Alternaria section Alternaria: Species, formae speciales or pathotypes?
Identifieur interne : 000315 ( Ncbi/Curation ); précédent : 000314; suivant : 000316Alternaria section Alternaria: Species, formae speciales or pathotypes?
Auteurs : J. H. C. Woudenberg [Pays-Bas] ; M. F. Seidl [Pays-Bas] ; J. Z. Groenewald [Pays-Bas] ; M. De Vries [Pays-Bas] ; J. B. Stielow [Pays-Bas] ; B. P. H. J. Thomma [Pays-Bas] ; P. W. Crous [Pays-Bas, Afrique du Sud]Source :
- Studies in Mycology [ 0166-0616 ] ; 2015.
Abstract
The cosmopolitan fungal genus
Url:
DOI: 10.1016/j.simyco.2015.07.001
PubMed: 26951037
PubMed Central: 4774270
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section <italic>Alternaria</italic>
: Species, <italic>formae speciales</italic>
or pathotypes?</title>
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<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>
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<country xml:lang="fr">Pays-Bas</country>
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<affiliation wicri:level="4"><nlm:aff id="aff2">Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands</nlm:aff>
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<author><name sortKey="Seidl, M F" sort="Seidl, M F" uniqKey="Seidl M" first="M. F." last="Seidl">M. F. Seidl</name>
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<wicri:regionArea>Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen</wicri:regionArea>
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<author><name sortKey="Groenewald, J Z" sort="Groenewald, J Z" uniqKey="Groenewald J" first="J. Z." last="Groenewald">J. Z. Groenewald</name>
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<country xml:lang="fr">Pays-Bas</country>
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<author><name sortKey="De Vries, M" sort="De Vries, M" uniqKey="De Vries M" first="M." last="De Vries">M. De Vries</name>
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<country xml:lang="fr">Pays-Bas</country>
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<author><name sortKey="Stielow, J B" sort="Stielow, J B" uniqKey="Stielow J" first="J. B." last="Stielow">J. B. Stielow</name>
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<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 wicri:level="4"><nlm:aff id="aff2">Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
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<author><name sortKey="Crous, P W" sort="Crous, P W" uniqKey="Crous P" first="P. W." last="Crous">P. W. Crous</name>
<affiliation wicri:level="1"><nlm:aff id="aff1">CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht</wicri:regionArea>
<wicri:noRegion>3584 CT Utrecht</wicri:noRegion>
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<affiliation wicri:level="4"><nlm:aff id="aff2">Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen</wicri:regionArea>
<orgName type="university">Université de Wageningue</orgName>
<placeName><settlement type="city">Wageningue</settlement>
<region nuts="2">Gueldre (province)</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff3">Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa</nlm:aff>
<country xml:lang="fr">Afrique du Sud</country>
<wicri:regionArea>Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002</wicri:regionArea>
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<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>
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<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>
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