypes?</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Woudenberg</surname><given-names>J.H.C.</given-names></name><email>j.woudenberg@cbs.knaw.nl</email><xref rid="aff1" ref-type="aff">1</xref><xref rid="aff2" ref-type="aff">2</xref><xref rid="cor1" ref-type="corresp">∗</xref></contrib><contrib contrib-type="author"><name><surname>Seidl</surname><given-names>M.F.</given-names></name><xref rid="aff2" ref-type="aff">2</xref></contrib><contrib contrib-type="author"><name><surname>Groenewald</surname><given-names>J.Z.</given-names></name><xref rid="aff1" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>de Vries</surname><given-names>M.</given-names></name><xref rid="aff1" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Stielow</surname><given-names>J.B.</given-names></name><xref rid="aff1" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Thomma</surname><given-names>B.P.H.J.</given-names></name><xref rid="aff2" ref-type="aff">2</xref></contrib><contrib contrib-type="author"><name><surname>Crous</surname><given-names>P.W.</given-names></name><xref rid="aff1" ref-type="aff">1</xref><xref rid="aff2" ref-type="aff">2</xref><xref rid="aff3" ref-type="aff">3</xref></contrib></contrib-group><aff id="aff1"><label>1</label>CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands</aff><aff id="aff2"><label>2</label>Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands</aff><aff id="aff3"><label>3</label>Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa</aff><author-notes><corresp id="cor1"><label>∗</label><italic>Correspondence</italic>: J.H.C. Woudenberg <email>j.woudenberg@cbs.knaw.nl</email></corresp></author-notes><pub-date pub-type="pmc-release"><day>25</day><month>8</month><year>2015</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><month>9</month><year>2015</year></pub-date><pub-date pub-type="epub"><day>25</day><month>8</month><year>2015</year></pub-date><volume>82</volume><fpage>1</fpage><lpage>21</lpage><permissions><copyright-statement>Copyright © 2015, CBS-KNAW Fungal Biodiversity Centre. Production and hosting by ELSEVIER B.V.</copyright-statement><copyright-year>2015</copyright-year><copyright-holder>CBS-KNAW Fungal Biodiversity Centre</copyright-holder><license license-type="CC BY-NC-ND" xlink:href="http://creativecommons.org/licenses/by-nc-nd/4.0/"><license-p>This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).</license-p></license></permissions><abstract><p>The cosmopolitan fungal genus <italic>Alternaria</italic> consists of multiple saprophytic and pathogenic species. Based on phylogenetic and morphological studies, the genus is currently divided into 26 sections. <italic>Alternaria</italic> sect. <italic>Alternaria</italic> contains most of the small-spored <italic>Alternaria</italic> species with concatenated conidia, including important plant, human and postharvest pathogens. Species within sect. <italic>Alternaria</italic> have been mostly described based on morphology and / or host-specificity, yet molecular variation between them is minimal. To investigate whether the described morphospecies within sect. <italic>Alternaria</italic> are supported by molecular data, whole-genome sequencing of nine <italic>Alternaria</italic> morphospecies supplemented with transcriptome sequencing of 12 <italic>Alternaria</italic> morphospecies as well as multi-gene sequencing of 168 <italic>Alternaria</italic> isolates was performed. The assembled genomes ranged in size from 33.3–35.2 Mb within sect. <italic>Alternaria</italic> and from 32.0–39.1 Mb for all <italic>Alternaria</italic> genomes. The number of repetitive sequences differed significantly between the different <italic>Alternaria</italic> genomes; ranging from 1.4–16.5 %. The repeat content within sect. <italic>Alternaria</italic> was relatively low with only 1.4–2.7 % of repeats. Whole-genome alignments revealed 96.7–98.2 % genome identity between sect. <italic>Alternaria</italic> isolates, compared to 85.1–89.3 % genome identity for isolates from other sections to the <italic>A. alternata</italic> reference genome. Similarly, 1.4–2.8 % and 0.8–1.8 % single nucleotide polymorphisms (SNPs) were observed in genomic and transcriptomic sequences, respectively, between isolates from sect. <italic>Alternaria</italic>, while the percentage of SNPs found in isolates from different sections compared to the <italic>A. alternata</italic> reference genome was considerably higher; 8.0–10.3 % and 6.1–8.5 %. The topology of a phylogenetic tree based on the whole-genome and transcriptome reads was congruent with multi-gene phylogenies based on commonly used gene regions. Based on the genome and transcriptome data, a set of core proteins was extracted, and primers were designed on two gene regions with a relatively low degree of conservation within sect. <italic>Alternaria</italic> (96.8 and 97.3 % conservation). Their potential discriminatory power within sect. <italic>Alternaria</italic> was tested next to nine commonly used gene regions in sect. <italic>Alternaria</italic>, namely the SSU, LSU, ITS, <italic>gapdh</italic>, <italic>rpb2</italic>, <italic>tef1</italic>, <italic>Alt a 1</italic>, <italic>endoPG</italic> and OPA10-2 gene regions. The phylogenies from the two gene regions with a relatively low conservation, KOG1058 and KOG1077, could not distinguish the described morphospecies within sect. <italic>Alternaria</italic> more effectively than the phylogenies based on the commonly used gene regions for <italic>Alternaria</italic>. Based on genome and transcriptome comparisons and molecular phylogenies, <italic>Alternaria</italic> sect. <italic>Alternaria</italic> consists of only 11 phylogenetic species and one species complex. Thirty-five morphospecies, which cannot be distinguished based on the multi-gene phylogeny, are synonymised under <italic>A. alternata</italic>. By providing guidelines for the naming and identification of phylogenetic species in <italic>Alternaria</italic> sect. <italic>Alternaria</italic>, this manuscript provides a clear and stable species classification in this section.</p></abstract><kwd-group><title>Key words</title><kwd><italic>Alternaria alternata</italic></kwd><kwd><italic>Alternaria arborescens</italic> species complex</kwd><kwd>Multi-gene phylogeny</kwd><kwd>Transcriptome sequencing</kwd><kwd>Whole-genome sequencing</kwd></kwd-group></article-meta></front><body><sec id="sec1"><title>Introduction</title><p><italic>Alternaria</italic> sect. <italic>Alternaria</italic> contains most of the small-spored <italic>Alternaria</italic> species with concatenated conidia. Almost 60 morphological or host-specific species can be assigned to this section, including the type species of the genus <italic>Alternaria</italic>, <italic>A. alternata</italic> (<xref rid="bib61" ref-type="bibr">Woudenberg <italic>et al.</italic> 2013</xref>). <italic>Alternaria alternata</italic> is known as the cause of leaf spot and other diseases in over 100 host species of plants (<xref rid="bib39" ref-type="bibr">Rotem 1994</xref>), but also as postharvest disease in various crops (<xref rid="bib6" ref-type="bibr">Coates & Johnson 1997</xref>) and of upper respiratory tract infections and asthma in humans (<xref rid="bib25" ref-type="bibr">Kurup <italic>et al.</italic> 2000</xref>). Other important plant pathogens in sect. <italic>Alternaria</italic> include <italic>A. longipes</italic>, the causal agent of brown spot of tobacco, <italic>A. mali</italic>, the causal agent of Alternaria blotch of apple, <italic>A. gaisen</italic>, the causal agent of black spot of Japanese pear and <italic>A. arborescens</italic>, the causal agent of stem canker of tomato. The first descriptions of the <italic>A. alternata</italic>, <italic>A. tenuissima</italic>, <italic>A. cheiranthi</italic> and <italic>A. brassicicola</italic> species-groups, based on sporulation patterns, were made by <xref rid="bib43" ref-type="bibr">Simmons (1995)</xref>. More recent molecular-based studies revealed that <italic>Alternaria</italic> species cluster in several distinct species clades, now referred to as sections (<xref rid="bib26" ref-type="bibr">Lawrence <italic>et al.</italic> 2013,</xref><xref rid="bib61" ref-type="bibr">Woudenberg <italic>et al.</italic> 2013</xref>), which do not always correlate with the species-groups that were delineated based on morphological characteristics. Currently, 26 <italic>Alternaria</italic> sections are recognised based on molecular phylogenies (<xref rid="bib61" ref-type="bibr">Woudenberg, 2013</xref>, <xref rid="bib60" ref-type="bibr">Woudenberg et al., 2014</xref><xref rid="bib10" ref-type="bibr">Grum-Grzhimaylo <italic>et al.</italic> 2015</xref>). So far, species within sect. <italic>Alternaria</italic> have been mostly described based on morphology and / or host-specificity; yet the molecular variation between them is minimal. The standard gene regions used for the delimitation of <italic>Alternaria</italic> species are not able to delineate species within sect. <italic>Alternaria</italic> (<xref rid="bib34" ref-type="bibr">Peever et al., 2004</xref>, <xref rid="bib4" ref-type="bibr">Andrew et al., 2009</xref>). Multiple molecular methods have been tested or proposed for distinguishing the small-spored <italic>Alternaria</italic> species, including random amplified polymorphic DNA (<xref rid="bib37" ref-type="bibr">Roberts <italic>et al.</italic> 2000</xref>), amplified fragment length polymorphism (<xref rid="bib48" ref-type="bibr">Somma <italic>et al.</italic> 2011</xref>), selective subtractive hybridisation (<xref rid="bib36" ref-type="bibr">Roberts <italic>et al.</italic> 2012</xref>) and sequence characterised amplified genomic regions (<xref rid="bib51" ref-type="bibr">Stewart <italic>et al.</italic> 2013a</xref>). However, none of these methods successfully distinguished all morphospecies described within sect. <italic>Alternaria</italic>.</p><p>The terms <italic>forma specialis</italic> and pathotype have been used to describe isolates that are morphologically indistinguishable from <italic>A. alternata</italic>, but infect particular hosts. At least 16 different <italic>f. sp.</italic> epithets occur in the literature, of which most were raised to species level by <xref rid="bib45" ref-type="bibr">Simmons (2007)</xref>. <xref rid="bib31" ref-type="bibr">Nishimura & Kohmoto (1983)</xref> proposed that <italic>Alternaria</italic> strains with identical morphology but producing different host-selective toxins (HST) should be defined as distinct pathotypes of <italic>Alternaria</italic>. Currently there are seven pathotypes of <italic>A. alternata</italic> described (<xref rid="bib3" ref-type="bibr">Akimitsu <italic>et al.</italic> 2014</xref>), but this term is not widely adopted.</p><p>Because most morphospecies within sect. <italic>Alternaria</italic> cannot be distinguished based on sequences of standard housekeeping genes (<xref rid="bib4" ref-type="bibr">Andrew <italic>et al.</italic> 2009</xref>), whole-genome sequencing technologies can be applied to search for genes, which can distinguish (most of) the described species (<xref rid="bib26" ref-type="bibr">Lawrence <italic>et al.</italic> 2013</xref>). Since the introduction of next generation sequencing (NGS) many fungal genomes have become available for study, with the 1 000 fungal genomes project (<xref rid="bib49" ref-type="bibr">Spatafora 2011</xref>) as a public stimulant for generating this kind of data. Currently there are two publicly available <italic>Alternaria</italic> genomes at NCBI (National Center for Biotechnology Information), namely <italic>A. brassicicola</italic>, sect. <italic>Brassicicola</italic> (BioProject PRJNA34523), and <italic>A. arborescens</italic>, sect. <italic>Alternaria</italic> (BioProject PRJNA78243).</p><p>In this study, whole-genome sequences of four <italic>Alternaria</italic> spp. from sect. <italic>Alternaria</italic> and five <italic>Alternaria</italic> spp. from five other sections were generated, and supplemented by transcriptome sequences of nine <italic>Alternaria</italic> spp. from sect. <italic>Alternaria</italic> and three <italic>Alternaria</italic> spp. from three other sections of <italic>Alternaria</italic>. Species were selected based on their phylogenetic position (<xref rid="bib61" ref-type="bibr">Woudenberg <italic>et al.</italic> 2013</xref>) in such a way that they are representative of the genus <italic>Alternaria</italic>, from the sister section of sect. <italic>Alternaria</italic>, sect. <italic>Alternantherae</italic> (<italic>A. alternantherae</italic>), to the most distant section, sect. <italic>Crivellia</italic> (<italic>A. papaveraceae</italic>). Within sect. <italic>Alternaria</italic>, species were selected based on their economic importance. Based on the genome and transcriptome data, two gene regions with relatively low conservation, the eukaryotic orthologous group (KOG) protein loci, KOG1058 (96.8 % conservation) and KOG1077 (97.3 % conservation), were identified and tested for their potential discriminatory power within sect. <italic>Alternaria</italic>. Together with a standard multi-gene phylogeny of 168 <italic>Alternaria</italic> isolates based on sequences of parts of nine gene regions, namely the internal transcribed spacer regions 1 and 2 and intervening 5.8S nrDNA (ITS), the 18S nrDNA (SSU), the 28S nrDNA (LSU), glyceraldehyde-3-phosphate dehydrogenase (<italic>gapdh</italic>), RNA polymerase second largest subunit (<italic>rpb2</italic>), translation elongation factor 1-alpha (<italic>tef1</italic>), <italic>Alternaria</italic> major allergen gene (<italic>Alt a 1</italic>), endopolygalacturonase (<italic>endoPG</italic>) and an anonymous gene region (OPA10-2), an attempt was made to create a clear and stable phylogenetic species classification in <italic>Alternaria</italic> sect. <italic>Alternaria</italic>.</p></sec><sec id="sec2"><title>Material and methods</title><sec id="sec2.1"><title>Isolates</title><p>One-hundred-and-sixty-eight <italic>Alternaria</italic> strains, including 64 (ex-)type or representative strains, present at the CBS-KNAW Fungal Biodiversity Centre (CBS), Utrecht, The Netherlands, were included in this study (<xref rid="tbl1" ref-type="table">Table 1</xref>) based on the phylogenetic position derived from their ITS sequence. A “representative isolate” refers to the strain used to describe the species based on morphology in <italic>The</italic> Alternaria <italic>Identification Manual</italic> (<xref rid="bib45" ref-type="bibr">Simmons 2007</xref>). Freeze-dried strains were revived in 2 mL malt / peptone (50 % / 50 %) and subsequently transferred to oatmeal agar (OA) (<xref rid="bib7" ref-type="bibr">Crous <italic>et al.</italic> 2009</xref>). Strains stored in liquid nitrogen were transferred to OA directly from the −185 °C storage.</p></sec><sec id="sec2.2"><title>DNA and RNA isolation for NGS</title><p>The genomes of four <italic>Alternaria</italic> spp. from sect. <italic>Alternaria</italic> and five <italic>Alternaria</italic> spp. from five other sections (<xref rid="tbl2" ref-type="table">Table 2</xref>) as well as the transcriptome profiles of nine <italic>Alternaria</italic> spp. from sect. <italic>Alternaria</italic> and three <italic>Alternaria</italic> spp. representing three other sections of <italic>Alternaria</italic> were sequenced (<xref rid="tbl3" ref-type="table">Table 3</xref>). Species were selected based on their economic importance and their phylogenetic position, with the intention to be representative of the entire genus <italic>Alternaria</italic> with a focus on sect. <italic>Alternaria</italic>. Isolates were grown in malt peptone (MP) (<xref rid="bib7" ref-type="bibr">Crous <italic>et al.</italic> 2009</xref>) supplemented with 1 × BME vitamin solution (Sigma-Aldrich<sup>®</sup> Chemie B.V., Zwijndrecht, The Netherlands) in a shaking incubator, at 25 °C, in the dark, for 3 d. When growth was observed, cultures were mixed in a blender and transferred to fresh MP with vitamin solution, and returned to the shaking incubator for another 2–3 d. When sufficient growth was observed, the mycelium was harvested with a Whatman No. 4 filter disk and a Buchner funnel, attached to a vacuum flask.</p><p>For isolating DNA, QIAGEN Genomic 100/G tips (QIAGEN Benelux B.V., Venlo, The Netherlands) were used and processed following the lysis protocol for tissue in the QIAGEN Blood & Cell Culture DNA kit. The following alternative steps, as suggested by the protocol, were followed. The mycelium, of which a maximum of 4 g (wet weight) was used, was grinded to a fine powder with liquid nitrogen in a pre-cooled mortar and pestle. Proteinase K stock solution was added to the solution, after which it was incubated for 2 h at 50 °C in a shaking incubator running at 700 rpm. Prewarmed QF buffer (50 °C) was used to elute the genomic DNA, and after precipitation the DNA was centrifuged at 4 °C for 20 min at 8 500 × g.</p><p>For isolating RNA, the QIAGEN RNeasy Midi kit was used following the protocol for isolation of total RNA from animal tissues including the optional on-column DNase digestion. For the disruption of the tissue and homogenisation of the lysate, the mortar and pestle with needle and syringe homogenisation method, as described in the protocol, was followed. All centrifuge steps are performed at room temperature at 4 000 × g. When necessary, a final standard LiCl purification was performed.</p></sec><sec id="sec2.3"><title>NGS</title><p>DNA sequence and RNA sequence library preparation (500 bp insert) for Illumina<sup>®</sup> sequencing and the sequencing itself (100-bp paired end reads) were performed at the Applied Biosystematics Group of Plant Research International (PRI, Wageningen).</p><p>DNA sequence library preparation for Ion Torrent™ sequencing was performed at the CBS. The Ion Torrent™ library preparation was carried out using the Ion Xpress™ Fragment Library Kit (Thermo Fisher Scientific, Bleiswijk, The Netherlands), with 180 ng of DNA. Adapter ligation, size selection and nick repair were performed as described in the Ion Torrent™ protocol using the Ion Xpress™ Plus Fragment Library Kit (Thermo Fisher Scientific), with a shearing time of 13 min. The 2100 Bioanalyzer system (Agilent Technologies Netherlands BV, Amstelveen, The Netherlands) and the associated High Sensitivity DNA Analysis kit (Agilent Technologies) were used to determine the quality and concentration of the libraries. The amount of library required for template preparation was calculated using the Template Dilution Factor calculation described in the protocol (DNA concentration diluted to 42 pM). Emulsion PCR and enrichment steps were carried out using the Ion PGM™ Template OT2 200 Kit (Thermo Fisher Scientific) and associated protocol. The enrichment percentage was determent via the Ion Sphere™ Quality Control Kit (Thermo Fisher Scientific) and was performed between the emulsion PCR and the enrichment step. Sequencing was performed using the Ion PGM™ Sequencing 200 Kit v. 2 (Thermo Fisher Scientific) with an Ion 318™ Chip Kit v. 2 (Thermo Fisher Scientific).</p></sec><sec id="sec2.4"><title>Genome assembly and mapping</title><p><italic>De novo</italic> genome assembly of the Illumina<sup>®</sup> paired-end reads were quality-filtered and assembled using the A5 pipeline v. 13.01.2014 (<xref rid="bib55" ref-type="bibr">Tritt <italic>et al.</italic> 2012</xref>) and <italic>de novo</italic> genome assembly of Ion Torrent™ reads was performed using Newbler v. 2.9 (454 Life Sciences, Roche Applied Science, Branford, CT, USA). Repeats in the assembled genomes were identified using <italic>de novo</italic> repeat detection with RepeatModeler (<xref rid="bib46" ref-type="bibr">Smit & Hubley 2008</xref>) followed by genome-wide repeat annotation using RepeatMasker (<xref rid="bib47" ref-type="bibr">Smit <italic>et al.</italic> 1996</xref>), combining the <italic>de novo</italic> repeats with previously described repeat families from RepBase Update (release 31-04-2014) (<xref rid="bib22" ref-type="bibr">Jurka <italic>et al.</italic> 2005</xref>).</p><p>Whole-genome alignments were performed using NUCmer, part of the MUMmer v. 3.1 package (<xref rid="bib24" ref-type="bibr">Kurtz <italic>et al.</italic> 2004</xref>), using the “mum” option to find matches unique in query and reference. Subsequently, the average identity of the aligned sequences was calculated using dnadiff, part of MUMmer v. 3.1.</p><p>Genomic variants were inferred using GATK v. 3.3 (<xref rid="bib8" ref-type="bibr">DePristo <italic>et al.