PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.

<h4>Background</h4>In environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylo...

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Autores principales:	Stéphane Mahé, Marie Duhamel, Thomas Le Calvez, Laetitia Guillot, Ludmila Sarbu, Anthony Bretaudeau, Olivier Collin, Alexis Dufresne, E Toby Kiers, Philippe Vandenkoornhuyse
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/47f04160ae044460bfce83a8af28ea19
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spelling	oai:doaj.org-article:47f04160ae044460bfce83a8af28ea192021-11-18T07:05:45ZPHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.1932-620310.1371/journal.pone.0043117https://doaj.org/article/47f04160ae044460bfce83a8af28ea192012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23028445/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>In environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept. Such analysis requires that the reference sequences are well identified and deposited in public-access databases. However, many entries in the public sequence databases are problematic in terms of quality and reliability and these data require screening to ensure correct phylogenetic interpretation.<h4>Methods and principal findings</h4>To facilitate phylogenetic inferences and phylogenetic assignment, we introduce a fungal sequence database. The database PHYMYCO-DB comprises fungal sequences from GenBank that have been filtered to satisfy stringent sequence quality criteria. For the first release, two widely used molecular taxonomic markers were chosen: the nuclear SSU rRNA and EF1-α gene sequences. Following the automatic extraction and filtration, a manual curation is performed to remove problematic sequences while preserving relevant sequences useful for phylogenetic studies. As a result of curation, ~20% of the automatically filtered sequences have been removed from the database. To demonstrate how PHYMYCO-DB can be employed, we test a set of environmental Chytridiomycota sequences obtained from deep sea samples.<h4>Conclusion</h4>PHYMYCO-DB offers the tools necessary to: (i) extract high quality fungal sequences for each of the 5 fungal phyla, at all taxonomic levels, (ii) extract already performed alignments, to act as 'reference alignments', (iii) launch alignments of personal sequences along with stored data. A total of 9120 SSU rRNA and 672 EF1-α high-quality fungal sequences are now available. The PHYMYCO-DB is accessible through the URL http://phymycodb.genouest.org/.Stéphane MahéMarie DuhamelThomas Le CalvezLaetitia GuillotLudmila SarbuAnthony BretaudeauOlivier CollinAlexis DufresneE Toby KiersPhilippe VandenkoornhuysePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 9, p e43117 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Stéphane Mahé Marie Duhamel Thomas Le Calvez Laetitia Guillot Ludmila Sarbu Anthony Bretaudeau Olivier Collin Alexis Dufresne E Toby Kiers Philippe Vandenkoornhuyse PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.
description	<h4>Background</h4>In environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept. Such analysis requires that the reference sequences are well identified and deposited in public-access databases. However, many entries in the public sequence databases are problematic in terms of quality and reliability and these data require screening to ensure correct phylogenetic interpretation.<h4>Methods and principal findings</h4>To facilitate phylogenetic inferences and phylogenetic assignment, we introduce a fungal sequence database. The database PHYMYCO-DB comprises fungal sequences from GenBank that have been filtered to satisfy stringent sequence quality criteria. For the first release, two widely used molecular taxonomic markers were chosen: the nuclear SSU rRNA and EF1-α gene sequences. Following the automatic extraction and filtration, a manual curation is performed to remove problematic sequences while preserving relevant sequences useful for phylogenetic studies. As a result of curation, ~20% of the automatically filtered sequences have been removed from the database. To demonstrate how PHYMYCO-DB can be employed, we test a set of environmental Chytridiomycota sequences obtained from deep sea samples.<h4>Conclusion</h4>PHYMYCO-DB offers the tools necessary to: (i) extract high quality fungal sequences for each of the 5 fungal phyla, at all taxonomic levels, (ii) extract already performed alignments, to act as 'reference alignments', (iii) launch alignments of personal sequences along with stored data. A total of 9120 SSU rRNA and 672 EF1-α high-quality fungal sequences are now available. The PHYMYCO-DB is accessible through the URL http://phymycodb.genouest.org/.
format	article
author	Stéphane Mahé Marie Duhamel Thomas Le Calvez Laetitia Guillot Ludmila Sarbu Anthony Bretaudeau Olivier Collin Alexis Dufresne E Toby Kiers Philippe Vandenkoornhuyse
author_facet	Stéphane Mahé Marie Duhamel Thomas Le Calvez Laetitia Guillot Ludmila Sarbu Anthony Bretaudeau Olivier Collin Alexis Dufresne E Toby Kiers Philippe Vandenkoornhuyse
author_sort	Stéphane Mahé
title	PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.
title_short	PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.
title_full	PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.
title_fullStr	PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.
title_full_unstemmed	PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.
title_sort	phymyco-db: a curated database for analyses of fungal diversity and evolution.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/47f04160ae044460bfce83a8af28ea19
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PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.

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