Reducing the number of accepted species in Aspergillus series Nigri
Creators: name: Bian, Cai
name: Kusuya, Yoko
name: Sklenář, František
name: D'hooge, Elizabet
name: Yaguchi, Takashi
name: Ban, Sayaka
name: Visagie, Cobus M.
name: Houbraken, Jos
name: Takahashi, Hiroki
name: Hubka, Vit
Publisher: name: Zenodo
Year: 2022
Subjects: Aspergillus luchuensis
Aspergillus niger
Aspergillus tubingensis
clinical fungi
indoor fungi
infraspecific variability
multigene phylogeny
multispecies coalescence model
ochratoxin A
species delimitation

description: The <em>Aspergillus</em> series <em>Nigri</em> contains biotechnologically and medically important species. They can produce hazardous mycotoxins, which is relevant due to the frequent occurrence of these species on foodstuffs and in the indoor environment. The taxonomy of the series has undergone numerous rearrangements, and currently, there are 14 species accepted in the series, most of which are considered cryptic. Species-level identifications are, however, problematic or impossible for many isolates even when using DNA sequencing or MALDI-TOF mass spectrometry, indicating a possible problem in the definition of species limits or the presence of undescribed species diversity. To re-examine the species boundaries, we collected DNA sequences from three phylogenetic markers (<em>benA</em>, <em>CaM</em> and <em>RPB2</em>) for 276 strains from series <em>Nigri</em> and generated 18 new whole-genome sequences. With the three-gene dataset, we employed phylogenetic methods based on the multispecies coalescence model, including four single-locus methods (GMYC, bGMYC, PTP and bPTP) and one multilocus method (STACEY). From a total of 15 methods and their various settings, 11 supported the recognition of only three species corresponding to the three main phylogenetic lineages: <em>A</em>. <em>niger</em>, <em>A</em>. <em>tubingensis</em> and <em>A</em>. <em>brasiliensis</em>. Similarly, recognition of these three species was supported by the GCPSR approach (Genealogical Concordance Phylogenetic Species Recognition) and analysis in DELINEATE software. We also showed that the phylogeny based on <em>benA</em>, <em>CaM</em> and <em>RPB2</em> is suboptimal and displays significant differences from a phylogeny constructed using 5 752 single-copy orthologous proteins; therefore, the results of the delimitation methods may be subject to a higher than usual level of uncertainty. To overcome this, we randomly selected 200 genes from these genomes and performed ten independent STACEY analyses, each with 20 genes. All analyses supported the recognition of only one species in the <em>A</em>. <em>niger</em> and <em>A</em>. <em>brasiliensis</em> lineages, while one to four species were inconsistently delimited in the <em>A</em>. <em>tubingensis</em> lineage. After considering all of these results and their practical implications, we propose that the revised series <em>Nigri</em> includes six species: <em>A</em>. <em>brasiliensis</em>, <em>A</em>. <em>eucalypticola</em>, <em>A</em>. <em>luchuensis</em> (syn. <em>A</em>. <em>piperis</em>), <em>A</em>. <em>niger</em> (syn. <em>A</em>. <em>vinaceus</em> and <em>A</em>. <em>welwitschiae</em>), <em>A</em>. <em>tubingensis</em> (syn. <em>A</em>. <em>chiangmaiensis</em>, <em>A</em>. <em>costaricensis</em>, <em>A</em>. <em>neoniger</em> and <em>A</em>. <em>pseudopiperis</em>) and <em>A</em>. <em>vadensis</em>. We also showed that the intraspecific genetic variability in the redefined <em>A</em>. <em>niger</em> and <em>A</em>. <em>tubingensis</em> does not deviate from that commonly found in other aspergilli. We supplemented the study with a list of accepted species, synonyms and unresolved names, some of which may threaten the stability of the current taxonomy.
description: Funding provided by: Ministerstvo Zdravotnictví Ceské Republiky<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100003243<br>Award Number: NU21-05-00681Funding provided by: Charles University Research Centre Program*<br>Crossref Funder Registry ID: <br>Award Number: 204069Funding provided by: Akademie Věd České Republiky<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100004240<br>Award Number: Long-term Research Development Project RVO: 61388971Funding provided by: Charles University Grant Agency<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100007543<br>Award Number: GAUK 380821Funding provided by: JST SPRING*<br>Crossref Funder Registry ID: <br>Award Number: JPMJSP2109Funding provided by: Plant Health and Protection - Agricultural Research Council (ARC-PHP)*<br>Crossref Funder Registry ID: <br>Award Number: 110441, FBIS170406226088Funding provided by: Japan Society for the Promotion of Science<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001691<br>Award Number: 20F20772