</italic> 2011</xref>). Briefly, genomic or transcriptomic reads were mapped against a reference genome (<italic>A. alternata</italic> CBS 916.96) using BWA (<xref rid="bib27" ref-type="bibr">Li & Durbin 2009</xref>) using the BWA-MEM algorithm v. 0.7.5a-r405. Transcript reads were trimmed prior to mapping using fastx-tools. Duplicated reads were identified and marked using Picard tools (<ext-link ext-link-type="uri" xlink:href="http://broadinstitute.github.io/picard" id="intref0010">http://broadinstitute.github.io/picard</ext-link>). Using GATK, transcript reads were splitted into exons and overhangs were removed. Subsequently, transcript and genomic reads were locally realigned to minimise the number of mismatches over all reads. Afterwards, genomic variants (SNPs) were called using GATK's UnifiedGenotyper (standard call and emitting threshold of 20; haploid organisms), and the resulting SNPs were filtered based on quality (Qual = 50), depth (DP = 10) and allelic frequency (AF = 0.9).</p><p>Conserved eukaryotic orthologous group (KOG) proteins were identified using the Core Eukaryotic Genes Mapping Approach (CEGMA) pipeline (<xref rid="bib33" ref-type="bibr">Parra <italic>et al.</italic> 2007</xref>). The conservation table was constructed from the five available genomes of sect. <italic>Alternaria</italic> to avoid alignment problems that could affect the conservation values.</p><p>The reference sequence alignment-based phylogeny builder (REALPHY) v. 1.09 (<xref rid="bib5" ref-type="bibr">Bertels <italic>et al.</italic> 2014</xref>) was used to construct a phylogenetic tree based on the whole-genome and transcriptome reads and the previously assembled <italic>Alternaria</italic> genomes. Briefly, short reads (genome and transcriptome) as well as short sequence fragments (100 nt) derived from the previously assembled genomes were mapped against the reference genome (<italic>A. alternata</italic> CBS 916.96) using Bowtie2. Subsequently, polymorphic as well as non-polymorphic sites were filtered (per base quality [20], coverage [10] and polymorphism frequency [0.95]) and extracted. Only sites that were present in all species were retained. The derived pseudo-molecule was used to infer a maximum likelihood phylogenetic tree using PhyML using the generalised time reversible (GTR) nucleotide substitution model. The robustness of the phylogeny was assessed by 1 000 bootstrap replicates.</p></sec><sec id="sec2.5"><title>PCR and sequencing</title><p>DNA extraction for gene sequencing was performed using the UltraClean™ Microbial DNA isolation kit (MoBio Laboratories, Carlsbad, CA, USA), according to the manufacturer's instructions. The SSU, LSU, ITS, <italic>gapdh</italic>, <italic>rpb2</italic> and the <italic>tef1</italic> gene regions were amplified and sequenced as described in <xref rid="bib61" ref-type="bibr">Woudenberg <italic>et al.</italic> (2013)</xref> and the <italic>Alt a 1</italic> gene as described in <xref rid="bib60" ref-type="bibr">Woudenberg <italic>et al.</italic> (2014)</xref>. The <italic>endoPG</italic> and OPA10-2 gene regions were amplified using the primers PG3 and PG2b and OPA10-2L and OPA10-2R (<xref rid="bib4" ref-type="bibr">Andrew <italic>et al.</italic> 2009</xref>). For the KOG1058 and KOG1077 gene regions the primers KOG1058F2 (5′-GAG TCA CGT TAY CGC ASC-3′) and KOG1058R2 (5′-TGG CTK ACG GAR ACG-3′) and KOG1077F2 (5′-GGA GCA GTC GGG CAA CG-3′) and KOG1077R2 (5′-ATT CRT GTT GTA CRA TCG C-3′) were designed from the genomic data. The PCRs were performed in an Applied Biosystems<sup>®</sup> 2720 Thermal Cycler (Thermo Fisher Scientific), in a total volume of 12.5 μL. The PCR mixtures consisted of 1 μL genomic DNA, 1× NH<sub>4</sub> reaction buffer (Bioline, Luckenwalde, Germany), 2 mM (<italic>endoPG</italic>, OPA10-2) or 1.6 mM MgCl<sub>2</sub> (KOG1058, KOG1077), 20 μM of each dNTP, 0.2 μM of each primer and 0.5 U <italic>Taq</italic> DNA polymerase (Bioline). The PCR conditions consisted of an initial denaturation step of 5 min at 94 °C followed by 40 cycles of 30 s at 94 °C, 30 s at 50 °C and 30 s at 72 °C for <italic>endoPG</italic>, 35 cycles of 30 s at 94 °C, 30 s at 62 °C and 45 s at 72 °C for OPA10-2, and 35 cycles of 30 s at 94 °C, 30 s at 59 °C and 60 s at 72 °C for KOG1058 and KOG1077, and a final elongation step of 7 min at 72 °C. The PCR products were sequenced in both directions using the PCR primers and a BigDye<sup>®</sup> Terminator v. 3.1 Cycle Sequencing Kit (Thermo Fisher Scientific), and analysed with an ABI Prism 3730xl DNA Analyser (Thermo Fisher Scientific) according to the manufacturer's instructions. Consensus sequences were computed from forward and reverse sequences using the BioNumerics v. 4.61 software package (Applied Maths, St-Martens-Latem, Belgium). All generated sequences were deposited in GenBank (<xref rid="tbl1" ref-type="table">Table 1</xref>).</p></sec><sec id="sec2.6"><title>Phylogenetic analyses</title><p>Multiple sequence alignments of individual data partitions were generated with MAFFT v. 7 (<ext-link ext-link-type="uri" xlink:href="http://mafft.cbrc.jp/alignment/server/index.html" id="intref0015">http://mafft.cbrc.jp/alignment/server/index.html</ext-link>), and manually adjusted. The best nucleotide substitution model for each partition was determined with Findmodel (<ext-link ext-link-type="uri" xlink:href="http://www.hiv.lanl.gov/content/sequence/findmodel/findmodel.html" id="intref0020">http://www.hiv.lanl.gov/content/sequence/findmodel/findmodel.html</ext-link>). For the ITS and OPA10-2 partitions a K80 model with a gamma-distributed rate variation was suggested, for the SSU, LSU, <italic>tef1</italic> and <italic>Alt a 1</italic> partitions a HKY model, with gamma-distributed rate variation for LSU and <italic>Alt a 1</italic>, for the <italic>gapdh</italic>, <italic>rpb2</italic> and KOG1077 partitions a TrN model with gamma-distributed rate variation and for the <italic>endoPG</italic> and KOG1058 partitions a GTR model with gamma-distributed rate variation. Bayesian analyses were performed with MrBayes v. 3.1.2 (<xref rid="bib18" ref-type="bibr">Huelsenbeck and Ronquist, 2001</xref>, <xref rid="bib38" ref-type="bibr">Ronquist and Huelsenbeck, 2003</xref>) on the individual data partitions as well as the combined aligned dataset. The Markov Chain Monte Carlo (MCMC) analysis used four chains and started from a random tree topology. The sample frequency was set at 500 for the combined analysis and the less informative loci (SSU, LSU, ITS and <italic>tef1</italic>) and at 100 for the remaining loci. The temperature value of the heated chain was 0.1 and the run stopped when the average standard deviation of split frequencies fell below 0.01. Burn-in was set to 25 % after which the likelihood values were stationary. Tracer v. 1.5.0 (<xref rid="bib35" ref-type="bibr">Rambaut & Drummond 2009</xref>) was used to confirm the convergence of chains. A maximum-likelihood analysis including 500 bootstrap replicates using RAxML v. 7.2.6 (<xref rid="bib50" ref-type="bibr">Stamatakis & Alachiotis 2010</xref>) was additionally run on the combined aligned dataset. Sequences of <italic>A. alternantherae</italic> (CBS 124392) were used as outgroup. The resulting trees were printed with TreeView v. 1.6.6 (<xref rid="bib32" ref-type="bibr">Page 1996</xref>) and, together with the alignments, deposited into TreeBASE (<ext-link ext-link-type="uri" xlink:href="http://www.treebase.org" id="intref0025">http://www.treebase.org</ext-link>).</p></sec><sec id="sec2.7"><title>Phylogenetic species recognition and naming in <italic>Alternaria</italic> sect. <italic>Alternaria</italic></title><p>Individual gene trees were generated as described in the “Phylogenetic analyses” part above and examined manually. A species clade was only recognised as unique if it was well-supported and monophyletic with all of its included isolates in multiple single-gene phylogenies, and no incongruencies were observed in the other single-gene phylogenies, <italic>e.g.</italic> the included isolates clustered together in all single-gene phylogenies. Unique molecular markers for the recognised species, which separates them from the other species in sect. <italic>Alternaria</italic>, are described with the species below and listed in a table which can be downloaded from the CBS-KNAW website (<ext-link ext-link-type="uri" xlink:href="http://www.cbs.knaw.nl/index.php/studies-in-mycology" id="intref0030">www.cbs.knaw.nl/index.php/studies-in-mycology</ext-link>) or requested from the author. Unique fixed nucleotide positions were derived from the respective alignments of the separate loci deposited in TreeBASE based on a comparison of the sequences of all isolates from the specific species to the sequences of all isolates of the other recognised species within sect. <italic>Alternaria</italic>.</p><p>To further standardise the taxonomic terms used, the trinomial system introduced by <xref rid="bib39" ref-type="bibr">Rotem (1994)</xref> is favoured. When differences in host affinity are observed within the isolates of one (of the above-defined) species, the third epithet, the <italic>forma specialis</italic>, defines the affinity to this specific host in accordance with the produced toxin causing this affinity. When different toxins are produced on the same host, but these toxins affect different host species, the term pathotype should be used in addition. All isolates which are not confined to specific hosts and / or toxins should retain only the binomial name until such specificity is found. For examples, please refer to the species notes under <italic>A. alternata</italic> below and to the <xref rid="sec4" ref-type="sec">Discussion</xref>.</p></sec></sec><sec id="sec3"><title>Results</title><sec id="sec3.1"><title>NGS</title><p>Nine <italic>Alternaria</italic> (morpho)species were sequenced using Ion Torrent™ or Illumina<sup>®</sup> sequencing technologies, yielding between 38× and >260× average genome coverage (<xref rid="tbl2" ref-type="table">Table 2</xref>). The assembled genomes ranged in size from 33.3–35.2 Mb within sect. <italic>Alternaria</italic> and from 32.0–39.1 Mb for all <italic>Alternaria</italic> genomes (<xref rid="tbl2" ref-type="table">Table 2</xref>). To characterise the assembled genomes, the repetitive complement of each individual genome was identified and classified using a combination of <italic>de novo</italic> prediction and identification of known repetitive elements. Surprisingly, the number of repetitive sequences differed significantly between different <italic>Alternaria</italic> genomes. Within sect. <italic>Alternaria</italic>, the number of repetitive sequences is relatively low; only 1.4–2.7 % of each genome was classified as repetitive (<xref rid="tbl2" ref-type="table">Table 2</xref>). In contrast, <italic>A. avenicola</italic> and <italic>A. alternantherae</italic> carry significantly higher percentages of repetitive elements, >10 % and >15 %, respectively (<xref rid="tbl2" ref-type="table">Table 2</xref>).</p><p>To assess the genomic differences between the included species, whole-genome alignments to the reference genome of <italic>A. alternata</italic> (CBS 916.96) were performed. These alignments revealed 96.7–98.2 % genome identity within sect. <italic>Alternaria</italic> compared to 85.1–89.3 % genome identity between isolates from other sections with <italic>A. alternata</italic>. Furthermore, the number of single nucleotide polymorphisms (SNPs) between the different species were assessed by mapping genomic reads to the reference genome of <italic>A. alternata</italic> (CBS 916.96). Between isolates from sect. <italic>Alternaria</italic>, 1.4–2.8 % SNPs were observed, while the percentage of SNPs found in isolates from different sections was considerably higher, ranging from 8.0–10.3 % (<xref rid="tbl2" ref-type="table">Table 2</xref>).</p><p>To further characterise the genus, deep transcriptome sequences of 12 isolates were derived that were mapped to the reference isolate of <italic>A. alternata</italic> (CBS 916.96). In this case, 0.8–1.8 % SNPs among the isolates from sect. <italic>Alternaria</italic> were observed, while the isolates from other sections displayed 6.1–8.5 % SNPs (<xref rid="tbl3" ref-type="table">Table 3</xref>).</p><p>Marker genes with potential discriminatory power were identified by predicting a set of conserved eukaryotic genes (KOG) in the genomes of the five assembled sect. <italic>Alternaria</italic> genomes using the CEGMA pipeline. Out of 380 included KOGs, 326 (86 %) had a conservation level of ≥98 %. Therefore, we focused on the 25 KOGs with the lowest degree of conservation, ranging from 83.0–97.3 %, and evaluated their discriminatory power. KOGs that were not able to distinguish all morphospecies included in the whole-genome and transcriptome sequencing were immediately rejected. Primers spanning the first 5 introns of KOG1058 and KOG1077 were designed (see the “<xref rid="sec2.5" ref-type="sec">PCR and sequencing</xref>” part of the “<xref rid="sec2" ref-type="sec">Material and Methods</xref>”). These proteins were found on place 16 and 23 in the conservation table and both act in the vesicle coat complex, although in different systems; namely COPI versus AP-2.</p><p>The pseudo-molecule derived from the whole-genome and transcriptome reads with REALPHY contained 1 750 944 nt. The topology from the REALPHY phylogeny (<xref rid="fig1" ref-type="fig">Fig. 1</xref>) corresponds to the multi-gene phylogeny based on a five-gene combined dataset (fig. 3 in <xref rid="bib26" ref-type="bibr">Lawrence <italic>et al.</italic> 2013</xref>) and a three-gene combined dataset (fig. 1 in <xref rid="bib61" ref-type="bibr">Woudenberg <italic>et al.</italic> 2013</xref>). Section <italic>Alternantherae</italic> and sect. <italic>Porri</italic> are the sister sections of sect. <italic>Alternaria</italic>, while sect. <italic>Infectoriae</italic> and sect. <italic>Crivellia</italic>, are the most distant sections (<xref rid="fig1" ref-type="fig">Fig. 1</xref>).</p></sec><sec id="sec3.2"><title>Gene-based phylogeny and identification</title><p>From the 168 isolates included in the multi-gene phylogeny, the amplification and / or sequencing of two isolates for the <italic>rpb2</italic> gene, three for the <italic>Alt a 1</italic> gene, one for the <italic>endoPG</italic> gene and four for the OPA10-2 regions failed (<xref rid="tbl1" ref-type="table">Table 1</xref>); these genes were included as missing data in the combined analysis. The aligned sequences of the SSU (1 021 aligned characters), LSU (849 aligned characters), ITS (523 aligned characters), <italic>gapdh</italic> (579 aligned characters), <italic>tef1</italic> (241 aligned characters), <italic>rpb2</italic> (753 aligned characters), <italic>Alt a 1</italic> (473 aligned characters), <italic>endoPG</italic> (448 aligned characters) and OPA10-2 (634 aligned characters) gene regions contained 6, 9, 27, 60, 42, 87, 110, 59 and 123 unique site patterns, respectively. Because of the low informative value of the SSU and LSU sequences (6 / 9 unique site patterns out of 1 021 / 849 aligned characters) these genes were excluded from the multi-gene phylogeny. The multi-gene phylogeny based on the remaining seven gene regions contained 3 651 characters including alignment gaps, which, after discarding the burn-in phase, resulted in a 50 % majority rule consensus tree based on 15 002 trees from two runs (<xref rid="fig2" ref-type="fig">Fig. 2</xref>).</p><p>The alignments of the additional gene regions that were sequenced, KOG1058 and KOG1077, consisted of 921 and 781 aligned characters, respectively, of which 118 and 78 were unique site patterns. The amplification and / or sequencing of the KOG1077 gene failed in six of the 49 isolates, representing the species <italic>A. alstroemeriae</italic>, <italic>A. iridiaustralis</italic> and <italic>A. jacinthicola</italic> (<xref rid="tbl4" ref-type="table">Table 4</xref>). Since the KOG1077 sequences could not separate <italic>A. longipes</italic> from <italic>A. gossypina</italic>, no further effort was put in optimising the primers to obtain the missing data.</p><p>Although the single-gene phylogenies are not fully congruent in terms of species resolution (see TreeBASE), 11 clades can be distinguished consistently within the single-gene phylogenies and in the multi-gene phylogeny (<xref rid="fig2" ref-type="fig">Fig. 2</xref>). Eight of those are single species clades representing <italic>A. alstroemeriae</italic>, <italic>A. betae-kenyensis</italic>, <italic>A. eichhorniae</italic>, <italic>A. gaisen</italic>, <italic>A. iridiaustralis</italic>, <italic>A. jacinthicola</italic>, <italic>A. longipes</italic>, and <italic>A. tomato</italic>. Three further clades constitute numerous morphospecies, which are synonymised here under <italic>A. burnsii</italic>, <italic>A. gossypina</italic> and the <italic>A. arborescens</italic> species complex (AASC). However, the majority of the isolates (105 / 168), representing 35 morphospecies, do not form clear phylogenetic clades. The subclades that are formed by these isolates are incongruent between the different gene regions sequenced; no two genes show the same groupings from any of the 100 plus isolates. These morphospecies are synonymised below under <italic>A. alternata</italic>.</p><p>None of the genes sequenced in this study enabled us to distinguish all of the phylogenetic species recognised here on its own (<xref rid="tbl4" ref-type="table">Table 4</xref>). The commonly used <italic>gapdh</italic> sequence could distinguish all species, except the <italic>A. arborescens</italic> species complex (AASC), from <italic>A. alternata</italic>. Five genes, namely <italic>rpb2</italic>, OPA10-2, <italic>Alt a 1</italic>, <italic>endoPG</italic> and KOG1058, could separate all species from <italic>A. alternata</italic>, but failed to separate different pairs of other species from one another (see <xref rid="tbl4" ref-type="table">Table 4</xref>). The SSU, LSU and ITS genes were least successful in separating the species accepted in this study. The unique fixed nucleotides per gene region are provided below under the treatment of each species, and are summarised in a table which can be downloaded from the CBS-KNAW website (<ext-link ext-link-type="uri" xlink:href="http://www.cbs.knaw.nl/index.php/studies-in-mycology" id="intref0035">www.cbs.knaw.nl/index.php/studies-in-mycology</ext-link>) or requested from the author.</p></sec><sec id="sec3.3"><title>Phylogenetic species in sect. <italic>Alternaria</italic></title><p><bold><italic>Alternaria alstroemeriae</italic></bold> E.G. Simmons & C.F. Hill, CBS Biodiversity Ser. (Utrecht) 6: 444. 2007.</p><p><italic>Specimens examined</italic>: <bold>Australia</bold>, from leaf of <italic>Alstroemeria</italic> sp. (<italic>Alstroemeriaceae</italic>), Jul. 2005, C.F. Hill, culture <bold>ex-type</bold> CBS 118809 = E.G.S. 52.068. <bold>USA</bold>, California, Sacramento, from leaf spot of <italic>Alstroemeria</italic> sp., before Apr. 2002, D. Fogle, CBS 118808 = E.G.S. 50.116.</p><p><italic>Unique fixed nucleotides</italic>: <bold><italic>gapdh</italic></bold> position 485 (T); <bold><italic>rpb2</italic></bold> position 162 (G); <bold><italic>tef1</italic></bold> position 52 (C), 143 (C), 165 (T), 205 (G); <bold>OPA10-2</bold> position 120 (T), 151 (T), 303 (G), 318 (G), 330 (C), 390 (G), 417 (C), 486 (G); <bold><italic>Alt a 1</italic></bold> position 157 (T), 178 (T), 404 (A); <bold><italic>endoPG</italic></bold> position 37 (A), 46 (C), 316 (T); <bold>KOG1058</bold> position 51 (C), 514 (T), 533 (C).</p><p><bold><italic>Alternaria alternata</italic></bold> (Fr.) Keissl., Beih. Bot. Centralbl., Abt. 2, 29: 434. 1912.</p><p><italic>Basionym</italic>: <italic>Torula alternata</italic> Fr., Syst. Mycol. (Lundae) 3: 500. 1832. (nom. sanct.)</p><p>= <italic>Alternaria tenuis</italic> Nees, Syst. Pilze (Würzburg): 72. 1816 [1816–1817].</p><p>= <italic>Helminthosporium tenuissimum</italic> Kunze ex Nees & T. Nees, Nova Acta Acad. Caes. Leop.-Carol. German. Nat. Cur. 9: 242. 1818.</p><p>≡ <italic>Macrosporium tenuissimum</italic> (Nees & T. Nees) Fr., Syst. Mycol. 3: 374. 1832. (nom. sanct.)</p><p>≡ <italic>Clasterosporium tenuissimum</italic> (Nees & T. Nees: Fr.) Sacc., Sylloge Fungorum (Abellini) 4: 393. 1886.</p><p>≡ <italic>Alternaria tenuissima</italic> (Nees & T. Nees: Fr.) Wiltshire, Trans. Brit. Mycol. Soc. 18: 157. 1933.</p><p>= <italic>Macrosporium fasciculatum</italic> Cooke & Ellis, Grevillea 6: 6. 1877.