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Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank

Genus Xylodon consists of white-rot fungi that grow on both angiosperms and gymnosperms. With resupinate and adnate basidiomes, Xylodon species have been classified into other resupinate genera for a long time. Upon the integration of molecular assessments, the taxonomy of the genus has been revised...

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Autores principales: Cho, Yoonhee, Kim, Ji Seon, Dai, Yu-Cheng, Gafforov, Yusufjon, Lim, Young Woon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8667721/
https://www.ncbi.nlm.nih.gov/pubmed/34966599
http://dx.doi.org/10.7717/peerj.12625
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author Cho, Yoonhee
Kim, Ji Seon
Dai, Yu-Cheng
Gafforov, Yusufjon
Lim, Young Woon
author_facet Cho, Yoonhee
Kim, Ji Seon
Dai, Yu-Cheng
Gafforov, Yusufjon
Lim, Young Woon
author_sort Cho, Yoonhee
collection PubMed
description Genus Xylodon consists of white-rot fungi that grow on both angiosperms and gymnosperms. With resupinate and adnate basidiomes, Xylodon species have been classified into other resupinate genera for a long time. Upon the integration of molecular assessments, the taxonomy of the genus has been revised multiple times over the years. However, the emendations were poorly reflected in studies and public sequence databases. In the present study, the genus Xylodon in Korea was evaluated using molecular and morphological analyses of 172 specimens collected in the period of 2011 to 2018. The host types and geographical distributions were also determined for species delimitation. Furthermore, public sequences that correspond to the Xylodon species in Korea were assessed to validate their identities. Nine Xylodon species were identified in Korea, with three species new to the country. Morphological differentiation and identification of some species were challenging, but all nine species were clearly divided into well-resolved clades in the phylogenetic analyses. Detailed species descriptions, phylogeny, and a key to Xylodon species in Korea are provided in the present study. A total of 646 public ITS and nrLSU sequences corresponding to the nine Xylodon species were found, each with 404 (73.1%) and 57 (61.3%) misidentified or labeled with synonymous names. In many cases, sequences released before the report of new names have not been revised or updated. Revisions of these sequences are arranged in the present study. These amendments may be used to avoid the misidentification of future sequence-based identifications and concurrently prevent the accumulation of misidentified sequences in GenBank.
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spelling pubmed-86677212021-12-28 Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank Cho, Yoonhee Kim, Ji Seon Dai, Yu-Cheng Gafforov, Yusufjon Lim, Young Woon PeerJ Bioinformatics Genus Xylodon consists of white-rot fungi that grow on both angiosperms and gymnosperms. With resupinate and adnate basidiomes, Xylodon species have been classified into other resupinate genera for a long time. Upon the integration of molecular assessments, the taxonomy of the genus has been revised multiple times over the years. However, the emendations were poorly reflected in studies and public sequence databases. In the present study, the genus Xylodon in Korea was evaluated using molecular and morphological analyses of 172 specimens collected in the period of 2011 to 2018. The host types and geographical distributions were also determined for species delimitation. Furthermore, public sequences that correspond to the Xylodon species in Korea were assessed to validate their identities. Nine Xylodon species were identified in Korea, with three species new to the country. Morphological differentiation and identification of some species were challenging, but all nine species were clearly divided into well-resolved clades in the phylogenetic analyses. Detailed species descriptions, phylogeny, and a key to Xylodon species in Korea are provided in the present study. A total of 646 public ITS and nrLSU sequences corresponding to the nine Xylodon species were found, each with 404 (73.1%) and 57 (61.3%) misidentified or labeled with synonymous names. In many cases, sequences released before the report of new names have not been revised or updated. Revisions of these sequences are arranged in the present study. These amendments may be used to avoid the misidentification of future sequence-based identifications and concurrently prevent the accumulation of misidentified sequences in GenBank. PeerJ Inc. 2021-12-10 /pmc/articles/PMC8667721/ /pubmed/34966599 http://dx.doi.org/10.7717/peerj.12625 Text en © 2021 Cho et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Cho, Yoonhee
Kim, Ji Seon
Dai, Yu-Cheng
Gafforov, Yusufjon
Lim, Young Woon
Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank
title Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank
title_full Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank
title_fullStr Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank
title_full_unstemmed Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank
title_short Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank
title_sort taxonomic evaluation of xylodon (hymenochaetales, basidiomycota) in korea and sequence verification of the corresponding species in genbank
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8667721/
https://www.ncbi.nlm.nih.gov/pubmed/34966599
http://dx.doi.org/10.7717/peerj.12625
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