</p><p>≡ <italic>Alternaria fasciculata</italic> (Cooke & Ellis) l.R. Jones & Grout, Bull. Torrey Bot. Club 24: 257. 1897.</p><p>= <italic>Macrosporium caudatum</italic> Cooke & Ellis, Grevillea 6: 87. 1878.</p><p>≡ <italic>Alternaria caudata</italic> (Cooke & Ellis) E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 496. 2007.</p><p>= <italic>Macrosporium maydis</italic> Cooke & Ellis, Grevillea 6: 87. 1878.</p><p>= <italic>Macrosporium inquinans</italic> Cooke & Ellis, Grevillea 7: 39. 1878.</p><p>= <italic>Macrosporium meliloti</italic> Peck, Rep. (Annual) NewYork State Mus. Nat. Hist. 33: 28. 1880.</p><p>= <italic>Macrosporium erumpens</italic> Cooke, Grevillea 12: 32. 1883.</p><p>≡ <italic>Alternaria erumpens</italic> (Cooke) Joly, Le Genre <italic>Alternaria</italic>: 199. 1964.</p><p>= <italic>Macrosporium martindalei</italic> Ellis & G. Martin, Amer. Naturalist 18: 189. 1884.</p><p>≡ <italic>Alternaria martindalei</italic> (Ellis & G. Martin) Joly, Le Genre <italic>Alternaria</italic>: 209. 1964.</p><p>= <italic>Macrosporium polytrichi</italic> Peck, Rep. (Annual) NewYork State Mus. Nat. Hist. 34: 31. 1890.</p><p>= <italic>Macrosporium podophylli</italic> Ellis & Everh., Proc. Acad. Nat. Sci. Philadelphia 43: 92. 1891.</p><p>≡ <italic>Alternaria podophylli</italic> (Ellis & Everhart) Joly, Le Genre <italic>Alternaria</italic>: 212. 1964.</p><p>= <italic>Macrosporium seguierii</italic> Allescher, Hedwigia 33: 75. 1894.</p><p>= <italic>Macrosporium amaranthi</italic> Peck, Bull. Torrey Bot. Club 22: 493. 1895.</p><p>≡ <italic>Alternaria amaranthi</italic> (Peck) J. van Hook, Proc. Indiana Acad. Sci. 1920: 214. 1921.</p><p>= <italic>Alternaria citri</italic> Ellis & N. Pierce, Bot. Gaz. (Crawfordville) 33: 234. 1902.</p><p>= <italic>Alternaria ribis</italic> Bubák & Ranojević, Ann. Mycol. 8: 400. 1910.</p><p>= <italic>Alternaria mali</italic> Roberts, J. Agric. Res. 2: 58. 1914.</p><p>= <italic>Alternaria palandui</italic> Ayyangar, Bull. Agric. Res. Inst., Pusa 179: 14. 1928.</p><p>= <italic>Alternaria lini</italic> Dey, Indian J. Agric. Sci. 3: 881. 1933.</p><p>= <italic>Alternaria tenuissima</italic> var. <italic>godetiae</italic> Neerg., Trans. Brit. Mycol. Soc. 18: 157. 1933.</p><p>≡ <italic>Alternaria godetiae</italic> (Neerg.) Neerg., Aarsberetn. J. E. Ohlens Enkes Plantepatol. Lab. 10: 14. 1945.</p><p>= <italic>Macrosporium pruni-mahalebi</italic> Săvulescu & Sandu, Hedwigia 75: 228. 1935.</p><p>= <italic>Alternaria rumicicola</italic> R.L. Mathur, J.P. Agnihotri & Tyagi, Curr. Sci. 31: 297. 1962.</p><p>= <italic>Alternaria tenuissima</italic> var. <italic>verruculosa</italic> S. Chowdhury, Proc. Natl. Acad. Sci. India, Sect. B, Biol. Sci. 36: 301. 1966.</p><p>= <italic>Alternaria angustiovoidea</italic> E.G. Simmons, Mycotaxon 25: 198. 1986.</p><p>= <italic>Alternaria pellucida</italic> E.G. Simmons, Mycotaxon 37: 102. 1990.</p><p>= <italic>Alternaria rhadina</italic> E.G. Simmons, Mycotaxon 48: 101. 1993.</p><p>= <italic>Alternaria destruens</italic> E.G. Simmons, Mycotaxon 68: 419. 1998.</p><p>= <italic>Alternaria broussonetiae</italic> T.Y. Zhang, W.Q. Chen & M.X. Gao, Mycotaxon 72: 439. 1999.</p><p>= <italic>Alternaria citriarbusti</italic> E.G. Simmons, Mycotaxon 70: 287. 1999.</p><p>= <italic>Alternaria citrimacularis</italic> E.G. Simmons, Mycotaxon 70: 277. 1999.</p><p>= <italic>Alternaria dumosa</italic> E.G. Simmons, Mycotaxon 70: 310. 1999.</p><p>= <italic>Alternaria interrupta</italic> E.G. Simmons, Mycotaxon 70: 306. 1999.</p><p>= <italic>Alternaria limoniasperae</italic> E.G. Simmons, Mycotaxon 70: 272. 1999.</p><p>= <italic>Alternaria perangusta</italic> E.G. Simmons, Mycotaxon 70: 303. 1999.</p><p>= <italic>Alternaria tenuissima</italic> var. <italic>alliicola</italic> T.Y. Zhang, Mycotaxon 72: 450. 1999.</p><p>= <italic>Alternaria toxicogenica</italic> E.G. Simmons, Mycotaxon 70: 294. 1999.</p><p>= <italic>Alternaria turkisafria</italic> E.G. Simmons, Mycotaxon 70: 290. 1999.</p><p>= <italic>Alternaria sanguisorbae</italic> M.X. Gao & T.Y. Zhang, Mycosystema 19: 456. 2000.</p><p>= <italic>Alternaria platycodonis</italic> Z.Y. Zhang & H. Zhang, Flora Fungorum Sin., <italic>Alternaria</italic>: 66. 2003.</p><p>= <italic>Alternaria yali-inficiens</italic> R.G. Roberts [as ‘<italic>yaliinficiens</italic>’], Pl. Dis. 89: 142. 2005.</p><p>= <italic>Alternaria astragali</italic> Wangeline & E.G. Simmons, Mycotaxon 99: 84. 2007.</p><p>= <italic>Alternaria brassicinae</italic> E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 532. 2007.</p><p>= <italic>Alternaria citricancri</italic> E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 542. 2007.</p><p>= <italic>Alternaria daucifolii</italic> E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 518. 2007.</p><p>= <italic>Alternaria herbiphorbicola</italic> E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 608. 2007.</p><p>= <italic>Alternaria pulvinifungicola</italic> E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 514. 2007.</p><p>= <italic>Alternaria postmessia</italic> E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 598. 2007.</p><p>= <italic>Alternaria seleniiphila</italic> Wangeline & E.G. Simmons, Mycotaxon 99: 86. 2007.</p><p>= <italic>Alternaria soliaegyptiaca</italic> E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 506. 2007.</p><p>= <italic>Alternaria tomaticola</italic> E.G. Simmons & Chellemi, CBS Biodiversity Ser. (Utrecht) 6: 528. 2007.</p><p>= <italic>Alternaria vaccinii</italic> E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 432. 2007.</p><p>= <italic>Alternaria viniferae</italic> Yong Wang bis, Y.Y. Than, K.D. Hyde, X.H. Li, Mycol. Progr. 13: 1124. 2014.</p><p><italic>Type and representative specimens examined</italic>: <bold>Canada</bold>, Manitoba, from <italic>Euphorbia esula</italic> (<italic>Euphorbiaceae</italic>), 1982, K. Mortensen, culture <bold>ex-type</bold> of <italic>A. angustiovoidea</italic> CBS 195.86 = E.G.S. 36.172 = DAOM 185214. <bold>China</bold>, Hebei, from fruit of <italic>Pyrus bretschneideri</italic> (<italic>Rosaceae</italic>), 2001, R.G. Roberts, culture <bold>ex-type</bold> of <italic>A. yali-inficiens</italic> CBS 121547 = E.G.S. 50.048; Shaanxi, Hanzhong, from <italic>Platycodon grandiflorus</italic> (<italic>Campanulaceae</italic>), before Dec. 2001, T.Y. Zhang, culture <bold>ex-type</bold> of <italic>A. platycodonis</italic> CBS 121348 = E.G.S. 50.070; Shangdong, Changqing, from <italic>Broussonetia papyrifera</italic> (<italic>Moraceae</italic>), 13 Sep. 1996, T.Y. Zhang, culture <bold>ex-type</bold> of <italic>A. broussonetiae</italic> CBS 121455 = E.G.S. 50.078; Shangdong, Jinan, from <italic>Sanguisorba officinalis</italic> (<italic>Rosaceae</italic>), 19 Sep. 1996, M.X. Gao, culture <bold>ex-type</bold> of <italic>A. sanguisorbae</italic> CBS 121456 = E.G.S. 50.080. <bold>Denmark</bold>, Sjaelland, Clausdal, from <italic>Godetia</italic> sp. (<italic>Onagraceae</italic>), 27 Jul. 1942, P. Neergaard, culture <bold>ex-type</bold> of <italic>A. godetiae</italic> CBS 117.44 = E.G.S. 06.190 = VKM F-1870. <bold>Egypt</bold>, Sabet, from soil, before Jan. 1933, culture <bold>ex-type</bold> of <italic>A. soliaegyptiaca</italic> CBS 103.33 = E.G.S. 35.182 = IHEM 3319. <bold>India</bold>, from <italic>Arachis hypogaea</italic> (<italic>Fabaceae</italic>), 1 Dec. 1980, L.V. Gangawane, culture <bold>ex-epitype</bold> CBS 916.96 = CBS 110977 = CBS 115616 = E.G.S. 34.016 = IMI 254138. <bold>Israel</bold>, from <italic>Minneola tangelo</italic> (<italic>Rutaceae</italic>), before Nov. 1996, Z. Solel, culture <bold>ex-type</bold> of <italic>A. interrupta</italic> CBS 102603 = E.G.S. 45.011; Mayan Zvi, from <italic>Minneola tangelo</italic>, before Nov. 1996, Z. Solel, culture <bold>ex-type</bold> of <italic>A. dumosa</italic> CBS 102604 = E.G.S. 45.007. <bold>Japan</bold>, from fruit of <italic>Citrus unshiu</italic> (<italic>Rutaceae</italic>), 1968, K. Tubaki, culture <bold>ex-type</bold> of <italic>A. pellucida</italic> CBS 479.90 = E.G.S. 29.028; from leaf of <italic>Pyrus pyrifolia</italic> (<italic>Rosaceae</italic>), 1990, K. Nagano, culture <bold>ex-type</bold> of <italic>A. rhadina</italic> CBS 595.93. <bold>Turkey</bold>, Kuzucuoglu, from <italic>Minneola tangelo</italic>, May 1996, Y. Canihos, culture <bold>ex-type</bold> of <italic>A. turkisafria</italic> CBS 102599 = E.G.S. 44.166; Adana region, from <italic>Minneola tangelo</italic>, May 1996, Y. Canihos, culture <bold>ex-type</bold> of <italic>A. perangusta</italic> CBS 102602 = E.G.S. 44.160. <bold>UK</bold>, from <italic>Dianthus chinensis</italic> (<italic>Caryophyllaceae</italic>), 20 Feb. 1981, A.S. Taylor, representative isolate of <italic>A. tenuissima</italic> CBS 918.96 = E.G.S. 34.015 = IMI 255532. <bold>USA</bold>, from <italic>Malus sylvestris</italic> (<italic>Rosaceae</italic>), before Dec. 1924, J.W. Roberts, culture <bold>ex-type</bold> of <italic>A. mali</italic> CBS 106.24 = E.G.S. 38.029 = ATCC 13963; Arizona, Yuma, from <italic>Brassica oleracea</italic> (<italic>Brassicaceae</italic>), Apr. 1982, R.H. Morrison, culture <bold>ex-type</bold> of <italic>A. brassicinae</italic> CBS 118811 = E.G.S. 35.158; California, from fruit of <italic>Citrus sinensis</italic> (<italic>Rutaceae</italic>), before Nov. 1947, D.E. Bliss, representative isolate of <italic>A. citri</italic> CBS 102.47 = E.G.S. 02.062; California, Los Angeles, from <italic>Citrus paradisi</italic> (<italic>Rutaceae</italic>), 12 Jul. 1947, L. Davis, culture ex-type of <italic>A. citricancri</italic> CBS 119543 = E.G.S. 12.160; Colorado, from leaf of <italic>Allium</italic> sp. (<italic>Alliaceae</italic>), F.A. Weiss, culture <bold>ex-epitype</bold> of <italic>A. palandui</italic> CBS 121336 = E.G.S. 37.005 = ATCC 11680; Colorado, Fort Collins, from the root of <italic>Stanleya pinnata</italic> (<italic>Brassicaceae</italic>), 19 Jun. 2002, A. Wangeline, culture <bold>ex-type</bold> of <italic>A. seleniiphila</italic> CBS 127671 = E.G.S. 52.121; Florida, Lake Alfred, from leaf lesion of <italic>Citrus jambhiri</italic> (<italic>Rutaceae</italic>), before Jul. 1997, culture <bold>ex-type</bold> of <italic>A. limoniasperae</italic> CBS 102595 = E.G.S. 45.100; Florida, Lake Alfred, from leaf lesion of <italic>Citrus jambhiri</italic>, before Jul. 1997, culture <bold>ex-type</bold> of <italic>A. citrimacularis</italic> CBS 102596 = E.G.S. 45.090; Florida, Lake Alfred, from leaf spot of <italic>Minneola tangelo</italic>, before Feb. 1998, culture <bold>ex-type</bold> of <italic>A. citriarbusti</italic> CBS 102598 = E.G.S. 46.141; Florida, Lake Alfred, from <italic>Minneola tangelo</italic>, 19 Dec. 1980, J.O. Whiteside, culture <bold>ex-type</bold> of <italic>A. postmessia</italic> CBS 119399 = E.G.S. 39.189; Florida, Quincy, from <italic>Solanum lycopersicum</italic> (<italic>Solanaceae</italic>), June 1996, D. Chellemi, culture <bold>ex-type</bold> of <italic>A. tomaticola</italic> CBS 118814 = E.G.S. 44.048; Florida, Wauchula, from <italic>Citrus reticulata</italic> (<italic>Rutaceae</italic>), 6 Jun. 1975, J.O. Whiteside, culture <bold>ex-type</bold> of <italic>A. toxicogenica</italic> CBS 102600 = E.G.S. 39.181 = ATCC 38963; Florida, Zellwood, from <italic>Daucus carota</italic> (<italic>Apiaceae</italic>), Jan. 1984, R.H. Morrison, culture <bold>ex-type</bold> of <italic>A. daucifolii</italic> CBS 118812 = E.G.S. 37.050; Iowa, from <italic>Quercus</italic> sp. (<italic>Fagaceae</italic>), 28 Jul. 1953, A. Engelhard, culture <bold>ex-type</bold> of <italic>A. pulvinifungicola</italic> CBS 194.86 = E.G.S. 04.090 = QM 1347; Maryland, from <italic>Euphorbia esula</italic>, before Dec. 1991, culture <bold>ex-type</bold> of <italic>A. herbiphorbicola</italic> CBS 119408 = E.G.S. 40.140; Massachusetts, Hadley, from fruit of <italic>Cucumis sativus</italic> (<italic>Cucurbitaceae</italic>), 24 Sep. 1984, E.G. Simmons, representative isolate of <italic>A. caudata</italic> CBS 121544 = E.G.S. 38.022; Massachusetts, Rochester, from <italic>Cuscuta gronovii</italic> (<italic>Convolvulaceae</italic>), Aug. 1997, F. Caruso, culture <bold>ex-type</bold> isolate of <italic>A. destruens</italic> CBS 121454 = E.G.S. 46.069; New Jersey, from <italic>Vaccinium</italic> sp. (<italic>Ericaceae</italic>), Oct. 1973, R.A. Cappellini, culture <bold>ex-type</bold> of <italic>A. vaccinii</italic> CBS 118818 = E.G.S. 31.032; Wyoming, Laramie, from the root of <italic>Astragalus bisulcatus</italic> (<italic>Fabaceae</italic>), 8 Jun. 2002, A. Wangeline, culture <bold>ex-type</bold> of <italic>A. astragali</italic> CBS 127672 = E.G.S. 52.122. <bold>Unknown</bold>, from <italic>Linum usitatissimum</italic> (<italic>Linaceae</italic>), before Jul. 1934, P.K. Dey, culture <bold>ex-type</bold> of <italic>A. lini</italic> CBS 106.34 = E.G.S. 06.198 = DSM 62019 = MUCL 10030.</p><p><italic>Notes</italic>: Both the names <italic>Torula alternata</italic> and <italic>Macrosporium tenuissimum</italic> represent sanctioned names by Fries (1832), with the basionym of <italic>tenuissimum</italic> (1818) being the older. However, the well-established name of the type species of <italic>Alternaria</italic>, <italic>A. alternata</italic> is retained above the older name <italic>A. tenuissima</italic>, as this would result in confusion among the user community, and be counterproductive. A proposal to conserve <italic>A. alternata</italic> over <italic>A. tenuissima</italic> will be compiled for submission to the Nomenclature Committee of Fungi. The isolate CBS 447.86, isolated from <italic>Malva</italic> sp. in Marocco, was stored in the CBS collection as <italic>Alternaria malvae</italic>. The original description of <italic>A. malvae</italic> was from leaf lesions of <italic>Malva crispa</italic>, from Seine-Inférieure (now called Seine-Maritime), France. Therefore <italic>A. malvae</italic> is not synonymised under <italic>A. alternata</italic>. The isolate CBS 106.34, send to the CBS by Dey in 1934 together with a reprint of his paper describing <italic>A. lini</italic>, is recognised as an ex-type isolate. Therefore <italic>A. lini</italic> is synonymised under <italic>A. alternata</italic>. The very recently described <italic>A. viniferae</italic> is synonymised based on the published <italic>gapdh</italic> and <italic>Alt a 1</italic> sequences, which cluster within <italic>A. alternata</italic>. Because of the relative high sequence variability amongst the <italic>A. alternata</italic> isolates, no unique fixed nucleotides are assigned to <italic>A. alternata</italic>. Three <italic>formae speciales</italic> of <italic>A. alternata</italic> are currently recognised; <italic>A. alternata f. sp. mali</italic> for isolates producing the AM-toxin, <italic>f. sp. fragariae</italic> for isolates producing the AF-toxin, and <italic>f. sp. citri</italic> with two pathotypes, <italic>i.e. f. sp. citri</italic> pathotype rough lemon for isolates producing the ACR-toxin, and <italic>f. sp. citri</italic> pathotype tangerine for isolates producing the ACT-toxin.</p><p><bold><italic>Alternaria betae-kenyensis</italic></bold> E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 530. 2007.</p><p><italic>Specimen examined</italic>: <bold>Kenya</bold>, from <italic>Beta vulgaris</italic> var. <italic>cicla</italic> (<italic>Chenopodiaceae</italic>), before Jun. 2001, <bold>ex-type</bold> CBS 118810 = E.G.S. 49.159 = IMI 385709.</p><p><italic>Unique fixed nucleotides</italic>: <bold>ITS</bold> position 464 (C); <bold><italic>gapdh</italic></bold> position 28 (C), 55 (A), 512 (T); <bold><italic>rpb2</italic></bold> position 204 (T), 363 (T), 369 (G), 447 (G), 468 (T), 480 (A), 507 (A), 627 (G); <bold><italic>tef1</italic></bold> position 213 (G), 218 (C); <bold>OPA10-2</bold> position 63 (C), 177 (A), 199 (G), 276 (T), 309 (T), 534 (C), 567 (A), 591 (A); <bold><italic>Alt a 1</italic></bold> position 55 (A), 155 (A), 311 (G), 338 (T), 359 (C), 365 (C), 379 (C), 440 (T), 473 (A); <bold><italic>endoPG</italic></bold> position 10 (T), 286 (T), 295 (T), 372 (G); <bold>KOG1058</bold> position 156 (C), 522 (T), 869 (G); <bold>KOG1077</bold> position 121 (A), 178 (C), 373 (A), 402 (C), 763 (C).</p><p><bold><italic>Alternaria burnsii</italic></bold> Uppal, Patel & Kamat, Indian J. Agric. Sci. 8: 49. 1938. <xref rid="fig3" ref-type="fig">Fig. 3</xref>.</p><p>= <italic>Alternaria tinosporae</italic> E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 508. 2007.</p><p>= <italic>Alternaria rhizophorae</italic> E.G. Simmons, CBS Biodiversity Ser. (Utrecht) 6: 510. 2007.</p><p><italic>Specimens examined</italic>: <bold>India</bold>, from <italic>Cuminum cyminum</italic> (<italic>Apiaceae</italic>), before Dec. 1938, B.N. Uppal, culture <bold>ex-type</bold> of <italic>A. burnsii</italic> CBS 107.38; Saznakhali, from infected leaf of <italic>Rhizophora mucronata</italic> (<italic>Rhizophoraceae</italic>), 14 Mar. 1995, <bold>ex-type</bold> of <italic>A. rhizophorae</italic> CBS 118816 = E.G.S. 43.145 = IMI 368045; Punjab, from <italic>Tinospora cordifolia</italic> (<italic>Menispermaceae</italic>), before Sept. 1987, culture <bold>ex-type</bold> of <italic>A. tinosporae</italic> CBS 118817 = E.G.S. 39.14 = IMI 318433; from human sputum, Anuradha, CBS 130264. <bold>Mozambique</bold>, from stem of <italic>Gossypium</italic> sp. (<italic>Malvaceae</italic>), Aug. 1950, Quintanilha, CBS 110.50. <bold>UK</bold>, from <italic>Sorghum</italic> sp. (<italic>Poaceae</italic>), 19 Dec. 1985, M. Kalicz, CBS 879.95 = IMI 300779. <bold>Unknown</bold>, from <italic>Gomphrena globosa</italic> (<italic>Amaranthaceae</italic>), before Mar. 1927, K. Togashi, CBS 108.27.</p><p><italic>Unique fixed nucleotides</italic>: <bold><italic>endoPG</italic></bold> position 196 (C), 199 (A).</p><p><italic>Notes</italic>: Although <italic>A. burnsii</italic> only has two unique fixed nucleotides, the species can easily be distinguished from <italic>A. alternata</italic> using molecular data. The low number of unique fixed nucleotides is due to its close phylogenetic relationship to <italic>A. tomato</italic> and <italic>A. jacinthicola</italic>. Most of the nucleotide differences present between <italic>A. burnsii</italic> and the <italic>A. alternata</italic> isolates are also present in the <italic>A. tomato</italic> and / or <italic>A. jacinthicola</italic> isolates.</p><p><bold><italic>Alternaria eichhorniae</italic></bold> Nag Raj & Ponnappa, Trans. Brit. Mycol. Soc. 55: 124. 1970.</p><p><italic>Specimens examined</italic>: <bold>India</bold>, Karnataka, Bangalore, from leaf of <italic>Eichhornia crassipes</italic> (<italic>Pontederiaceae</italic>), 28 Feb. 1966, R. Charudattan, culture <bold>ex-type</bold> CBS 489.92 = ATCC 22255 = ATCC 46777 = ATCC 201659 = IMI 121518. <bold>Indonesia</bold>, from leaf of <italic>Eichhornia crassipes</italic>, before Dec. 1996, representative culture CBS 119778 = E.G.S. 45.026 = IMI 372968.</p><p><italic>Unique fixed nucleotides</italic>: <bold>ITS</bold> position 105 (T); <bold><italic>gapdh</italic></bold> position 36 (G), 162 (G), 168 (T), 509 (A); <bold><italic>rpb2</italic></bold> position 6 (T), 549 (G); <bold><italic>tef1</italic></bold> position 12 (C), 31 (G), 223 (G); <bold>OPA10-2</bold> position 123 (G), 366 (C), 387 (A), 582 (T), 600 (A); <bold><italic>Alt a 1</italic></bold> position 67 (T), 130 (A), 298 (A), 356 (A), 397 (C); <bold><italic>endoPG</italic></bold> position 29 (A), 68 (C), 79 (T), 130 (A), 148 (T), 152 (A), 173 (A), 316 (G), 369 (C), 376 (C), 378 (T); <bold>KOG1058</bold> position 16 (C), 64 (T), 254 (C), 268 (T), 269 (G), 270 (G), 278 (G), 298 (C), 536 (C), 694 (G), 711 (C); <bold>KOG1077</bold> position 62 (T), 162 (C), 166 (C), 189 (C), 195 (C), 234 (G), 235 (C), 348 (C), 350 (C), 564 (A), 685 (A), 715 (A), 776 (T).</p><p><bold><italic>Alternaria gaisen</italic></bold> Nagano ex Hara, Sakumotsu Byorigaku, Edn 4: 263. 1928.</p><p>≡ <italic>Alternaria gaisen</italic> Nagano, J. Jap. Soc. Hort. Sci. 32: 16–19. 1920. (nom. illegit., Art. 39.1).</p><p>= <italic>Alternaria kikuchiana</italic> S. Tanaka, Mem. Coll. Agric. Kyoto Univ., Phytopathol. Ser. 28: 27. 1933.</p><p>= <italic>Macrosporium nashi</italic> Miura, Flora of Manchuria and East Mongolia, Part III Cryptogams, Fungi: 513. 1928.</p><p><italic>Specimens examined</italic>: <bold>Japan</bold>, Tottori, from <italic>Pyrus pyrifolia</italic> (<italic>Rosaceae</italic>), Jul. 1990, E.G. Simmons, representative isolate CBS 118488 = E.G.S. 90.0391; Tottori, from <italic>Pyrus pyrifolia</italic>, 11 Jul. 1990, E.G. Simmons, representative isolate CBS 632.93 = E.G.S. 90.0512. <bold>Netherlands</bold>, host unknown, Aug. 2011, S. I. R. Videira, SV01.</p><p><italic>Unique fixed nucleotides</italic>: <bold><italic>gapdh</italic></bold> position 383 (C), 473 (A); <bold><italic>rpb2</italic></bold> position 207 (T), 540 (G); <bold><italic>tef1</italic></bold> position 241 (T); <bold><italic>Alt a 1</italic></bold> position 1 (A), 13 (T), 97 (A), 339 (T), 345 (G), 413 (C); <bold><italic>endoPG</italic></bold> position 130 (C), 172 (A), 250 (T), 361 (T); <bold>KOG1058</bold> position 707 (G); <bold>KOG1077</bold> position 174 (A).</p><p><bold><italic>Alternaria gossypina</italic></bold> (Thüm.) J.C.F. Hopkins, Trans. Brit. Mycol. Soc. 16: 136. 1931. <xref rid="fig4" ref-type="fig">Fig. 4</xref>.</p><p><italic>Basionym</italic>: <italic>Macrosporium gossypinum</italic> Thüm., Herb. Mycol. Oecon.: no. 513. 1877.</p><p>= <italic>Alternaria grisea</italic> Szilv., Arch. Hydrobiol. 3: 546. 1936.</p><p>= <italic>Alternaria colombiana</italic> E.G. Simmons, Mycotaxon 70: 298. 1999.</p><p>= <italic>Alternaria tangelonis</italic> E.G. Simmons, Mycotaxon 70: 282. 1999.</p><p><italic>Type</italic>: (<bold>Lectotype</bold>, designated in Simmons 2003) <bold>USA</bold>, South Carolina, Aiken, from stems of dead <italic>Gossypinum herbaceum</italic>, 1876, H.W. Ravenel, <italic>Macrosporium gossypinum</italic> BPI 445306.</p><p><italic>Specimens examined</italic>: <bold>Colombia</bold>, Chinchiná, from fruit lesion of <italic>Minneola tangelo</italic> (<italic>Rutaceae</italic>), before Nov. 1996, B. L. Castro, culture <bold>ex-type</bold> of <italic>A. colombiana</italic> CBS 102601 = E.G.S. 45.017. <bold>Sumatra</bold>, Toba Heath, from soil, before Jun. 1936, A. von Szilvinyi, culture <bold>ex-type</bold> of <italic>A. grisea</italic> CBS 107.36. <bold>USA</bold>, Florida, from <italic>Minneola tangelo</italic>, before Aug. 1997, culture <bold>ex-type</bold> of <italic>A. tangelonis</italic> CBS 102597 = E.G.S. 45.114. <bold>Zimbabwe</bold>, from <italic>Gossypium</italic> sp. (<italic>Malvaceae</italic>), before Mar. 1932, J.C.F. Hopkins, culture <bold>ex-type</bold> of <italic>A. gossypina</italic> CBS 104.32. <bold>Unknown</bold>, from <italic>Malus domestica</italic> (<italic>Rosaceae</italic>), before Jun. 1923, A.S. Horne, CBS 100.23.</p><p><italic>Unique fixed nucleotides</italic>: <bold>OPA10-2</bold> position 172 (T); <bold>KOG1058</bold> position 19 (A), 20 (A).</p><p><italic>Notes</italic>: Although <italic>A. gossypina</italic> only has three unique fixed nucleotides, the species can easily be distinguished from <italic>A. alternata</italic> using molecular data. The low number of unique fixed nucleotides is due to its close phylogenetic relationship to <italic>A. longipes</italic>. Most of the nucleotide differences present between <italic>A. gossypina</italic> and the <italic>A. alternata</italic> isolates are also present in the <italic>A. longipes</italic> isolates. The isolate of <italic>A. gossypina</italic> deposited to the CBS by J.C.F. Hopkins, CBS 104.32, is recognised as ex-type culture of <italic>A. gossypina</italic> and the isolate of <italic>A. grisea</italic> deposited at the CBS by A. von Szilvinyi, CBS 107.36, is recognised as ex-type isolate of <italic>A. grisea</italic>. The isolate CBS 100.23, from <italic>Malus domestica</italic>, was deposited at the CBS as <italic>A. grossulariae</italic>. The original type description of this species, however, was from <italic>Grossularia</italic> sp., from Riga, Letland. Therefore <italic>A. grossulariae</italic> is not synonymised under <italic>A. gossypina</italic> based on this isolate pending the recollection of authentic material of the former species. By synonymising <italic>A. grisea</italic>, <italic>A. colombiana</italic> and <italic>A. tangelonis</italic> under <italic>A. gossypina</italic>, this species now has become an <italic>Alternaria</italic> species with a broad host range including host species from the <italic>Rutaceae</italic>, <italic>Malvaceae</italic> and <italic>Rosaceae</italic>.</p><p><bold><italic>Alternaria iridiaustralis</italic></bold> E.G. Simmons, Alcorn & C.F. Hill, CBS Biodiversity Ser. (Utrecht) 6: 434. 2007.</p><p><italic>Specimens examined</italic>: <bold>Australia</bold>, Queensland, Brisbane, from <italic>Iris</italic> sp. (<italic>Iridaceae</italic>), Oct. 1995, J. Alcorn, culture <bold>ex-type</bold> CBS 118486 = E.G.S. 43.014; Queensland, Brisbane, from <italic>Iris</italic> sp., Oct. 1996, J. Alcorn, CBS 118487 = E.G.S. 44.147. <bold>New Zealand</bold>, Auckland, Grey Lynn, from leaf of <italic>Iris</italic> sp., 7 Jan. 2001, C.F. Hill, CBS 118404 = E.G.S. 49.078.</p><p><italic>Unique fixed nucleotides</italic>: <bold>ITS</bold> position 475 (A); <bold><italic>gapdh</italic></bold> position 33 (A), 171 (T), 174 (A), 186 (C), 218 (G), 365 (A); <bold><italic>rpb2</italic></bold> position 12 (T), 489 (T), 516 (T), 591 (C); <bold><italic>tef1</italic></bold> position 9 (G), 43 (T), 238 (G); <bold>OPA10-2</bold> position 27 (G), 209 (C), 226 (A), 243 (G), 270 (C), 273 (A), 297 (C), 339 (T), 435 (A), 486 (A); <bold><italic>Alt a 1</italic></bold> position 28 (T), 73 (C), 97 (G), 109 (T), 111 (G), 224 (A), 256 (T), 266 (A), 267 (G), 350 (G), 361 (A), 388 (C); <bold><italic>endoPG</italic></bold> position 87 (A), 93 (G), 101 (G), 210 (A), 219 (T), 338 (A), 340 (T), 374 (A); <bold>KOG1058</bold> position 25 (C), 48 (A), 498 (C), 569 (T).</p><p><bold><italic>Alternaria jacinthicola</italic></bold> Dagno & M.H. Jijakli, J. Yeast Fungal Res. 2: 102. 2011.</p><p>= <italic>Alternaria capsicicola</italic> A. Nasehi, J. Kadir & F. Abed-Ashtiani, Mycol. Progr. 13: 1044. 2014. (nom. inval., Art. 8.1, Melbourne Code).</p><p><italic>Specimens examined</italic>: <bold>Mali</bold>, from leaf of <italic>Eichhornia crassipes</italic> (<italic>Pontederiaceae</italic>), 2006, K. Dagno, culture <bold>ex-type</bold> CBS 133751 = MUCL 53159. <bold>Mauritius</bold>, from leaf spot of <italic>Arachis hypogaea</italic> (<italic>Fabaceae</italic>), 2 Sep. 1959, S. Felix, CBS 878.95 = IMI 77934b. <bold>Unknown</bold>, from imported fruit of <italic>Cucumis melo</italic> (<italic>Cucurbitaceae</italic>) bought in Dutch supermarket, Feb. 2013, U. Damm, UD03.</p><p><italic>Unique fixed nucleotides</italic>: <bold><italic>gapdh</italic></bold> position 479 (A); <bold><italic>rpb2</italic></bold> position 6 (T), 549 (G); <bold>OPA10-2</bold> position 159 (C); <bold><italic>Alt a 1</italic></bold> position 295 (C), 353 (C), 364 (G); <bold><italic>endoPG</italic></bold> position 19 (T).</p><p><italic>Notes</italic>: Although <italic>A. jacinthicola</italic> only has a few unique fixed nucleotides, the species can easily be distinguished from <italic>A. alternata</italic> using molecular data. The low number of unique fixed nucleotides is due to its close phylogenetic relationship to <italic>A. tomato</italic> and <italic>A. burnsii</italic>. Most of the nucleotide differences present between <italic>A. jacinthicola</italic> and the <italic>A. alternata</italic> isolates are also present in the <italic>A. tomato</italic> and / or <italic>A. burnsii</italic> isolates. By including two other isolates with <italic>A. jacinthicola</italic>, it has become an <italic>Alternaria</italic> species with a broad host range including species from the <italic>Pontederiaceae</italic>, <italic>Cucurbitaceae</italic> and <italic>Fabaceae</italic>. The recently described <italic>A. capsicicola</italic> (<xref rid="bib29" ref-type="bibr">Nasehi <italic>et al.</italic> 2014</xref>) is synonymised under <italic>A. jacinthicola</italic> based on its <italic>Alt a 1</italic> (<ext-link ext-link-type="uri" xlink:href="ncbi-n:KJ508068" id="intref0040">KJ508068</ext-link>, <ext-link ext-link-type="uri" xlink:href="ncbi-n:KJ508069" id="intref0045">KJ508069</ext-link>) and <italic>gapdh</italic> (<ext-link ext-link-type="uri" xlink:href="ncbi-n:KJ508064" id="intref0050">KJ508064</ext-link>, <ext-link ext-link-type="uri" xlink:href="ncbi-n:KJ508065" id="intref0055">KJ508065</ext-link>) sequences which are 100 % identical to <italic>A. jacinthicola</italic>. The name <italic>A. capsicicola</italic> is invalid, as two accessions were designated as holotype specimens.</p><p><bold><italic>Alternaria longipes</italic></bold> (Ellis & Everh.) E.W. Mason, Mycol. Pap. 2: 19. 1928.</p><p><italic>Basionym</italic>: <italic>Macrosporium longipes</italic> Ellis & Everh., J. Mycol. 7: 134. 1892.</p><p>= <italic>Alternaria brassicae var. tabaci</italic> Preissecker, Fachliche Mitt. Österr. Tabakregie 16: 4. 1916.</p><p><italic>Specimens examined</italic>: <bold>USA</bold>, North Carolina, from <italic>Nicotiana tabacum</italic> (<italic>Solanaceae</italic>), 1967, E.G. Simmons, CBS 917.96; North Carolina, from <italic>Nicotiana tabacum</italic>, before Nov. 1971, representative isolate CBS 540.94 = E.G.S. 30.033 = QM 9589; North Carolina, Colombus County, from <italic>Nicotiana tabacum</italic>, Aug. 1963, E.G. Simmons, CBS 539.94 = QM 8438; North Carolina, from <italic>Nicotiana tabacum</italic>, before Nov. 1971, representative isolate CBS 121332 = E.G.S. 30.048; North Carolina, from <italic>Nicotiana tabacum</italic>, before Nov. 1971, representative isolate CBS 121333 = E.G.S. 30.051. <bold>Unknown</bold>, from leaf spot of <italic>Nicotiana tabacum</italic>, before Oct. 1935, W.B. Tisdale, CBS 113.35.</p><p><italic>Unique fixed nucleotides</italic>: <bold>SSU</bold> position 654 (G); <bold>ITS</bold> position 491 (C); <bold><italic>gapdh</italic></bold> position 144 (G); <bold>OPA10-2</bold> position 51 (T), 85 (G); <bold>KOG1058</bold> position 848 (C).</p><p><italic>Notes</italic>: Although <italic>A. longipes</italic> only has a few unique fixed nucleotides, the species can easily be distinguished from <italic>A. alternata</italic> using molecular data. The low number of unique fixed nucleotides is due to its close phylogenetic relationship to <italic>A. gossypina</italic>. Most of the nucleotide differences present between <italic>A. longipes</italic> and the <italic>A. alternata</italic> isolates are also present in the <italic>A. gossypina</italic> isolates.</p><p><bold><italic>Alternaria tomato</italic></bold> (Cooke) L.R. Jones, Bull. Torrey Bot. Club 23: 353. 1896.</p><p><italic>Basionym</italic>: <italic>Macrosporium tomato</italic> Cooke, Grevillea 12: 32. 1883.</p><p><italic>Specimens examined</italic>: <bold>Unknown</bold>, from <italic>Solanum lycopersicum</italic> (<italic>Solanaceae</italic>), before Apr. 1930, A.A. Bailey, CBS 103.30; from <italic>Solanum lycopersicum</italic>, before Mar. 1935, G.F. Weber, CBS 114.35.</p><p><italic>Unique fixed nucleotides</italic>: <bold><italic>gapdh</italic></bold> position 356 (T); <bold><italic>rpb2</italic></bold> position 21 (T), 252 (C), 567 (C); <bold><italic>tef1</italic></bold> position 36 (T); <bold><italic>Alt a 1</italic></bold> position 187 (G); <bold>KOG1058</bold> position 60 (A), 183 (A); <bold>KOG1077</bold> position 588 (T).</p><p><italic>Notes</italic>: Although <italic>A. tomato</italic> only has a few unique fixed nucleotides, the species can easily be distinguished from <italic>A. alternata</italic> using molecular data. The low number of unique fixed nucleotides is due to its close phylogenetic relationship to <italic>A. burnsii</italic> and <italic>A. jacinthicola</italic>. Most of the nucleotide differences present between <italic>A. tomato</italic> and the <italic>A. alternata</italic> isolates are also present in the <italic>A. burnsii</italic> and / or <italic>A. jacinthicola</italic> isolates.</p><p><bold><italic>Alternaria arborescens</italic> species complex</bold> (<xref rid="fig5" ref-type="fig">Fig. 5</xref>).</p><p><bold><italic>Alternaria arborescens</italic></bold> E.G. Simmons, Mycotaxon 70: 356. 1999.</p><p><bold><italic>Alternaria cerealis</italic></bold> E.G. Simmons & C.F. Hill, CBS Biodiversity Ser. (Utrecht) 6: 600. 2007.</p><p><bold><italic>Alternaria geophila</italic></bold> Dasz., Bull. Soc. Bot. Genève, 2 Sér. 4: 294. 1912.</p><p><bold><italic>Alternaria senecionicola</italic></bold> E.G. Simmons & C.F. Hill, CBS Biodiversity Ser. (Utrecht) 6: 658. 2007.</p><p><italic>Type specimens examined</italic>: <bold>New Zealand</bold>, Auckland, Grey Lynn, from blighted <italic>Senecio skirrhodon</italic> (<italic>Compositae</italic>), Jul. 2000, C.F. Hill, culture <bold>ex-type</bold> of <italic>A. senecionicola</italic> CBS 119545 = E.G.S. 48.130; Auckland, from <italic>Avena sativa</italic> (<italic>Gramineae</italic>), Nov. 1995, C.F. Hill, culture <bold>ex-type</bold> of <italic>A. cerealis</italic> CBS 119544 = E.G.S. 43.072. <bold>Switzerland</bold>, from peat soil, before 1913, W. Daszewska, culture <bold>ex-type</bold> of <italic>A. geophila</italic> CBS 101.13. <bold>USA</bold>, California, from <italic>Solanum lycopersicum</italic> (<italic>Solanaceae</italic>), 23 Apr. 1990, D. Gilchrist, culture <bold>ex-type</bold> of <italic>A. arborescens</italic> CBS 102605 = E.G.S. 39.128.</p><p><italic>Unique fixed nucleotides</italic>: <bold><italic>rpb2</italic></bold> position 18 (A), 385 (T); <bold><italic>tef1</italic></bold> position 42 (T), 44 (A), 111 (G); <bold>OPA10-2</bold> position 330 (G), 504 (C); <bold><italic>Alt a 1</italic></bold> position 333 (T); <bold><italic>endoPG</italic></bold> position 349 (C); <bold>KOG1058</bold> position 625 (C); <bold>KOG1077</bold> position 207 (A), 276 (−), 429 (G), 651 (T).</p><p><italic>Notes</italic>: Although <italic>A. geophila</italic> is the oldest name in this species complex, the well-known name <italic>A. arborescens</italic> is retained above the relatively unknown name <italic>A. geophila</italic> for the species complex. The morphospecies present in this complex could not be resolved with the set of partial gene sequences used in this study and a more detailed study, possibly using whole-genome sequences of additional isolates from this species complex, is needed. Should this species complex be resolved and <italic>A. geophila</italic> and <italic>A. arborescens</italic> have to be synonymised, priority of the name <italic>A. arborescens</italic> over <italic>A. geophila</italic> is strongly suggested. The isolate CBS 126.60 was deposited in the CBS collection as <italic>A. maritima</italic>; however, the type material of <italic>A. maritima</italic> is unknown, and therefore <italic>A. maritima</italic> is not included within the AASC pending the recollection of suitable material of <italic>A. maritima</italic>.</p></sec></sec><sec id="sec4"><title>Discussion</title><p>The aim of the present study was to employ genome comparisons and molecular phylogenies to clarify the species present in <italic>Alternaria</italic> sect. <italic>Alternaria</italic>. The <italic>Alternaria</italic> genomes generated in this study ranged in size from 32.0–39.1 Mb (<xref rid="tbl2" ref-type="table">Table 2</xref>), which can only be partly explained by differences in repeat content between the genomes. The isolates with the highest repeat content, <italic>A. avenicola</italic> (∼12 % repeats) and <italic>A. alternantherae</italic> (∼16 % repeats), have a relatively large genome size (39.1 and 35.0 Mb), but <italic>A. infectoria</italic> with a genome size of 36.5 Mb contains only ∼5 % of repeats (<xref rid="tbl2" ref-type="table">Table 2</xref>). The percentage of repeats within sect. <italic>Alternaria</italic> is relatively low, 1.4–2.7 %, with the highest percentage of repeats in the <italic>A. arborescens</italic> genome. The isolates which are now named <italic>A. alternata</italic>, only ranged from 1.4–1.7 %. The genome assembly shows a high similarity between the isolates within sect. <italic>Alternaria</italic>; 96.7–98.2 % genome identity within sect. <italic>Alternaria</italic>, compared to 85.1–89.3 % genome identity between isolates from other sections with the reference genome of <italic>A. alternata</italic> (CBS 916.96). This is confirmed by the percentage of SNPs found in the whole-genome and transcriptome reads; 1.4–2.8 % and 0.8–1.8 % SNPs in respectively the whole-genome and transcriptome reads between isolates from sect. <italic>Alternaria</italic>, compared to 8.0–10.3 % and 6.1–8.5 % SNPs found in isolates from different sections with the <italic>A. alternata</italic> reference genome. The phylogenetic species boundaries proposed here for sect. <italic>Alternaria</italic> are corroborated by the percentage of SNPs found in both the genome and transcriptome studies. The morphospecies now synonymised under <italic>A. alternata</italic> show 1.4–1.5 % SNPs in their whole-genome reads compared to 2.8 % in <italic>A. gaisen</italic> and ≤1 % of SNPs in their transcriptome reads compared to the reference isolate, while the species retained as separate, <italic>A. gaisen</italic> and <italic>A. arborescens</italic>, both show 1.8 % of SNPs in the transcriptome reads.</p><p>To be able to determine whether an isolate should be referred to as <italic>forma specialis</italic> or pathotype, the species boundaries should first be firmly established. From the seven described pathotypes of <italic>A. alternata</italic> (<xref rid="bib3" ref-type="bibr">Akimitsu <italic>et al.</italic> 2014</xref>), two are now recognised as separate phylogenetic species in sect. <italic>Alternaria</italic>, namely <italic>A. gaisen</italic> and <italic>A. longipes</italic>, and one belongs to the <italic>A. arborescens</italic> species complex (AASC). The terms <italic>forma specialis</italic> (<italic>e.g.</italic><xref rid="bib30" ref-type="bibr">Neergaard, 1945</xref>, <xref rid="bib21" ref-type="bibr">Joly, 1964</xref>, <xref rid="bib9" ref-type="bibr">Grogan et al., 1975</xref>, <xref rid="bib57" ref-type="bibr">Yoon et al., 1989</xref>, <xref rid="bib56" ref-type="bibr">Vakalounakis, 1989</xref>) and pathotype (<xref rid="bib31" ref-type="bibr">Nishimura & Kohmoto 1983</xref>) have both been used to specify the host affinity of strains of <italic>A. alternata</italic>. This affinity to a specific host is in most cases caused by the ability to produce a unique host-specific toxin (HST), which is needed for infection of the specific host. We propose here to standardise the taxonomic terms used according to Rotem's approach (<xref rid="bib39" ref-type="bibr">1994</xref>). He favoured the use of the trinomial system in which the third epithet, the <italic>forma specialis</italic>, defines the affinity to a specific host in accordance with the produced toxin. When different toxins are produced on the same host, but these toxins affect different host species, like for instance on <italic>Citrus</italic> where the ACT- and / or ACR-toxin can be produced by the same <italic>f. sp</italic>., which affect tangerine and / or rough lemon, respectively (<xref rid="bib28" ref-type="bibr">Masanuka <italic>et al.</italic> 2005</xref>), the term pathotype will be used. The four previously described pathotypes which still reside in <italic>A. alternata</italic> (<xref rid="bib3" ref-type="bibr">Akimitsu <italic>et al.</italic> 2014</xref>), will therefore be named <italic>A. alternata f. sp. mali</italic> for isolates producing the AM-toxin, <italic>f. sp. fragariae</italic> for isolates producing the AF-toxin, <italic>f. sp. citri</italic> pathotype rough lemon for isolates producing the ACR-toxin, and <italic>f. sp. citri</italic> pathotype tangerine for isolates producing the ACT-toxin. All <italic>A. alternata</italic> isolates which are not confined to specific hosts and / or toxins should retain only the binomial name until such specificity is found. Multiple studies showed that HST gene clusters are located on small conditionally dispensable (CD) chromosomes (<xref rid="bib53" ref-type="bibr">Tanaka and Tsuge, 2000</xref>, <xref rid="bib15" ref-type="bibr">Hatta et al., 2002</xref>, <xref rid="bib2" ref-type="bibr">Akamatsu, 2004</xref>, <xref rid="bib11" ref-type="bibr">Harimoto et al., 2007</xref>, <xref rid="bib12" ref-type="bibr">Harimoto et al., 2008</xref>, <xref rid="bib16" ref-type="bibr">Hu et al., 2012</xref>) which can be lost (<xref rid="bib20" ref-type="bibr">Johnson <italic>et al.</italic> 2001</xref>) or gained (<xref rid="bib41" ref-type="bibr">Salamiah et al., 2001</xref>, <xref rid="bib28" ref-type="bibr">Masanuka et al., 2005</xref>, <xref rid="bib1" ref-type="bibr">Akagi et al., 2009</xref>), making an isolate either non-pathogenic or pathogenic to the specific host affected by the HST. With the species boundaries set in this study, this loss or gain of a specific gene cluster will not change the binomial part of the species name of an isolate.</p><p><xref rid="bib51" ref-type="bibr">Stewart <italic>et al.</italic> (2013a)</xref> have suggested that sequence data derived from SCARs would provide sufficient resolution to address lower level phylogenetic hypotheses in <italic>Alternaria</italic>. The authors developed SCARs from randomly amplified and cloned RAPD-PCR amplicons of which six of the 19 tested on small-spored <italic>Alternaria</italic> isolates were highly polymorphic. One of them was too variable which made it difficult to align and amplify this region; the remaining five were all more variable then ITS, <italic>gapdh</italic> and <italic>tef1</italic>, but only one (OPA10-2) showed a higher variability than <italic>endoPG</italic>. The other four were equally variable as or slightly more variable than <italic>endoPG</italic>. Both <italic>endoPG</italic> and OPA10-2 are used in the multi-gene phylogeny presented here, but could only distinguish 11 species of the 52 morphospecies previously described. Also, the molecular phylogenies obtained from the relative low conservative genes based on genome sequencing, KOG1058 and KOG1077, could not provide sufficient resolution to distinguish the known morphospecies. The incongruencies between the single-gene phylogenies, together with the high similarity found in the sequenced genomes of sect. <italic>Alternaria</italic> and the low SNP count derived by the genomic and transcriptomic data between isolates of sect. <italic>Alternaria</italic> led to the conclusion to synonymise 35 <italic>Alternaria</italic> morphospecies under <italic>A. alternata</italic>. As mentioned above, the detection of host-specific toxins could eventually give rise to several new <italic>formae speciales</italic> of <italic>A. alternata</italic>.</p><p>In a later study the same authors (<xref rid="bib52" ref-type="bibr">Stewart <italic>et al.</italic> 2014</xref>) estimated the evolutionary histories of four nuclear loci on a worldwide sample of <italic>A. alternata</italic> isolates, causing citrus brown spot, using the coalescent theory. Next to the phylogenetic species concepts for estimating the species boundaries, two approaches were used that incorporate uncertainty in gene genealogies when lineage sorting and non-reciprocal monophyly of gene trees is common. The coalescent analyses revealed that the phylogenetic lineages are strongly influenced by incomplete lineage sorting and recombination. Also a study of the mating system of <italic>A. alternata</italic> isolates causing citrus brown spot found signatures of recombination (<xref rid="bib59" ref-type="bibr">Stewart <italic>et al</italic>. 2013b</xref>). <xref rid="bib4" ref-type="bibr">Andrew <italic>et al.</italic> (2009)</xref> already hypothesised that recombination and incomplete lineage sorting could explain the significant incongruence they found among gene genealogies in a four-gene species phylogeny on small-spored <italic>Alternaria</italic>, and the several putative recombination events that were identified within two non-coding regions. In agreement with our findings, little support was found for most of the morphospecies, when using these quantitative species recognition approaches.</p><p>Most of the synonymised morphospecies (10 / 35 species) under <italic>A. alternata</italic> were described in 2007 (<xref rid="bib45" ref-type="bibr">Simmons</xref>), and are only based on a single isolate that was collected long before the year of description (<italic>A. brassicinae</italic>, <italic>A. citricancri</italic>, <italic>A. herbiphorbicola</italic>, <italic>A. pulvinifungicola</italic>, <italic>A. postmessia</italic>, <italic>A. soliaegyptiaca</italic>, <italic>A. vaccinii</italic>). As far as known, no new isolates of these species were reported in literature after their original description. Studies on the presence of host-specific toxins in these isolates could show if they should become a new <italic>f. sp.</italic> of <italic>A. alternata</italic>. Nine of the synonymised morphospecies are described in a paper on the classification of citrus pathogens (<xref rid="bib44" ref-type="bibr">Simmons 1999</xref>). The validity of all these small-spored species described from citrus was already questioned by a molecular study performed in later years (<xref rid="bib34" ref-type="bibr">Peever <italic>et al.</italic> 2004</xref>). The authors already advocated that all small-spored citrus-associated isolates of <italic>Alternaria</italic> should collapse into a single phylogenetic species, <italic>A. alternata</italic>. Also the validity of the name <italic>A. mali</italic>, the causal agent of Alternaria blotch of apple, which occurs on the European quarantine lists, was questioned in recent years (<xref rid="bib40" ref-type="bibr">Rotondo et al., 2012</xref>, <xref rid="bib14" ref-type="bibr">Harteveld et al., 2013</xref>). The authors describe the association of multiple <italic>Alternaria</italic> species-groups with leaf blotch and fruit spot diseases of apple in Italy and Australia respectively, and could not separate the <italic>A. mali</italic> reference isolate from ‘<italic>A. tenuissima</italic>’ isolates with molecular data. Based on the approach described in the present study, the only way to distinguish <italic>A. alternata f. sp. mali</italic>, which is of high importance as quarantine organism, is to detect the AM-toxin that gives the name to these isolates (<xref rid="bib19" ref-type="bibr">Johnson <italic>et al.</italic> 2000</xref>).</p><p>The isolates constituting the AASC show some internal molecular and morphological variation, but can only clearly be separated from the <italic>A. alternata</italic> cluster based on molecular data. Both <italic>A. cerealis</italic> and <italic>A. senecionicola</italic> were marked by <xref rid="bib45" ref-type="bibr">Simmons (2007)</xref> as having an arborescent-like sporulation pattern, but not all isolates from the AASC display this typical arborescent-like sporulation pattern (<xref rid="fig5" ref-type="fig">Fig. 5</xref>). This is illustrated by the fact that 12 out of the 28 isolates, which cluster in the AASC, were stored in the CBS collection as either <italic>A. alternata</italic> or <italic>A. tenuissima</italic> (<xref rid="tbl1" ref-type="table">Table 1</xref>). Because of the inconsistencies in morphology and molecular data in the AASC, more research is needed before conclusions can be drawn on the phylogenetic species present in this complex. Next to the known pathogenicity of <italic>A. arborescens</italic> on tomato, caused by the production of the AL-toxin, studies on <italic>Alternaria</italic> spp. show that isolates from the AASC can also cause diseases on apple (<xref rid="bib40" ref-type="bibr">Rotondo et al., 2012</xref>, <xref rid="bib14" ref-type="bibr">Harteveld et al., 2013</xref>, <xref rid="bib13" ref-type="bibr">Harteveld et al., 2014</xref>) and can act as postharvest pathogens on apple and citrus (<xref rid="bib23" ref-type="bibr">Kang et al., 2002</xref>, <xref rid="bib42" ref-type="bibr">Serdani et al., 2002</xref>). The presence of multiple human isolates in the AASC stresses the importance of additional research on this species complex. To our knowledge, <italic>A. arborescens</italic> was not previously recognised as being of medical importance. One recent publication (<xref rid="bib17" ref-type="bibr">Hu <italic>et al.</italic> 2014</xref>) does describe <italic>A. arborescens</italic> as the causative agent of a cutaneous Alternariosis in a healthy person, but the identification was based on ITS alone, a locus which cannot distinguish <italic>A. arborescens</italic> from multiple other species now recognised in sect. <italic>Alternaria</italic> (<xref rid="tbl4" ref-type="table">Table 4</xref>). In the end it might well be that <italic>A. arborescens</italic> needs the same treatment as <italic>A. alternata</italic>, and that it will be divided into different <italic>formae speciales</italic> based on the specific host they infect, and the toxin gene cluster they exploit.</p><p>The need for this research is stressed by examining recent publications on <italic>Alternaria</italic> spp. from sect. <italic>Alternaria</italic>. Two <italic>Alternaria</italic> species that were both argued as new based on phylogenetic data, and which were published during the writing of this manuscript, are both placed in synonymy under an older species name in this study. Based on molecular comparisons, <italic>Alternaria capsicicola</italic> (<xref rid="bib29" ref-type="bibr">Nasehi <italic>et al.</italic> 2014</xref>) is synonymised under <italic>A. jacinthicola</italic>, and <italic>A. viniferae</italic> (<xref rid="bib54" ref-type="bibr">Tao <italic>et al.</italic> 2014</xref>) is synonymised under <italic>A. alternata</italic>. Furthermore, the recent descriptions based on ITS alone of <italic>A. arborescens</italic> as the cause of cutaneous Alternariosis in a healthy person (<xref rid="bib17" ref-type="bibr">Hu <italic>et al.</italic> 2014</xref>) and of <italic>A. longipes</italic> as the cause of a severe leaf spot disease on potato (<xref rid="bib58" ref-type="bibr">Shoaib <italic>et al.</italic> 2014</xref>) need to be re-investigated by employing a more robust molecular dataset. As already mentioned above, <italic>A. arborescens</italic> cannot be separated from <italic>A. alternata</italic> based on the ITS region alone, and the 1 unique fixed nucleotide in the ITS sequence which separates <italic>A. longipes</italic> from <italic>A. alternata</italic> is not present in the ITS sequence from the isolate causing the leaf spot in potato. These are most likely not the only examples of species of <italic>Alternaria</italic> sect. <italic>Alternaria</italic> treated in recently published manuscripts that need to be confirmed by, or subjected to, a multilocus sequence analysis in light of the present study. The research presented here will hopefully make the correct identification of species in sect. <italic>Alternaria</italic> easier for other researchers confronted with these species.</p></sec><sec id="sec5"><title>Conclusions</title><p>Based on genome comparisons and molecular phylogenies, <italic>Alternaria</italic> sect. <italic>Alternaria</italic> consists of 11 phylogenetic species and one species complex. Thirty-five morphospecies, which cannot reliably be distinguished based on the multi-gene phylogeny, are synonymised under <italic>A. alternata</italic>. When a specific HST-gene cluster is demonstrated in an <italic>A. alternata</italic> isolate, this isolate will be named as a <italic>f. sp</italic>. of <italic>A. alternata</italic>. Currently three <italic>formae speciales</italic> of <italic>A. alternata</italic> are recognised, of which <italic>f. sp</italic>. <italic>citri</italic> consists of two pathotypes, according to the host species the HST acts upon. The AASC can be distinguished from all species now recognised within sect. <italic>Alternaria</italic>, but the inconsistencies in morphology and molecular data makes further research necessary. By providing guidelines for the naming and identification of phylogenetic species in <italic>Alternaria</italic> sect. <italic>Alternaria</italic>, a stable and consistent taxonomic treatment of this section can hopefully be accomplished for the future. 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Simmons (1920–2013) for his monumental taxonomic revision of <italic>Alternaria</italic> over the past few decades, and especially for making his strains available to facilitate this study. The research was supported by the Dutch Ministry of Education, Culture and Science through an endowment of the FES programme “Making the tree of life work”. Research in the laboratory of BPHJT is supported by the Research Council for Earth and Life Sciences (ALW) of the Netherlands Organisation for Scientific Research (NWO). Ion Torrent sequencing at the CBS-KNAW was financially supported by the <funding-source id="gs1">European Community Research Infrastructures</funding-source> program under FP7 call ‘Synthesis of Systematic Resources’, grant number 226506-CP-CSA-Infra.</p></ack><fn-group><fn id="d32e6235"><p id="ntpara0010">Peer review under responsibility of CBS-KNAW Fungal Biodiversity Centre.</p></fn></fn-group></back><floats-group><fig id="fig1"><label>Fig. 1</label><caption><p>PhyML tree based on the whole-genome and transcriptome reads of 15 <italic>Alternaria</italic> species using REALPHY. The bootstrap support values are given at the nodes; thickened lines indicate a fully supported node. The grey box represents species which are now synonymised under <italic>A. alternata</italic>. The tree was rooted to <italic>A. papaveraceae</italic> (CBS 116607).</p></caption><graphic xlink:href="gr1"></graphic></fig><fig id="fig2"><label>Fig. 2</label><caption><p>Bayesian 50 % majority rule consensus tree based on the ITS, <italic>gapdh</italic>, <italic>tef1</italic>, <italic>rpb2</italic>, <italic>Alt a 1</italic>, <italic>endoPG</italic> and OPA10-2 sequences of 168 <italic>Alternaria</italic> strains. The Bayesian posterior probabilities >0.75 (PP) and RAxML bootstrap support values >65 (ML) are given at the nodes (PP / ML). Thickened lines indicate a PP of 1.0 and ML of 100. Species names between parentheses represent synonymised species names. Ex-type strains are indicated with T and representative strains with R. The ex-type strains of here recognised species are printed in <bold>bold</bold> face. The tree was rooted to <italic>A. alternantherae</italic> (CBS 124392).</p></caption><graphic xlink:href="gr2"></graphic></fig><fig id="fig3"><label>Fig. 3</label><caption><p><italic>Alternaria burnsii</italic> conidia and conidiophores. A–B. CBS 108.27. C–D. CBS 879.95. E–F. CBS 118816. G–H. CBS 118817. Scale bars = 10 μm.</p></caption><graphic xlink:href="gr3"></graphic></fig><fig id="fig4"><label>Fig. 4</label><caption><p><italic>Alternaria gossypina</italic> conidia and conidiophores. A–B. CBS 100.23. C–D. CBS 104.32. E–F. CBS 107.36. G–H. CBS 102597. Scale bars = 10 μm.</p></caption><graphic xlink:href="gr4"></graphic></fig><fig id="fig5"><label>Fig. 5</label><caption><p><italic>Alternaria arborescens</italic> species complex conidia and conidiophores. A–B. <italic>A. geophila</italic> CBS 101.13. C–D. <italic>A. arborescens</italic> CBS 102605. E–F. <italic>A. cerealis</italic> CBS 119544. G–H. <italic>A. senecionicola</italic> CBS 119545. Scale bars = 10 μm.</p></caption><graphic xlink:href="gr5"></graphic></fig><table-wrap id="tbl1" position="float"><label>Table 1</label><caption><p>Isolates used in this study and their GenBank accession numbers.</p></caption><table frame="hsides" rules="groups"><thead><tr><th>Species name and strain number<xref rid="tbl1fn1" ref-type="table-fn">1</xref><sup>,</sup><xref rid="tbl1fn2" ref-type="table-fn">2</xref></th><th>Locality, host / substrate</th><th colspan="11">GenBank accession numbers<xref rid="tbl1fn3" ref-type="table-fn">3</xref><hr></hr></th></tr><tr><th>SSU</th><th>LSU</th><th>ITS</th><th><italic>gapdh</italic></th><th><italic>tef1</italic></th><th><italic>rpb2</italic></th><th><italic>Alt a 1</italic></th><th><italic>endoPG</italic></th><th>OPA10-2</th><th>KOG1058</th><th>KOG1077</th></tr></thead><tbody><tr><td colspan="13"><bold><italic>Alternaria alstroemeriae</italic></bold></td></tr><tr><td>CBS 118808; E.G.S. 50.116<sup>R</sup></td><td>USA, <italic>Alstroemeria</italic> sp.</td><td>KP124917</td><td>KP124447</td><td>KP124296</td><td>KP124153</td><td>KP125071</td><td>KP124764</td><td>KP123845</td><td>KP123993</td><td>KP124601</td><td></td><td></td></tr><tr><td>CBS 118809; E.G.S. 52.068; MAFF 1219<sup>T</sup></td><td>Australia, <italic>Alstroemeria</italic> sp.</td><td>KP124918</td><td>KP124448</td><td>KP124297</td><td>KP124154</td><td>KP125072</td><td>KP124765</td><td>np</td><td>KP123994</td><td>KP124602</td><td>KP125226</td><td>np</td></tr><tr><td colspan="13"><bold><italic>Alternaria alternantherae</italic></bold></td></tr><tr><td>CBS 124392; HSAUP2798</td><td>China, <italic>Solanum melongena</italic></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584506" id="interref9000"><bold>KC584506</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584251" id="interref9005"><bold>KC584251</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584179" id="interref9010"><bold>KC584179</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584096" id="interref9015"><bold>KC584096</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584633" id="interref9020"><bold>KC584633</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584374" id="interref9025"><bold>KC584374</bold></ext-link></td><td>KP123846</td><td>np</td><td>np</td><td>KP125227</td><td>KP125275</td></tr><tr><td colspan="13"><bold><italic>Alternaria alternata</italic></bold></td></tr><tr><td>CBS 106.24; E.G.S. 38.029; ATCC 13963 (<italic>A. mali</italic><sup>T</sup>)</td><td>USA, <italic>Malus sylvestris</italic></td><td>KP124919</td><td>KP124449</td><td>KP124298</td><td>KP124155</td><td>KP125073</td><td>KP124766</td><td>KP123847</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY295020" id="intref0075"><bold>AY295020</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ800620" id="interref8000"><bold>JQ800620</bold></ext-link></td><td></td><td></td></tr><tr><td>CBS 104.26</td><td>Unknown, unknown</td><td>KP124920</td><td>KP124450</td><td>KP124299</td><td>KP124156</td><td>KP125074</td><td>KP124767</td><td>KP123848</td><td>KP123995</td><td>KP124603</td><td></td><td></td></tr><tr><td>CBS 107.27; ATCC 24463; QM 1736 (<italic>A. citri</italic>)</td><td>USA, <italic>Citrus limonium</italic></td><td>KP124921</td><td>KP124451</td><td>KP124300</td><td>KP124157</td><td>KP125075</td><td>KP124768</td><td>KP123849</td><td>KP123996</td><td>KP124604</td><td></td><td></td></tr><tr><td>CBS 154.31; IHEM 3320</td><td>USA, <italic>Staphylea trifolia</italic></td><td>KP124922</td><td>KP124452</td><td>KP124301</td><td>KP124158</td><td>KP125076</td><td>KP124769</td><td>KP123851</td><td>KP123998</td><td>KP124606</td><td></td><td></td></tr><tr><td>CBS 103.33; E.G.S. 35.182; IHEM 3319 (<italic>A. soliaegyptiaca</italic><sup>T</sup>)</td><td>Egypt, soil</td><td>KP124923</td><td>KP124453</td><td>KP124302</td><td>KP124159</td><td>KP125077</td><td>KP124770</td><td>KP123852</td><td>KP123999</td><td>KP124607</td><td>KP125228</td><td>KP125276</td></tr><tr><td>CBS 106.34; E.G.S. 06.198; DSM 62019; MUCL 10030 (<italic>A. lini</italic><sup>T</sup>)</td><td>Unknown, <italic>Linum usitatissimum</italic></td><td>KP124924</td><td>KP124454</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:Y17071" id="intref0080"><bold>Y17071</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646308" id="interref8005"><bold>JQ646308</bold></ext-link></td><td>KP125078</td><td>KP124771</td><td>KP123853</td><td>KP124000</td><td>KP124608</td><td></td><td></td></tr><tr><td>CBS 117.44; E.G.S. 06.190; VKM F-1870 (<italic>A. godetiae</italic><sup>T</sup>)</td><td>Denmark, <italic>Godetia</italic> sp.</td><td>KP124925</td><td>KP124455</td><td>KP124303</td><td>KP124160</td><td>KP125079</td><td>KP124772</td><td>KP123854</td><td>KP124001</td><td>KP124609</td><td>KP125229</td><td>KP125277</td></tr><tr><td>CBS 102.47; E.G.S. 02.062 (<italic>A. citri</italic><sup>R</sup>)</td><td>USA, <italic>Citrus sinensis</italic></td><td>KP124926</td><td>KP124456</td><td>KP124304</td><td>KP124161</td><td>KP125080</td><td>KP124773</td><td>KP123855</td><td>KP124002</td><td>KP124610</td><td></td><td></td></tr><tr><td>CBS 174.52; E.G.S. 39.1613; IMI 068086; QM 1278</td><td>USA, <italic>Anemone occidentalis</italic></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584578" id="interref9030"><bold>KC584578</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:DQ678068" id="interref8000a"><bold>DQ678068</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584228" id="interref9035"><bold>KC584228</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584152" id="interref9040"><bold>KC584152</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584704" id="interref9045"><bold>KC584704</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:DQ677964" id="interref8005a"><bold>DQ677964</bold></ext-link></td><td>KP123856</td><td>KP124003</td><td>KP124611</td><td></td><td></td></tr><tr><td>CBS 175.52; E.G.S. 35.1619; IMI 068085; QM 1277</td><td>USA, <italic>Juncus mertensianus</italic></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584577" id="interref9050"><bold>KC584577</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584320" id="interref9055"><bold>KC584320</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584227" id="interref9060"><bold>KC584227</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584151" id="interref9065"><bold>KC584151</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584703" id="interref9070"><bold>KC584703</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584445" id="interref9075"><bold>KC584445</bold></ext-link></td><td>KP123857</td><td>KP124004</td><td>KP124612</td><td></td><td></td></tr><tr><td>CBS 107.53; DSM 3187; IFO 5778 (<italic>A. kikuchiana</italic>)</td><td>Japan, <italic>Pyrus pyrifolia</italic></td><td>KP124927</td><td>KP124457</td><td>KP124305</td><td>KP124162</td><td>KP125081</td><td>KP124774</td><td>KP123858</td><td>KP124005</td><td>KP124613</td><td></td><td></td></tr><tr><td>CBS 686.68; LCP 1988 (<italic>A. tenuissima</italic>)</td><td>Sahara, desert sand</td><td>KP124928</td><td>KP124458</td><td>KP124306</td><td>KP124163</td><td>KP125082</td><td>KP124775</td><td>KP123859</td><td>KP124006</td><td>KP124614</td><td></td><td></td></tr><tr><td>CBS 826.68; IMI 265857 (<italic>A. nobilis</italic>)</td><td>Germany, <italic>Lolium</italic> sp.</td><td>KP124929</td><td>KP124459</td><td>KP124307</td><td>KP124164</td><td>KP125083</td><td>KP124776</td><td>KP123860</td><td>KP124007</td><td>np</td><td></td><td></td></tr><tr><td>CBS 612.72; DSM 62012 (<italic>A. cinerariae</italic>)</td><td>Germany, <italic>Senecio cineraria</italic></td><td>KP124930</td><td>KP124460</td><td>KP124308</td><td>KP124165</td><td>KP125084</td><td>KP124777</td><td>KP123861</td><td>KP124008</td><td>KP124615</td><td></td><td></td></tr><tr><td>CBS 795.72; ATCC 24127; IHEM 3789</td><td>USA, <italic>Plantago aristida</italic></td><td>KP124931</td><td>KP124461</td><td>KP124309</td><td>KP124166</td><td>KP125085</td><td>KP124778</td><td>KP123862</td><td>KP124009</td><td>KP124616</td><td></td><td></td></tr><tr><td>CBS 198.74 (<italic>A. chlamydospora</italic>)</td><td>Kuwait, soil</td><td>KP124932</td><td>KP124462</td><td>KP124310</td><td>KP124167</td><td>KP125086</td><td>np</td><td>KP123863</td><td>KP124010</td><td>KP124617</td><td></td><td></td></tr><tr><td>CBS 267.77 (<italic>A. citri</italic>)</td><td>USA, <italic>Citrus paradisi</italic></td><td>KP124933</td><td>KP124463</td><td>KP124311</td><td>KP124168</td><td>KP125087</td><td>KP124779</td><td>KP123864</td><td>KP124011</td><td>KP124618</td><td></td><td></td></tr><tr><td>CBS 603.78; E.G.S. 30.134; QM 9553</td><td>USA, air</td><td>KP124934</td><td>KP124464</td><td>KP124312</td><td>KP124169</td><td>KP125088</td><td>KP124780</td><td>KP123865</td><td>KP124012</td><td>KP124619</td><td></td><td></td></tr><tr><td>CBS 175.80 (<italic>A. septorioides</italic>)</td><td>Italy, unknown</td><td>KP124935</td><td>KP124465</td><td>KP124313</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646324" id="interref8010"><bold>JQ646324</bold></ext-link></td><td>KP125089</td><td>KP124781</td><td>KP123866</td><td>KP124013</td><td>KP124620</td><td></td><td></td></tr><tr><td>CBS 192.81 (<italic>A. citri</italic>)</td><td>Egypt, <italic>Citrus sinensis</italic></td><td>KP124936</td><td>KP124466</td><td>KP124314</td><td>KP124170</td><td>KP125090</td><td>KP124782</td><td>KP123867</td><td>KP124014</td><td>KP124621</td><td></td><td></td></tr><tr><td>CBS 620.83; ATCC 15052 (<italic>A. tenuissima</italic>)</td><td>USA, <italic>Nicotiana tabacum</italic></td><td>KP124937</td><td>KP124467</td><td>KP124315</td><td>KP124171</td><td>KP125091</td><td>KP124783</td><td>KP123868</td><td>KP124015</td><td>KP124622</td><td></td><td></td></tr><tr><td>CBS 194.86; E.G.S. 04.090; QM 1347 (<italic>A. pulvinifungicola</italic><sup>T</sup>)</td><td>USA, <italic>Quercus</italic> sp.</td><td>KP124938</td><td>KP124468</td><td>KP124316</td><td>KP124172</td><td>KP125092</td><td>KP124784</td><td>KP123869</td><td>KP124016</td><td>KP124623</td><td>KP125230</td><td>KP125278</td></tr><tr><td>CBS 195.86; E.G.S. 36.172; DAOM 185214 (<italic>A. angustiovoidea</italic><sup>T</sup>)</td><td>Canada, <italic>Euphorbia esula</italic></td><td>KP124939</td><td>KP124469</td><td>KP124317</td><td>KP124173</td><td>KP125093</td><td>KP124785</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646398" id="interref8015"><bold>JQ646398</bold></ext-link></td><td>KP124017</td><td>KP124624</td><td>KP125231</td><td>KP125279</td></tr><tr><td>CBS 447.86 (<italic>A. malvae</italic>)</td><td>Marocco, <italic>Malva</italic> sp.</td><td>KP124940</td><td>KP124470</td><td>KP124318</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646314" id="interref8020"><bold>JQ646314</bold></ext-link></td><td>KP125094</td><td>KP124786</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646397" id="interref8025"><bold>JQ646397</bold></ext-link></td><td>KP124018</td><td>KP124625</td><td></td><td></td></tr><tr><td>CBS 479.90; E.G.S. 29.028 (<italic>A. pellucida</italic><sup>T</sup>)</td><td>Japan, <italic>Citrus unshiu</italic></td><td>KP124941</td><td>KP124471</td><td>KP124319</td><td>KP124174</td><td>KP125095</td><td>KP124787</td><td>KP123870</td><td>KP124019</td><td>KP124626</td><td>KP125232</td><td>KP125280</td></tr><tr><td>CBS 595.93 (<italic>A. rhadina</italic><sup>T</sup>)</td><td>Japan, <italic>Pyrus pyrifolia</italic></td><td>KP124942</td><td>KP124472</td><td>KP124320</td><td>KP124175</td><td>KP125096</td><td>KP124788</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646399" id="interref8030"><bold>JQ646399</bold></ext-link></td><td>KP124020</td><td>KP124627</td><td></td><td></td></tr><tr><td>CBS 877.95 (<italic>A. tenuissima</italic>)</td><td>India, human, sinusitis</td><td>KP124943</td><td>KP124473</td><td>KP124321</td><td>KP124176</td><td>KP125097</td><td>KP124789</td><td>KP123871</td><td>KP124021</td><td>np</td><td></td><td></td></tr><tr><td>CBS 880.95; IMI 292915 (<italic>A. tenuissima</italic>)</td><td>Belgium, <italic>Fragaria vesca</italic></td><td>KP124944</td><td>KP124474</td><td>KP124322</td><td>KP124177</td><td>KP125098</td><td>KP124790</td><td>np</td><td>KP124022</td><td>KP124628</td><td></td><td></td></tr><tr><td>CBS 965.95; IMI 289679 (<italic>A. tenuissima</italic>)</td><td>India, <italic>Triticum</italic> sp.</td><td>KP124945</td><td>KP124475</td><td>KP124323</td><td>KP124178</td><td>KP125099</td><td>KP124791</td><td>KP123872</td><td>KP124023</td><td>KP124629</td><td></td><td></td></tr><tr><td>CBS 966.95; IMI 79630 (<italic>A. tenuissima</italic>)</td><td>India, <italic>Solanum lycopersicum</italic></td><td>KP124946</td><td>KP124476</td><td>KP124324</td><td>KP124179</td><td>KP125100</td><td>KP124792</td><td>KP123873</td><td>KP124024</td><td>KP124630</td><td></td><td></td></tr><tr><td>CBS 806.96</td><td>Papua New Guinea, <italic>Cyperaceae</italic></td><td>KP124947</td><td>KP124477</td><td>KP124325</td><td>KP124180</td><td>KP125101</td><td>KP124793</td><td>KP123874</td><td>KP124025</td><td>KP124631</td><td></td><td></td></tr><tr><td>CBS 916.96; E.G.S. 34.016; CBS 110977; CBS 115616; IMI 254138<sup>T</sup></td><td>India, <italic>Arachis hypogaea</italic></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584507" id="interref9080"><bold>KC584507</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:DQ678082" id="interref8010a"><bold>DQ678082</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AF347031" id="intref0085"><bold>AF347031</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY278808" id="intref0090"><bold>AY278808</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584634" id="interref9085"><bold>KC584634</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584375" id="interref9090"><bold>KC584375</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY563301" id="intref0095"><bold>AY563301</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ811978" id="interref8035"><bold>JQ811978</bold></ext-link></td><td>KP124632</td><td>KP125233</td><td>KP125281</td></tr><tr><td>CBS 918.96; E.G.S. 34.015; IMI 255532 (<italic>A. tenuissima</italic><sup>R</sup>)</td><td>UK, <italic>Dianthus chinensis</italic></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584567" id="interref9095"><bold>KC584567</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584311" id="interref9100"><bold>KC584311</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AF347032" id="intref0100"><bold>AF347032</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY278809" id="intref0105"><bold>AY278809</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584693" id="interref9105"><bold>KC584693</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584435" id="interref9110"><bold>KC584435</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY563302" id="intref0110"><bold>AY563302</bold></ext-link></td><td>KP124026</td><td>KP124633</td><td>KP125234</td><td>KP125282</td></tr><tr><td>CBS 911.97; IMI 056271 (<italic>A. tenuissima</italic>)</td><td>India, <italic>Artemisia brevifolia</italic></td><td>KP124948</td><td>KP124478</td><td>KP124326</td><td>KP124181</td><td>KP125102</td><td>KP124794</td><td>KP123875</td><td>KP124027</td><td>KP124634</td><td></td><td></td></tr><tr><td>CBS 639.97; IMI 366417</td><td>Greece, <italic>Helianthus annuus</italic></td><td>KP124949</td><td>KP124479</td><td>KP124327</td><td>KP124182</td><td>KP125103</td><td>KP124795</td><td>KP123876</td><td>KP124028</td><td>KP124635</td><td></td><td></td></tr><tr><td>CBS 102595; E.G.S. 45.100 (<italic>A. limoniasperae</italic><sup>T</sup>)</td><td>USA, <italic>Citrus jambhiri</italic></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584540" id="interref9115"><bold>KC584540</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584284" id="interref9120"><bold>KC584284</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:FJ266476" id="intref0115"><bold>FJ266476</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY562411" id="intref0120"><bold>AY562411</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584666" id="interref9125"><bold>KC584666</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584408" id="interref9130"><bold>KC584408</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY563306" id="intref0125"><bold>AY563306</bold></ext-link></td><td>KP124029</td><td>KP124636</td><td>KP125235</td><td>KP125283</td></tr><tr><td>CBS 102596; E.G.S. 45.090 (<italic>A. citrimacularis</italic><sup>T</sup>)</td><td>USA, <italic>Citrus jambhiri</italic></td><td>KP124950</td><td>KP124480</td><td>KP124328</td><td>KP124183</td><td>KP125104</td><td>KP124796</td><td>KP123877</td><td>KP124030</td><td>KP124637</td><td>KP125236</td><td>KP125284</td></tr><tr><td>CBS 102598; E.G.S. 46.141 (<italic>A. citriarbusti</italic><sup>T</sup>)</td><td>USA, <italic>Minneola tangelo</italic></td><td>KP124951</td><td>KP124481</td><td>KP124329</td><td>KP124184</td><td>KP125105</td><td>KP124797</td><td>KP123878</td><td>KP124031</td><td>KP124638</td><td>KP125237</td><td>KP125285</td></tr><tr><td>CBS 102599; E.G.S. 44.166 (<italic>A. turkisafria</italic><sup>T</sup>)</td><td>Turkey, <italic>Minneola tangelo</italic></td><td>KP124952</td><td>KP124482</td><td>KP124330</td><td>KP124185</td><td>KP125106</td><td>KP124798</td><td>KP123879</td><td>KP124032</td><td>KP124639</td><td>KP125238</td><td>KP125286</td></tr><tr><td>CBS 102600; E.G.S. 39.181; ATCC 38963 (<italic>A. toxicogenica</italic><sup>T</sup>)</td><td>USA, <italic>Citrus reticulata</italic></td><td>KP124953</td><td>KP124483</td><td>KP124331</td><td>KP124186</td><td>KP125107</td><td>KP124799</td><td>KP123880</td><td>KP124033</td><td>KP124640</td><td>KP125239</td><td>KP125287</td></tr><tr><td>CBS 102602; E.G.S. 44.160 (<italic>A. perangusta</italic><sup>T</sup>)</td><td>Turkey, <italic>Minneola tangelo</italic></td><td>KP124954</td><td>KP124484</td><td>KP124332</td><td>KP124187</td><td>KP125108</td><td>KP124800</td><td>KP123881</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY295023" id="intref0130"><bold>AY295023</bold></ext-link></td><td>KP124641</td><td>KP125240</td><td>KP125288</td></tr><tr><td>CBS 102603; E.G.S. 45.011 (<italic>A. interrupta</italic><sup>T</sup>)</td><td>Israel, <italic>Minneola tangelo</italic></td><td>KP124955</td><td>KP124485</td><td>KP124333</td><td>KP124188</td><td>KP125109</td><td>KP124801</td><td>KP123882</td><td>KP124034</td><td>KP124642</td><td></td><td></td></tr><tr><td>CBS 102604; E.G.S. 45.007 (<italic>A. dumosa</italic><sup>T</sup>)</td><td>Israel, <italic>Minneola tangelo</italic></td><td>KP124956</td><td>KP124486</td><td>KP124334</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY562410" id="intref0135"><bold>AY562410</bold></ext-link></td><td>KP125110</td><td>KP124802</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY563305" id="intref0140"><bold>AY563305</bold></ext-link></td><td>KP124035</td><td>KP124643</td><td>KP125241</td><td>KP125289</td></tr><tr><td>CBS 109455</td><td>Canada, human arm tissue</td><td>KP124957</td><td>KP124487</td><td>KP124335</td><td>KP124189</td><td>KP125111</td><td>KP124803</td><td>KP123883</td><td>KP124036</td><td>KP124644</td><td></td><td></td></tr><tr><td>CBS 109803</td><td>Germany, human skin</td><td>KP124958</td><td>KP124488</td><td>KP124336</td><td>KP124190</td><td>KP125112</td><td>KP124804</td><td>KP123884</td><td>KP124037</td><td>KP124645</td><td></td><td></td></tr><tr><td>CBS 110027</td><td>Germany, human eye</td><td>KP124959</td><td>KP124489</td><td>KP124337</td><td>KP124191</td><td>KP125113</td><td>KP124805</td><td>KP123885</td><td>KP124038</td><td>KP124646</td><td></td><td></td></tr><tr><td>CBS 110977; E.G.S. 34.016; CBS 916.96; CBS 115616<sup>T</sup></td><td>India, <italic>Arachis hypogaea</italic></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584507" id="interref9135"><bold>KC584507</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:DQ678082" id="interref8015a"><bold>DQ678082</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AF347031" id="intref0145"><bold>AF347031</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY278808" id="intref0150"><bold>AY278808</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584634" id="interref9140"><bold>KC584634</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584375" id="interref9145"><bold>KC584375</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY563301" id="intref0155"><bold>AY563301</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ811978" id="interref8040"><bold>JQ811978</bold></ext-link></td><td>KP124647</td><td></td><td></td></tr><tr><td>CBS 112249</td><td>Unknown, unknown</td><td>KP124960</td><td>KP124490</td><td>KP124338</td><td>KP124192</td><td>KP125114</td><td>KP124806</td><td>KP123886</td><td>KP124039</td><td>KP124648</td><td></td><td></td></tr><tr><td>CBS 112251 (<italic>A. arborescens</italic>)</td><td>Unknown, unknown</td><td>KP124961</td><td>KP124491</td><td>KP124339</td><td>KP124193</td><td>KP125115</td><td>KP124807</td><td>KP123887</td><td>KP124040</td><td>KP124649</td><td></td><td></td></tr><tr><td>CBS 112252 (<italic>A. tenuissima</italic>)</td><td>Unknown, unknown</td><td>KP124962</td><td>KP124492</td><td>KP124340</td><td>KP124194</td><td>KP125116</td><td>KP124808</td><td>KP123888</td><td>KP124041</td><td>KP124650</td><td></td><td></td></tr><tr><td>CBS 113013; CPC 4268 (<italic>A. tenuissima</italic>)</td><td>South Africa, <italic>Malus domestica</italic></td><td>KP124963</td><td>KP124493</td><td>KP124341</td><td>KP124195</td><td>KP125117</td><td>KP124809</td><td>KP123889</td><td>KP124042</td><td>KP124651</td><td></td><td></td></tr><tr><td>CBS 113014; CPC 4260 (<italic>A. tenuissima</italic>)</td><td>South Africa, <italic>Malus domestica</italic></td><td>KP124964</td><td>KP124494</td><td>KP124342</td><td>KP124196</td><td>KP125118</td><td>KP124810</td><td>KP123890</td><td>KP124043</td><td>KP124652</td><td></td><td></td></tr><tr><td>CBS 113015; CPC 4266 (<italic>A. tenuissima</italic>)</td><td>South Africa, <italic>Malus domestica</italic></td><td>KP124965</td><td>KP124495</td><td>KP124343</td><td>KP124197</td><td>KP125119</td><td>KP124811</td><td>KP123891</td><td>KP124044</td><td>KP124653</td><td></td><td></td></tr><tr><td>CBS 113024; CPC 4334</td><td>South Africa, <italic>Minneola tangelo</italic></td><td>KP124966</td><td>KP124496</td><td>KP124344</td><td>KP124198</td><td>KP125120</td><td>KP124812</td><td>KP123892</td><td>KP124045</td><td>KP124654</td><td></td><td></td></tr><tr><td>CBS 113025; CPC 4342</td><td>South Africa, <italic>Citrus clementina</italic></td><td>KP124967</td><td>KP124497</td><td>KP124345</td><td>KP124199</td><td>KP125121</td><td>KP124813</td><td>KP123893</td><td>KP124046</td><td>KP124655</td><td></td><td></td></tr><tr><td>CBS 113054; CPC 4263 (<italic>A. tenuissima</italic>)</td><td>South Africa, <italic>Malus domestica</italic></td><td>KP124968</td><td>KP124498</td><td>KP124346</td><td>KP124200</td><td>KP125122</td><td>KP124814</td><td>KP123894</td><td>KP124047</td><td>KP124656</td><td></td><td></td></tr><tr><td>CBS 115069; CPC 4254 (<italic>A. tenuissima</italic>)</td><td>South Africa, <italic>Malus domestica</italic></td><td>KP124969</td><td>KP124499</td><td>KP124347</td><td>KP124201</td><td>KP125123</td><td>KP124815</td><td>KP123895</td><td>KP124048</td><td>KP124657</td><td></td><td></td></tr><tr><td>CBS 115152; HKUCC 9099</td><td>China, <italic>Psychotria serpens</italic></td><td>KP124970</td><td>KP124500</td><td>KP124348</td><td>KP124202</td><td>KP125124</td><td>KP124816</td><td>KP123896</td><td>KP124049</td><td>KP124658</td><td></td><td></td></tr><tr><td>CBS 115188; CPC 4348</td><td>South Africa, <italic>Citrus clementina</italic></td><td>KP124971</td><td>KP124501</td><td>KP124349</td><td>KP124203</td><td>KP125125</td><td>KP124817</td><td>KP123897</td><td>KP124050</td><td>KP124659</td><td></td><td></td></tr><tr><td>CBS 115190; CPC 4340</td><td>South Africa, <italic>Citrus sinensis</italic></td><td>KP124972</td><td>KP124502</td><td>KP124350</td><td>KP124204</td><td>KP125126</td><td>KP124818</td><td>KP123898</td><td>KP124051</td><td>KP124660</td><td></td><td></td></tr><tr><td>CBS 115199; CPC 4327</td><td>South Africa, <italic>Minneola tangelo</italic></td><td>KP124973</td><td>KP124503</td><td>KP124351</td><td>KP124205</td><td>KP125127</td><td>KP124819</td><td>KP123899</td><td>KP124052</td><td>KP124661</td><td></td><td></td></tr><tr><td>CBS 115200; CPC 4325</td><td>South Africa, <italic>Minneola tangelo</italic></td><td>KP124974</td><td>KP124504</td><td>KP124352</td><td>KP124206</td><td>KP125128</td><td>KP124820</td><td>KP123900</td><td>KP124053</td><td>KP124662</td><td></td><td></td></tr><tr><td>CBS 115616; EGS 34.016; CBS 916.96; CBS 110977<sup>T</sup></td><td>India, <italic>Arachis hypogaea</italic></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584507" id="interref9150"><bold>KC584507</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:DQ678082" id="interref8020a"><bold>DQ678082</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AF347031" id="intref0160"><bold>AF347031</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY278808" id="intref0165"><bold>AY278808</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584634" id="interref9155"><bold>KC584634</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584375" id="interref9160"><bold>KC584375</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY563301" id="intref0170"><bold>AY563301</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ811978" id="interref8045"><bold>JQ811978</bold></ext-link></td><td>KP124663</td><td></td><td></td></tr><tr><td>CBS 116749</td><td>Netherlands, unknown</td><td>KP124975</td><td>KP124505</td><td>KP124353</td><td>KP124207</td><td>KP125129</td><td>KP124821</td><td>KP123901</td><td>KP124054</td><td>KP124664</td><td></td><td></td></tr><tr><td>CBS 117130</td><td>Italy, <italic>Arbutus unedo</italic></td><td>KP124976</td><td>KP124506</td><td>KP124354</td><td>KP124208</td><td>KP125130</td><td>KP124822</td><td>KP123902</td><td>KP124055</td><td>KP124665</td><td></td><td></td></tr><tr><td>CBS 117143</td><td>Italy, <italic>Capsicum annuum</italic></td><td>KP124977</td><td>KP124507</td><td>KP124355</td><td>KP124209</td><td>KP125131</td><td>KP124823</td><td>KP123903</td><td>KP124056</td><td>KP124666</td><td></td><td></td></tr><tr><td>CBS 118811; E.G.S. 35.158 (<italic>A. brassicinae</italic><sup>T</sup>)</td><td>USA, <italic>Brassica oleracea</italic></td><td>KP124978</td><td>KP124508</td><td>KP124356</td><td>KP124210</td><td>KP125132</td><td>KP124824</td><td>KP123904</td><td>KP124057</td><td>KP124667</td><td>KP125242</td><td>KP125290</td></tr><tr><td>CBS 118812; E.G.S. 37.050 (<italic>A. daucifolii</italic><sup>T</sup>)</td><td>USA, <italic>Daucus carota</italic></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584525" id="interref9165"><bold>KC584525</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584269" id="interref9170"><bold>KC584269</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584193" id="interref9175"><bold>KC584193</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584112" id="interref9180"><bold>KC584112</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584652" id="interref9185"><bold>KC584652</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584393" id="interref9190"><bold>KC584393</bold></ext-link></td><td>KP123905</td><td>KP124058</td><td>KP124668</td><td>KP125243</td><td>KP125291</td></tr><tr><td>CBS 118814; E.G.S. 44.048 (<italic>A. tomaticola</italic><sup>T</sup>)</td><td>USA, <italic>Solanum lycopersicum</italic></td><td>KP124979</td><td>KP124509</td><td>KP124357</td><td>KP124211</td><td>KP125133</td><td>KP124825</td><td>KP123906</td><td>KP124059</td><td>KP124669</td><td>KP125244</td><td>KP125292</td></tr><tr><td>CBS 118815; E.G.S. 51.132 (<italic>A. tomaticola</italic><sup>R</sup>)</td><td>USA, <italic>Solanum lycopersicum</italic></td><td>KP124980</td><td>KP124510</td><td>KP124358</td><td>KP124212</td><td>KP125134</td><td>KP124826</td><td>KP123907</td><td>KP124060</td><td>KP124670</td><td></td><td></td></tr><tr><td>CBS 118818; E.G.S. 31.032 (<italic>A. vaccinii</italic><sup>T</sup>)</td><td>USA, <italic>Vaccinium</italic> sp.</td><td>KP124981</td><td>KP124511</td><td>KP124359</td><td>KP124213</td><td>KP125135</td><td>KP124827</td><td>KP123908</td><td>KP124061</td><td>KP124671</td><td>KP125245</td><td>KP125293</td></tr><tr><td>CBS 119115</td><td>Greece, <italic>Prunus</italic> sp.</td><td>KP124982</td><td>KP124512</td><td>KP124360</td><td>KP124214</td><td>KP125136</td><td>KP124828</td><td>KP123909</td><td>KP124062</td><td>np</td><td></td><td></td></tr><tr><td>CBS 119399; E.G.S. 39.189 (<italic>A. postmessia</italic><sup>T</sup>)</td><td>USA, <italic>Minneola tangelo</italic></td><td>KP124983</td><td>KP124513</td><td>KP124361</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646328" id="interref8050"><bold>JQ646328</bold></ext-link></td><td>KP125137</td><td>KP124829</td><td>KP123910</td><td>KP124063</td><td>KP124672</td><td>KP125246</td><td>KP125294</td></tr><tr><td>CBS 119408; E.G.S. 40.140 (<italic>A. herbiphorbicola</italic><sup>T</sup>)</td><td>USA, <italic>Euphorbia esula</italic></td><td>KP124984</td><td>KP124514</td><td>KP124362</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646326" id="interref8055"><bold>JQ646326</bold></ext-link></td><td>KP125138</td><td>KP124830</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646410" id="interref8060"><bold>JQ646410</bold></ext-link></td><td>KP124064</td><td>KP124673</td><td>KP125247</td><td>KP125295</td></tr><tr><td>CBS 119543; E.G.S. 12.160 (<italic>A. citricancri</italic><sup>T</sup>)</td><td>USA, <italic>Citrus paradisi</italic></td><td>KP124985</td><td>KP124515</td><td>KP124363</td><td>KP124215</td><td>KP125139</td><td>KP124831</td><td>KP123911</td><td>KP124065</td><td>KP124674</td><td>KP125248</td><td>KP125296</td></tr><tr><td>CBS 120829</td><td>Greece, <italic>Punica granatum</italic></td><td>KP124986</td><td>KP124516</td><td>KP124364</td><td>KP124216</td><td>KP125140</td><td>KP124832</td><td>KP123912</td><td>KP124066</td><td>KP124675</td><td></td><td></td></tr><tr><td>CBS 121336; E.G.S. 37.005; ATCC 11680 (<italic>A. palandui</italic><sup>T</sup>)</td><td>USA, <italic>Allium</italic> sp.</td><td>KP124987</td><td>KP124517</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KJ862254" id="interref7000"><bold>KJ862254</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KJ862255" id="interref7005"><bold>KJ862255</bold></ext-link></td><td>KP125141</td><td>KP124833</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KJ862259" id="interref7010"><bold>KJ862259</bold></ext-link></td><td>KP124067</td><td>KP124676</td><td>KP125249</td><td>KP125297</td></tr><tr><td>CBS 121344; E.G.S. 45.003 (<italic>A. turkisafria</italic><sup>R</sup>)</td><td>Israel, <italic>Minneola tangelo</italic></td><td>KP124988</td><td>KP124518</td><td>KP124365</td><td>KP124217</td><td>KP125142</td><td>KP124834</td><td>KP123913</td><td>KP124068</td><td>KP124677</td><td></td><td></td></tr><tr><td>CBS 121346; E.G.S. 45.056 (<italic>A. turkisafria</italic><sup>R</sup>)</td><td>South Africa, <italic>Minneola tangelo</italic></td><td>KP124989</td><td>KP124519</td><td>KP124366</td><td>KP124218</td><td>KP125143</td><td>KP124835</td><td>KP123914</td><td>KP124069</td><td>KP124678</td><td></td><td></td></tr><tr><td>CBS 121348; E.G.S. 50.070 (<italic>A. platycodonis</italic><sup>T</sup>)</td><td>China, <italic>Platycodon grandiflorus</italic></td><td>KP124990</td><td>KP124520</td><td>KP124367</td><td>KP124219</td><td>KP125144</td><td>KP124836</td><td>KP123915</td><td>KP124070</td><td>KP124679</td><td>KP125250</td><td>KP125298</td></tr><tr><td>CBS 121454; E.G.S. 46.069 (<italic>A. destruens</italic><sup>T</sup>)</td><td>USA, <italic>Cuscuta gronovii</italic></td><td>KP124991</td><td>KP124521</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AF278836" id="intref0175"><bold>AF278836</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY278812" id="intref0180"><bold>AY278812</bold></ext-link></td><td>KP125145</td><td>KP124837</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646402" id="interref8065"><bold>JQ646402</bold></ext-link></td><td>KP124071</td><td>KP124680</td><td>KP125251</td><td>KP125299</td></tr><tr><td>CBS 121455; E.G.S. 50.078 (<italic>A. broussonetiae</italic><sup>T</sup>)</td><td>China, <italic>Broussonetia papyrifera</italic></td><td>KP124992</td><td>KP124522</td><td>KP124368</td><td>KP124220</td><td>KP125146</td><td>KP124838</td><td>KP123916</td><td>KP124072</td><td>KP124681</td><td>KP125252</td><td>KP125300</td></tr><tr><td>CBS 121456; E.G.S. 50.080; HSAUP 9600197 (<italic>A. sanguisorbae</italic><sup>T</sup>)</td><td>China, <italic>Sanguisorba officinalis</italic></td><td>KP124993</td><td>KP124523</td><td>KP124369</td><td>KP124221</td><td>KP125147</td><td>KP124839</td><td>KP123917</td><td>KP124073</td><td>KP124682</td><td>KP125253</td><td>KP125301</td></tr><tr><td>CBS 121492; HSAUP0207 (<italic>Ulocladium cucumisis</italic>)</td><td>China, <italic>Cucumis melo</italic></td><td>KP124994</td><td>KP124524</td><td>KP124370</td><td>KP124222</td><td>KP125148</td><td>KP124840</td><td>KP123918</td><td>KP124074</td><td>KP124683</td><td></td><td></td></tr><tr><td>CBS 121544; E.G.S. 38.022 (<italic>A. caudata</italic><sup>R</sup>)</td><td>USA, <italic>Cucumis sativus</italic></td><td>KP124995</td><td>KP124525</td><td>KP124371</td><td>KP124223</td><td>KP125149</td><td>KP124841</td><td>KP123919</td><td>KP124075</td><td>KP124684</td><td></td><td></td></tr><tr><td>CBS 121547; E.G.S. 50.048 (<italic>A. yali-inficiens</italic><sup>T</sup>)</td><td>China, <italic>Pyrus bretschneideri</italic></td><td>KP124996</td><td>KP124526</td><td>KP124372</td><td>KP124224</td><td>KP125150</td><td>KP124842</td><td>KP123920</td><td>KP124076</td><td>KP124685</td><td></td><td></td></tr><tr><td>CBS 124277 (<italic>A. tenuissima</italic>)</td><td>Denmark, <italic>Prunus</italic> sp.</td><td>KP124997</td><td>KP124527</td><td>KP124373</td><td>KP124225</td><td>KP125151</td><td>KP124843</td><td>KP123921</td><td>KP124077</td><td>KP124686</td><td></td><td></td></tr><tr><td>CBS 124278 (<italic>A. tenuissima</italic>)</td><td>Denmark, <italic>Prunus</italic> sp.</td><td>KP124998</td><td>KP124528</td><td>KP124374</td><td>KP124226</td><td>KP125152</td><td>KP124844</td><td>KP123922</td><td>KP124078</td><td>KP124687</td><td></td><td></td></tr><tr><td>CBS 125606</td><td>India, human</td><td>KP124999</td><td>KP124529</td><td>KP124375</td><td>KP124227</td><td>KP125153</td><td>KP124845</td><td>KP123923</td><td>KP124079</td><td>KP124688</td><td></td><td></td></tr><tr><td>CBS 126071 (<italic>A. tenuissima</italic>)</td><td>Namibia, soil</td><td>KP125000</td><td>KP124530</td><td>KP124376</td><td>KP124228</td><td>KP125154</td><td>KP124846</td><td>KP123924</td><td>KP124080</td><td>KP124689</td><td></td><td></td></tr><tr><td>CBS 126072 (<italic>A. tenuissima</italic>)</td><td>Namibia, soil</td><td>KP125001</td><td>KP124531</td><td>KP124377</td><td>KP124229</td><td>KP125155</td><td>KP124847</td><td>KP123925</td><td>KP124081</td><td>KP124690</td><td></td><td></td></tr><tr><td>CBS 126908</td><td>USA, soil</td><td>KP125002</td><td>KP124532</td><td>KP124378</td><td>KP124230</td><td>KP125156</td><td>KP124848</td><td>KP123926</td><td>KP124082</td><td>KP124691</td><td></td><td></td></tr><tr><td>CBS 126910 (<italic>A. tenuis</italic>)</td><td>USA, soil</td><td>KP125003</td><td>KP124533</td><td>KP124379</td><td>KP124231</td><td>KP125157</td><td>KP124849</td><td>KP123927</td><td>KP124083</td><td>KP124692</td><td></td><td></td></tr><tr><td>CBS 127334</td><td>USA, soil</td><td>KP125004</td><td>KP124534</td><td>KP124380</td><td>KP124232</td><td>KP125158</td><td>KP124850</td><td>KP123928</td><td>KP124084</td><td>KP124693</td><td></td><td></td></tr><tr><td>CBS 127671; E.G.S. 52.121 (<italic>A. seleniiphila</italic><sup>T</sup>)</td><td>USA, <italic>Stanleya pinnata</italic></td><td>KP125005</td><td>KP124535</td><td>KP124381</td><td>KP124233</td><td>KP125159</td><td>KP124851</td><td>KP123929</td><td>KP124085</td><td>KP124694</td><td></td><td></td></tr><tr><td>CBS 127672; E.G.S. 52.122 (<italic>A. astragali</italic><sup>T</sup>)</td><td>USA, <italic>Astragalus bisulcatus</italic></td><td>KP125006</td><td>KP124536</td><td>KP124382</td><td>KP124234</td><td>KP125160</td><td>KP124852</td><td>KP123930</td><td>KP124086</td><td>KP124695</td><td></td><td></td></tr><tr><td>CBS 130254</td><td>India, human sputum</td><td>KP125007</td><td>KP124537</td><td>KP124383</td><td>KP124235</td><td>KP125161</td><td>KP124853</td><td>KP123931</td><td>KP124087</td><td>KP124696</td><td></td><td></td></tr><tr><td>CBS 130255</td><td>India, human sputum</td><td>KP125008</td><td>KP124538</td><td>KP124384</td><td>KP124236</td><td>KP125162</td><td>KP124854</td><td>KP123932</td><td>KP124088</td><td>KP124697</td><td></td><td></td></tr><tr><td>CBS 130258</td><td>India, human sputum</td><td>KP125009</td><td>KP124539</td><td>KP124385</td><td>KP124237</td><td>KP125163</td><td>KP124855</td><td>KP123933</td><td>KP124089</td><td>KP124698</td><td></td><td></td></tr><tr><td>CBS 130259</td><td>India, human sputum</td><td>KP125010</td><td>KP124540</td><td>KP124386</td><td>KP124238</td><td>KP125164</td><td>KP124856</td><td>KP123934</td><td>KP124090</td><td>KP124699</td><td></td><td></td></tr><tr><td>CBS 130260</td><td>India, human sputum</td><td>KP125011</td><td>KP124541</td><td>KP124387</td><td>KP124239</td><td>KP125165</td><td>KP124857</td><td>KP123935</td><td>KP124091</td><td>KP124700</td><td></td><td></td></tr><tr><td>CBS 130261</td><td>India, human sputum</td><td>KP125012</td><td>KP124542</td><td>KP124388</td><td>KP124240</td><td>KP125166</td><td>KP124858</td><td>KP123936</td><td>KP124092</td><td>KP124701</td><td></td><td></td></tr><tr><td>CBS 130262</td><td>India, human sputum</td><td>KP125013</td><td>KP124543</td><td>KP124389</td><td>KP124241</td><td>KP125167</td><td>KP124859</td><td>KP123937</td><td>KP124093</td><td>KP124702</td><td></td><td></td></tr><tr><td>CBS 130263</td><td>India, human sputum</td><td>KP125014</td><td>KP124544</td><td>KP124390</td><td>KP124242</td><td>KP125168</td><td>KP124860</td><td>KP123938</td><td>KP124094</td><td>KP124703</td><td></td><td></td></tr><tr><td>CBS 130265</td><td>India, human sputum</td><td>KP125015</td><td>KP124545</td><td>KP124391</td><td>KP124243</td><td>KP125169</td><td>KP124861</td><td>KP123939</td><td>KP124095</td><td>KP124704</td><td></td><td></td></tr><tr><td colspan="13"><bold><italic>Alternaria arborescens</italic> SC</bold></td></tr><tr><td>CBS 101.13; E.G.S. 07.022; QM1765 (<italic>A. geophila</italic><sup>T</sup>)</td><td>Switzerland, peat soil</td><td>KP125016</td><td>KP124546</td><td>KP124392</td><td>KP124244</td><td>KP125170</td><td>KP124862</td><td>KP123940</td><td>KP124096</td><td>KP124705</td><td>KP125254</td><td>KP125302</td></tr><tr><td>CBS 105.24; IHEM 3123 (<italic>A. alternata</italic>)</td><td>Unknown, <italic>Solanum tuberosum</italic></td><td>KP125017</td><td>KP124547</td><td>KP124393</td><td>KP124245</td><td>KP125171</td><td>KP124863</td><td>KP123941</td><td>KP124097</td><td>KP124706</td><td></td><td></td></tr><tr><td>CBS 108.41; E.G.S. 44.087; ATCC 11892 (<italic>A. alternata</italic>)</td><td>Unknown, wood</td><td>KP125018</td><td>KP124548</td><td>KP124394</td><td>KP124246</td><td>KP125172</td><td>KP124864</td><td>KP123942</td><td>KP124098</td><td>KP124707</td><td></td><td></td></tr><tr><td>CBS 113.41; IHEM 3318 (<italic>A. alternata</italic>)</td><td>Unknown, <italic>Schizanthus</italic> sp.</td><td>KP125019</td><td>KP124549</td><td>KP124395</td><td>KP124247</td><td>KP125173</td><td>KP124865</td><td>KP123943</td><td>KP124099</td><td>KP124708</td><td></td><td></td></tr><tr><td>CBS 105.49 (<italic>A. alternata</italic>)</td><td>Italy, contaminant blood culture</td><td>KP125020</td><td>KP124550</td><td>KP124396</td><td>KP124248</td><td>KP125174</td><td>KP124866</td><td>KP123944</td><td>KP124100</td><td>KP124709</td><td></td><td></td></tr><tr><td>CBS 126.60; IMI 081622 (<italic>A. maritima</italic>)</td><td>UK, wood</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:GU456294" id="intref0185"><bold>GU456294</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:GU456317" id="intref0190"><bold>GU456317</bold></ext-link></td><td>KP124397</td><td>KP124249</td><td>KP125175</td><td>KP124867</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646390" id="interref8070"><bold>JQ646390</bold></ext-link></td><td>KP124101</td><td>KP124710</td><td></td><td></td></tr><tr><td>CBS 750.68; LCP 68.1989 (<italic>A. tenuissima</italic>)</td><td>France, <italic>Phaseolus vulgaris</italic></td><td>KP125021</td><td>KP124551</td><td>KP124398</td><td>KP124250</td><td>KP125176</td><td>KP124868</td><td>KP123945</td><td>KP124102</td><td>KP124711</td><td></td><td></td></tr><tr><td>CBS 102605; E.G.S. 39.128 (<italic>A. arborescens</italic><sup>T</sup>)</td><td>USA, <italic>Solanum lycopersicum</italic></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584509" id="interref9195"><bold>KC584509</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584253" id="interref9200"><bold>KC584253</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AF347033" id="intref0195"><bold>AF347033</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY278810" id="intref0200"><bold>AY278810</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584636" id="interref9205"><bold>KC584636</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584377" id="interref9210"><bold>KC584377</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY563303" id="intref0205"><bold>AY563303</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY295028" id="intref0210"><bold>AY295028</bold></ext-link></td><td>KP124712</td><td>KP125255</td><td>KP125303</td></tr><tr><td>CBS 109730 (<italic>A. arborescens</italic>)</td><td>USA, <italic>Solanum lycopersicum</italic></td><td>KP125022</td><td>KP124552</td><td>KP124399</td><td>KP124251</td><td>KP125177</td><td>KP124869</td><td>KP123946</td><td>KP124103</td><td>KP124713</td><td></td><td></td></tr><tr><td>CBS 112633; CPC 4244 (<italic>A. arborescens</italic>)</td><td>South Africa, <italic>Malus domestica</italic></td><td>KP125023</td><td>KP124553</td><td>KP124400</td><td>KP124252</td><td>KP125178</td><td>KP124870</td><td>KP123947</td><td>KP124104</td><td>KP124714</td><td></td><td></td></tr><tr><td>CBS 112749; CPC 4245 (<italic>A. arborescens</italic>)</td><td>South Africa, <italic>Malus domestica</italic></td><td>KP125024</td><td>KP124554</td><td>KP124401</td><td>KP124253</td><td>KP125179</td><td>KP124871</td><td>KP123948</td><td>KP124105</td><td>KP124715</td><td></td><td></td></tr><tr><td>CBS 115189; CPC 4345 (<italic>A. arborescens</italic>)</td><td>South Africa, <italic>Citrus clementina</italic></td><td>KP125025</td><td>KP124555</td><td>KP124402</td><td>KP124254</td><td>KP125180</td><td>KP124872</td><td>KP123949</td><td>KP124106</td><td>KP124716</td><td></td><td></td></tr><tr><td>CBS 115516; CPC 4247 (<italic>A. arborescens</italic>)</td><td>South Africa, <italic>Malus domestica</italic></td><td>KP125026</td><td>KP124556</td><td>KP124403</td><td>KP124255</td><td>KP125181</td><td>KP124873</td><td>KP123950</td><td>KP124107</td><td>KP124717</td><td></td><td></td></tr><tr><td>CBS 115517; CPC 4246 (<italic>A. arborescens</italic>)</td><td>South Africa, <italic>Malus domestica</italic></td><td>KP125027</td><td>KP124557</td><td>KP124404</td><td>KP124256</td><td>KP125182</td><td>KP124874</td><td>KP123951</td><td>KP124108</td><td>KP124718</td><td></td><td></td></tr><tr><td>CBS 116329 (<italic>A. alternata</italic>)</td><td>Germany, <italic>Malus domestica</italic></td><td>KP125028</td><td>KP124558</td><td>KP124405</td><td>KP124257</td><td>KP125183</td><td>KP124875</td><td>KP123952</td><td>KP124109</td><td>KP124719</td><td></td><td></td></tr><tr><td>CBS 117587 (<italic>A. alternata</italic>)</td><td>Netherlands, <italic>Brassica</italic> sp.</td><td>KP125029</td><td>KP124559</td><td>KP124406</td><td>KP124258</td><td>KP125184</td><td>KP124876</td><td>KP123953</td><td>KP124110</td><td>KP124720</td><td></td><td></td></tr><tr><td>CBS 118389; E.G.S. 90.131 (<italic>A. gaisen</italic><sup>R</sup>)</td><td>Japan, <italic>Pyrus pyrifolia</italic></td><td>KP125030</td><td>KP124560</td><td>KP124407</td><td>KP124259</td><td>KP125185</td><td>KP124877</td><td>KP123954</td><td>KP124111</td><td>KP124721</td><td></td><td></td></tr><tr><td>CBS 119544; E.G.S. 43.072 (<italic>A. cerealis</italic><sup>T</sup>)</td><td>New Zealand, <italic>Avena sativa</italic></td><td>KP125031</td><td>KP124561</td><td>KP124408</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646321" id="interref8075"><bold>JQ646321</bold></ext-link></td><td>KP125186</td><td>KP124878</td><td>KP123955</td><td>KP124112</td><td>KP124722</td><td>KP125256</td><td>KP125304</td></tr><tr><td>CBS 119545; E.G.S. 48.130 (<italic>A. senecionicola</italic><sup>T</sup>)</td><td>New Zealand, <italic>Senecio skirrhodon</italic></td><td>KP125032</td><td>KP124562</td><td>KP124409</td><td>KP124260</td><td>KP125187</td><td>KP124879</td><td>KP123956</td><td>KP124113</td><td>KP124723</td><td>KP125257</td><td>KP125305</td></tr><tr><td>CBS 123235 (<italic>A. alternata</italic>)</td><td>Denmark, human toenail</td><td>KP125033</td><td>KP124563</td><td>KP124410</td><td>KP124261</td><td>KP125188</td><td>KP124880</td><td>KP123957</td><td>KP124114</td><td>KP124724</td><td></td><td></td></tr><tr><td>CBS 123266 (<italic>A. alternata</italic>)</td><td>Denmark, human toenail</td><td>KP125034</td><td>KP124564</td><td>KP124411</td><td>KP124262</td><td>KP125189</td><td>KP124881</td><td>KP123958</td><td>KP124115</td><td>KP124725</td><td></td><td></td></tr><tr><td>CBS 123267 (<italic>A. alternata</italic>)</td><td>Denmark, human nail</td><td>KP125035</td><td>KP124565</td><td>KP124412</td><td>KP124263</td><td>KP125190</td><td>KP124882</td><td>KP123959</td><td>KP124116</td><td>KP124726</td><td></td><td></td></tr><tr><td>CBS 124274 (<italic>A. arborescens</italic>)</td><td>Denmark, <italic>Prunus</italic> sp.</td><td>KP125036</td><td>KP124566</td><td>KP124413</td><td>KP124264</td><td>KP125191</td><td>np</td><td>KP123960</td><td>KP124117</td><td>KP124727</td><td></td><td></td></tr><tr><td>CBS 124281 (<italic>A. arborescens</italic>)</td><td>Denmark, <italic>Triticum</italic> sp.</td><td>KP125037</td><td>KP124567</td><td>KP124414</td><td>KP124265</td><td>KP125192</td><td>KP124883</td><td>KP123961</td><td>KP124118</td><td>KP124728</td><td></td><td></td></tr><tr><td>CBS 124282 (<italic>A. arborescens</italic>)</td><td>Denmark, <italic>Hordeum vulgare</italic></td><td>KP125038</td><td>KP124568</td><td>KP124415</td><td>KP124266</td><td>KP125193</td><td>KP124884</td><td>KP123962</td><td>KP124119</td><td>KP124729</td><td></td><td></td></tr><tr><td>CBS 124283 (<italic>A. tenuissima</italic>)</td><td>Russia, <italic>Oryza</italic> sp.</td><td>KP125039</td><td>KP124569</td><td>KP124416</td><td>KP124267</td><td>KP125194</td><td>KP124885</td><td>KP123963</td><td>KP124120</td><td>KP124730</td><td></td><td></td></tr><tr><td>CBS 127263 (<italic>A. alternata</italic>)</td><td>Mexico, human nasal infection</td><td>KP125040</td><td>KP124570</td><td>KP124417</td><td>KP124268</td><td>KP125195</td><td>KP124886</td><td>KP123964</td><td>KP124121</td><td>KP124731</td><td></td><td></td></tr><tr><td>CPC 25266</td><td>Austria, <italic>Pyrus</italic> sp.</td><td>KP125041</td><td>KP124571</td><td>KP124418</td><td>KP124269</td><td>KP125196</td><td>KP124887</td><td>KP123965</td><td>KP124122</td><td>KP124732</td><td></td><td></td></tr><tr><td colspan="13"><bold><italic>Alternaria betae-kenyensis</italic></bold></td></tr><tr><td>CBS 118810; E.G.S. 49.159; IMI 385709<sup>T</sup></td><td>Kenya, <italic>Beta vulgaris</italic> var. <italic>cicla</italic></td><td>KP125042</td><td>KP124572</td><td>KP124419</td><td>KP124270</td><td>KP125197</td><td>KP124888</td><td>KP123966</td><td>KP124123</td><td>KP124733</td><td>KP125258</td><td>KP125306</td></tr><tr><td colspan="13"><bold><italic>Alternaria burnsii</italic></bold></td></tr><tr><td>CBS 108.27</td><td>Unknown, <italic>Gomphrena globosa</italic></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584601" id="interref9215"><bold>KC584601</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584343" id="interref9220"><bold>KC584343</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584236" id="interref9225"><bold>KC584236</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584162" id="interref9230"><bold>KC584162</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584727" id="interref9235"><bold>KC584727</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584468" id="interref9240"><bold>KC584468</bold></ext-link></td><td>KP123850</td><td>KP123997</td><td>KP124605</td><td></td><td></td></tr><tr><td>CBS 107.38; E.G.S. 06.185<sup>T</sup></td><td>India, <italic>Cuminum cyminum</italic></td><td>KP125043</td><td>KP124573</td><td>KP124420</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646305" id="interref8080"><bold>JQ646305</bold></ext-link></td><td>KP125198</td><td>KP124889</td><td>KP123967</td><td>KP124124</td><td>KP124734</td><td>KP125259</td><td>np</td></tr><tr><td>CBS 110.50; MUCL 10012 (<italic>A. gossypina</italic>)</td><td>Mozambique, <italic>Gossypium</italic> sp.</td><td>KP125044</td><td>KP124574</td><td>KP124421</td><td>KP124271</td><td>KP125199</td><td>KP124890</td><td>KP123968</td><td>KP124125</td><td>KP124735</td><td></td><td></td></tr><tr><td>CBS 879.95; IMI 300779 (<italic>A. tenuissima</italic>)</td><td>UK, <italic>Sorghum</italic> sp.</td><td>KP125045</td><td>KP124575</td><td>KP124422</td><td>KP124272</td><td>KP125200</td><td>KP124891</td><td>KP123969</td><td>KP124126</td><td>KP124736</td><td></td><td></td></tr><tr><td>CBS 118816; E.G.S. 43.145; IMI 368045 (<italic>A. rhizophorae</italic><sup>T</sup>)</td><td>India, <italic>Rhizophora mucronata</italic></td><td>KP125046</td><td>KP124576</td><td>KP124423</td><td>KP124273</td><td>KP125201</td><td>KP124892</td><td>KP123970</td><td>KP124127</td><td>KP124737</td><td>KP125260</td><td>KP125307</td></tr><tr><td>CBS 118817; E.G.S. 39.014; IMI 318433 (<italic>A. tinosporae</italic><sup>T</sup>)</td><td>India, <italic>Tinospora cordifolia</italic></td><td>KP125047</td><td>KP124577</td><td>KP124424</td><td>KP124274</td><td>KP125202</td><td>KP124893</td><td>KP123971</td><td>KP124128</td><td>KP124738</td><td>KP125261</td><td>KP125308</td></tr><tr><td>CBS 130264</td><td>India, human sputum</td><td>KP125048</td><td>KP124578</td><td>KP124425</td><td>KP124275</td><td>KP125203</td><td>KP124894</td><td>KP123972</td><td>KP124129</td><td>KP124739</td><td></td><td></td></tr><tr><td colspan="13"><bold><italic>Alternaria eichhorniae</italic></bold></td></tr><tr><td>CBS 489.92; ATCC 22255; ATCC 46777; IMI 121518<sup>T</sup></td><td>India, <italic>Eichhornia crassipes</italic></td><td>KP125049</td><td>KP124579</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC146356" id="interref9245"><bold>KC146356</bold></ext-link></td><td>KP124276</td><td>KP125204</td><td>KP124895</td><td>KP123973</td><td>KP124130</td><td>KP124740</td><td>KP125262</td><td>KP125309</td></tr><tr><td>CBS 119778; E.G.S. 45.026; IMI 37968<sup>R</sup></td><td>Indonesia, <italic>Eichhornia crassipes</italic></td><td>KP125050</td><td>KP124580</td><td>KP124426</td><td>KP124277</td><td>KP125205</td><td>KP124896</td><td>np</td><td>KP124131</td><td>KP124741</td><td>KP125263</td><td>KP125310</td></tr><tr><td colspan="13"><bold><italic>Alternaria gaisen</italic></bold></td></tr><tr><td>CBS 632.93; E.G.S. 90.512<sup>R</sup></td><td>Japan, <italic>Pyrus pyrifolia</italic></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584531" id="interref9250"><bold>KC584531</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584275" id="interref9255"><bold>KC584275</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584197" id="interref9260"><bold>KC584197</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584116" id="interref9265"><bold>KC584116</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584658" id="interref9270"><bold>KC584658</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584399" id="interref9275"><bold>KC584399</bold></ext-link></td><td>KP123974</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY295033" id="intref0215"><bold>AY295033</bold></ext-link></td><td>KP124742</td><td>KP125264</td><td>KP125311</td></tr><tr><td>CBS 118488; E.G.S. 90.391<sup>R</sup></td><td>Japan, <italic>Pyrus pyrifolia</italic></td><td>KP125051</td><td>KP124581</td><td>KP124427</td><td>KP124278</td><td>KP125206</td><td>KP124897</td><td>KP123975</td><td>KP124132</td><td>KP124743</td><td>KP125265</td><td>KP125312</td></tr><tr><td>CPC 25268</td><td>Portugal, unknown</td><td>KP125052</td><td>KP124582</td><td>KP124428</td><td>KP124279</td><td>KP125207</td><td>KP124898</td><td>KP123976</td><td>KP124133</td><td>KP124744</td><td></td><td></td></tr><tr><td colspan="13"><bold><italic>Alternaria gossypina</italic></bold></td></tr><tr><td>CBS 100.23 (<italic>A. grossulariae</italic>)</td><td>Unknown, <italic>Malus domestica</italic></td><td>KP125053</td><td>KP124583</td><td>KP124429</td><td>KP124280</td><td>KP125208</td><td>KP124899</td><td>KP123977</td><td>KP124134</td><td>KP124745</td><td></td><td></td></tr><tr><td>CBS 104.32<sup>T</sup></td><td>Zimbabwe, <italic>Gossypium</italic> sp.</td><td>KP125054</td><td>KP124584</td><td>KP124430</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646312" id="interref8085"><bold>JQ646312</bold></ext-link></td><td>KP125209</td><td>KP124900</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646395" id="interref8090"><bold>JQ646395</bold></ext-link></td><td>KP124135</td><td>KP124746</td><td></td><td></td></tr><tr><td>CBS 107.36 (<italic>A. grisea</italic><sup>T</sup>)</td><td>Indonesia, soil</td><td>KP125055</td><td>KP124585</td><td>KP124431</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646310" id="interref8095"><bold>JQ646310</bold></ext-link></td><td>KP125210</td><td>KP124901</td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:JQ646393" id="interref8100"><bold>JQ646393</bold></ext-link></td><td>KP124136</td><td>KP124747</td><td></td><td></td></tr><tr><td>CBS 102597; E.G.S. 45.114 (<italic>A. tangelonis</italic><sup>T</sup>)</td><td>USA, <italic>Minneola tangelo</italic></td><td>KP125056</td><td>KP124586</td><td>KP124432</td><td>KP124281</td><td>KP125211</td><td>KP124902</td><td>KP123978</td><td>KP124137</td><td>KP124748</td><td>KP125266</td><td>KP125313</td></tr><tr><td>CBS 102601; E.G.S. 45.017 (<italic>A. colombiana</italic><sup>T</sup>)</td><td>Colombia, <italic>Minneola tangelo</italic></td><td>KP125057</td><td>KP124587</td><td>KP124433</td><td>KP124282</td><td>KP125212</td><td>KP124903</td><td>KP123979</td><td>KP124138</td><td>KP124749</td><td>KP125267</td><td>KP125314</td></tr><tr><td colspan="13"><bold><italic>Alternaria iridiaustralis</italic></bold></td></tr><tr><td>CBS 118404; E.G.S. 49.078; MAFF 354A<sup>R</sup></td><td>New Zealand, <italic>Iris</italic> sp.</td><td>KP125058</td><td>KP124588</td><td>KP124434</td><td>KP124283</td><td>KP125213</td><td>KP124904</td><td>KP123980</td><td>KP124139</td><td>KP124750</td><td>KP125268</td><td>np</td></tr><tr><td>CBS 118486; E.G.S. 43.014<sup>T</sup></td><td>Australia, <italic>Iris</italic> sp.</td><td>KP125059</td><td>KP124589</td><td>KP124435</td><td>KP124284</td><td>KP125214</td><td>KP124905</td><td>KP123981</td><td>KP124140</td><td>KP124751</td><td></td><td></td></tr><tr><td>CBS 118487; E.G.S. 44.147<sup>R</sup></td><td>Australia, <italic>Iris</italic> sp.</td><td>KP125060</td><td>KP124590</td><td>KP124436</td><td>KP124285</td><td>KP125215</td><td>KP124906</td><td>KP123982</td><td>KP124141</td><td>KP124752</td><td></td><td></td></tr><tr><td colspan="13"><bold><italic>Alternaria jacinthicola</italic></bold></td></tr><tr><td>CBS 878.95; IMI 77934b (<italic>A. tenuissima</italic>)</td><td>Mauritius, <italic>Arachis hypogaea</italic></td><td>KP125061</td><td>KP124591</td><td>KP124437</td><td>KP124286</td><td>KP125216</td><td>KP124907</td><td>KP123983</td><td>KP124142</td><td>KP124753</td><td>KP125269</td><td>np</td></tr><tr><td>CBS 133751; MUCL 53159<sup>T</sup></td><td>Mali, <italic>Eichhornia crassipes</italic></td><td>KP125062</td><td>KP124592</td><td>KP124438</td><td>KP124287</td><td>KP125217</td><td>KP124908</td><td>KP123984</td><td>KP124143</td><td>KP124754</td><td>KP125270</td><td>np</td></tr><tr><td>CPC 25267</td><td>Unknown, <italic>Cucumis melo</italic> var. <italic>inodorus</italic></td><td>KP125063</td><td>KP124593</td><td>KP124439</td><td>KP124288</td><td>KP125218</td><td>KP124909</td><td>KP123985</td><td>KP124144</td><td>KP124755</td><td>KP125271</td><td>np</td></tr><tr><td colspan="13"><bold><italic>Alternaria longipes</italic></bold></td></tr><tr><td>CBS 113.35</td><td>Unknown, <italic>Nicotiana tabacum</italic></td><td>KP125064</td><td>KP124594</td><td>KP124440</td><td>KP124289</td><td>KP125219</td><td>KP124910</td><td>KP123986</td><td>KP124145</td><td>KP124756</td><td></td><td></td></tr><tr><td>CBS 539.94; QM 8438</td><td>USA, <italic>Nicotiana tabacum</italic></td><td>KP125065</td><td>KP124595</td><td>KP124441</td><td>KP124290</td><td>KP125220</td><td>KP124911</td><td>KP123987</td><td>KP124146</td><td>KP124757</td><td></td><td></td></tr><tr><td>CBS 540.94; E.G.S. 30.033; QM 9589<sup>R</sup></td><td>USA, <italic>Nicotiana tabacum</italic></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584541" id="interref9280"><bold>KC584541</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584285" id="interref9285"><bold>KC584285</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY278835" id="intref0220"><bold>AY278835</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY278811" id="intref0225"><bold>AY278811</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584667" id="interref9290"><bold>KC584667</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:KC584409" id="interref9295"><bold>KC584409</bold></ext-link></td><td><ext-link ext-link-type="uri" xlink:href="ncbi-n:AY563304" id="intref0230"><bold>AY563304</bold></ext-link></td><td>KP124147</td><td>KP124758</td><td>KP125272</td><td>KP125315</td></tr><tr><td>CBS 917.96</td><td>USA, <italic>Nicotiana tabacum</italic></td><td>KP125066</td><td>KP124596</td><td>KP124442</td><td>KP124291</td><td>KP125226</td><td>KP124912</td><td>KP123988</td><td>KP124148</td><td>KP124759</td><td></td><td></td></tr><tr><td>CBS 121332; E.G.S. 30.048<sup>R</sup></td><td>USA, <italic>Nicotiana tabacum</italic></td><td>KP125067</td><td>KP124597</td><td>KP124443</td><td>KP124292</td><td>KP125227</td><td>KP124913</td><td>KP123989</td><td>KP124149</td><td>KP124760</td><td></td><td></td></tr><tr><td>CBS 121333; E.G.S. 30.051<sup>R</sup></td><td>USA, <italic>Nicotiana tabacum</italic></td><td>KP125068</td><td>KP124598</td><td>KP124444</td><td>KP124293</td><td>KP125223</td><td>KP124914</td><td>KP123990</td><td>KP124150</td><td>KP124761</td><td></td><td></td></tr><tr><td colspan="13"><bold><italic>Alternaria tomato</italic></bold></td></tr><tr><td>CBS 103.30</td><td>Unknown, <italic>Solanum lycopersicum</italic></td><td>KP125069</td><td>KP124599</td><td>KP124445</td><td>KP124294</td><td>KP125224</td><td>KP124915</td><td>KP123991</td><td>KP124151</td><td>KP124762</td><td>KP125273</td><td>KP125316</td></tr><tr><td>CBS 114.35</td><td>Unknown, <italic>Solanum lycopersicum</italic></td><td>KP125070</td><td>KP124600</td><td>KP124446</td><td>KP124295</td><td>KP125225</td><td>KP124916</td><td>KP123992</td><td>KP124152</td><td>KP124763</td><td>KP125274</td><td>KP125317</td></tr></tbody></table><table-wrap-foot><fn id="tbl1fn1"><label>1</label><p id="ntpara0015">ATCC: American Type Culture Collection, Manassas, VA, USA; CBS: Culture collection of the Centraalbureau voor Schimmelcultures, Fungal Biodiversity Centre, Utrecht, The Netherlands; CPC: Personal collection of P.W. Crous, Utrecht, The Netherlands; DAOM: Canadian Collection of Fungal Cultures, Ottawa, Canada; DSM: German Collection of Microorganisms and Cell Cultures, Leibniz Institute, Braunschweig, Germany; E.G.S.: Personal collection of Dr. E.G. Simmons; HKUCC: The University of Hong Kong Culture Collection, Hong Kong, China; HSAUP: Department of Plant Pathology, Shandong Agricultural University, China; IFO: Institute for Fermentation Culture Collection, Osaka, Japan; IHEM: Biomedical Fungi and Yeast Collection of the Belgian Co-ordinated Collections of Micro-organisms (BCCM), Brussels, Belgium; IMI: Culture collection of CABI Europe UK Centre, Egham UK; LCP: Laboratory of Cryptogamy, National Museum of Natural History, Paris, France; MAFF: MAFF Genebank Project, Ministry of Agriculture, Forestry and Fisherie, Tsukuba, Japan; MUCL: (Agro)Industrial Fungi and Yeast Collection of the Belgian Co-ordinated Collections of Micro-organisms (BCCM), Louvain-la-Neuve, Belgium; QM: Quarter Master Culture Collection, Amherst, MA, USA; VKM: All-Russian Collection of Microorganisms, Moscow, Russia.</p></fn></table-wrap-foot><table-wrap-foot><fn id="tbl1fn2"><label>2</label><p id="ntpara0020">T: ex-type isolate; R: representative isolate; Species names between parentheses refer to the former species name.</p></fn></table-wrap-foot><table-wrap-foot><fn id="tbl1fn3"><label>3</label><p id="ntpara0025">Bold accession numbers are generated in other studies; np: no product.</p></fn></table-wrap-foot></table-wrap><table-wrap id="tbl2" position="float"><label>Table 2</label><caption><p>Assembly statistics of the <italic>Alternaria</italic> genomes.</p></caption><table frame="hsides" rules="groups"><thead><tr><th>Species</th><th>Strain number(s)</th><th>Section</th><th>Sequencing method</th><th>Size (Mb)</th><th>Coverage (approx.)</th><th>% Repeats</th><th>% Identity</th><th>% SNPs<xref rid="tbl2fn2" ref-type="table-fn">2</xref></th></tr></thead><tbody><tr><td><italic>A. alternata</italic></td><td>CBS 916.96<xref rid="tbl2fn3" ref-type="table-fn">3</xref></td><td><italic>Alternaria</italic></td><td>Illumina</td><td align="char">33.3</td><td>40×</td><td align="char">1.4</td><td>na<xref rid="tbl2fn3" ref-type="table-fn">3</xref></td><td>na<xref rid="tbl2fn3" ref-type="table-fn">3</xref></td></tr><tr><td><italic>A. arborescens</italic><xref rid="tbl2fn1" ref-type="table-fn">1</xref></td><td>E.G.S. 39.128 = CBS 102605</td><td><italic>Alternaria</italic></td><td>–</td><td align="char">33.9</td><td>–</td><td align="char">2.7</td><td>96.7</td><td>–</td></tr><tr><td><italic>A. citriarbusti</italic> (now <italic>A. alternata</italic>)</td><td>CBS 102598</td><td><italic>Alternaria</italic></td><td>Ion Torrent</td><td align="char">34.8</td><td>38×</td><td align="char">1.7</td><td>98.1</td><td>1.4</td></tr><tr><td><italic>A. gaisen</italic></td><td>CBS 118488</td><td><italic>Alternaria</italic></td><td>Illumina</td><td align="char">35.2</td><td>182×</td><td align="char">1.8</td><td>96.7</td><td>2.8</td></tr><tr><td><italic>A. tenuissima</italic> (now <italic>A. alternata</italic>)</td><td>CBS 918.96</td><td><italic>Alternaria</italic></td><td>Illumina</td><td align="char">33.5</td><td>260×</td><td align="char">1.4</td><td>98.2</td><td>1.5</td></tr><tr><td><italic>A. alternantherae</italic></td><td>CBS 124392</td><td><italic>Alternantherae</italic></td><td>Illumina</td><td align="char">35.0</td><td>210×</td><td align="char">16.5</td><td>89.3</td><td>8.0</td></tr><tr><td><italic>A. solani</italic></td><td>CBS 109157</td><td><italic>Porri</italic></td><td>Ion Torrent</td><td align="char">32.6</td><td>50×</td><td align="char">1.5</td><td>87.9</td><td>9.0</td></tr><tr><td><italic>A. avenicola</italic></td><td>CBS 121459</td><td><italic>Panax</italic></td><td>Illumina</td><td align="char">39.1</td><td>200×</td><td align="char">11.9</td><td>87.2</td><td>9.5</td></tr><tr><td><italic>A. infectoria</italic></td><td>CBS 210.86</td><td><italic>Infectoriae</italic></td><td>Illumina</td><td align="char">36.5</td><td>200×</td><td align="char">5.3</td><td>85.1</td><td>10.3</td></tr><tr><td><italic>A. papaveraceae</italic></td><td>CBS 116607</td><td><italic>Crivellia</italic></td><td>Illumina</td><td align="char">33.8</td><td>220×</td><td align="char">5.3</td><td>85.8</td><td>10.3</td></tr><tr><td><italic>A. brassicicola</italic><xref rid="tbl2fn1" ref-type="table-fn">1</xref></td><td>ATCC 96836 = CBS 118699</td><td><italic>Brassicicola</italic></td><td>–</td><td align="char">32.0</td><td>–</td><td align="char">7.1</td><td>86.6</td><td>–</td></tr></tbody></table><table-wrap-foot><fn id="tbl2fn1"><label>1</label><p id="ntpara0030">Publicly available genomes; <italic>A. arborescens</italic> downloaded from NCBI, <italic>A. brassisicola</italic> downloaded from JGI (<ext-link ext-link-type="uri" xlink:href="http://genome.jgi-psf.org/Altbr1/Altbr1.home.html" id="intref0235">http://genome.jgi-psf.org/Altbr1/Altbr1.home.html</ext-link>).</p></fn></table-wrap-foot><table-wrap-foot><fn id="tbl2fn2"><label>2</label><p id="ntpara0035">SNPs / covered base (>10×), duplicates removed.</p></fn></table-wrap-foot><table-wrap-foot><fn id="tbl2fn3"><label>3</label><p id="ntpara0040">Reference isolate.</p></fn></table-wrap-foot></table-wrap><table-wrap id="tbl3" position="float"><label>Table 3</label><caption><p>Assembly statistics of the <italic>Alternaria</italic> transcriptome profiles.</p></caption><table frame="hsides" rules="groups"><thead><tr><th>Species</th><th>Strain number</th><th>Section</th><th>% SNP<xref rid="tbl3fn2" ref-type="table-fn">2</xref></th></tr></thead><tbody><tr><td><italic>A. alternata</italic></td><td>CBS 916.96<xref rid="tbl3fn1" ref-type="table-fn">1</xref></td><td><italic>Alternaria</italic></td><td align="char">0.0</td></tr><tr><td><italic>A. arborescens</italic></td><td>CBS 102605</td><td><italic>Alternaria</italic></td><td align="char">1.8</td></tr><tr><td><italic>A. citriarbusti</italic> (now <italic>A. alternata</italic>)</td><td>CBS 102598</td><td><italic>Alternaria</italic></td><td align="char">1.0</td></tr><tr><td><italic>A. citricancri</italic> (now <italic>A. alternata</italic>)</td><td>CBS 119543</td><td><italic>Alternaria</italic></td><td align="char">0.9</td></tr><tr><td><italic>A. gaisen</italic></td><td>CBS 118488</td><td><italic>Alternaria</italic></td><td align="char">1.8</td></tr><tr><td><italic>A. mali</italic> (now <italic>A. alternata</italic>)</td><td>CBS 106.24</td><td><italic>Alternaria</italic></td><td align="char">0.9</td></tr><tr><td><italic>A. tenuissima</italic> (now <italic>A. alternata</italic>)</td><td>CBS 918.96</td><td><italic>Alternaria</italic></td><td align="char">0.8</td></tr><tr><td><italic>A. tomaticola</italic> (now <italic>A. alternata</italic>)</td><td>CBS 118814</td><td><italic>Alternaria</italic></td><td align="char">0.9</td></tr><tr><td><italic>A. toxicogenica</italic> (now <italic>A. alternata</italic>)</td><td>CBS 102600</td><td><italic>Alternaria</italic></td><td align="char">0.9</td></tr><tr><td><italic>A. alternantherae</italic></td><td>CBS 124392</td><td><italic>Alternantherae</italic></td><td align="char">6.1</td></tr><tr><td><italic>A. infectoria</italic></td><td>CBS 210.86</td><td><italic>Infectoriae</italic></td><td align="char">8.5</td></tr><tr><td><italic>A. papaveraceae</italic></td><td>CBS 116607</td><td><italic>Crivellia</italic></td><td align="char">8.4</td></tr></tbody></table><table-wrap-foot><fn id="tbl3fn1"><label>1</label><p id="ntpara0045">Reference isolate.</p></fn></table-wrap-foot><table-wrap-foot><fn id="tbl3fn2"><label>2</label><p id="ntpara0050">SNPs / covered base (>10×), duplicates removed.</p></fn></table-wrap-foot></table-wrap><table-wrap id="tbl4" position="float"><label>Table 4</label><caption><p>Comparison of gene ability to distinguish species in sect. <italic>Alternaria</italic>.</p></caption><table frame="hsides" rules="groups"><tbody><tr><td><inline-graphic xlink:href="fx1.gif"></inline-graphic></td></tr></tbody></table></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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