A database for ITS2 sequences from nematodes

BACKGROUND: Marker gene surveys have a wide variety of applications in species identification, population genetics, and molecular epidemiology. As these methods expand to new types of organisms and additional markers beyond 16S and 18S rRNA genes, comprehensive databases are a critical requirement f...

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Autores principales: Workentine, Matthew L., Chen, Rebecca, Zhu, Shawna, Gavriliuc, Stefan, Shaw, Nicolette, Rijke, Jill de, Redman, Elizabeth M., Avramenko, Russell W., Wit, Janneke, Poissant, Jocelyn, Gilleard, John S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Database
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7350610/
https://www.ncbi.nlm.nih.gov/pubmed/32650716
http://dx.doi.org/10.1186/s12863-020-00880-0
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author Workentine, Matthew L.
Chen, Rebecca
Zhu, Shawna
Gavriliuc, Stefan
Shaw, Nicolette
Rijke, Jill de
Redman, Elizabeth M.
Avramenko, Russell W.
Wit, Janneke
Poissant, Jocelyn
Gilleard, John S.
author_facet Workentine, Matthew L.
Chen, Rebecca
Zhu, Shawna
Gavriliuc, Stefan
Shaw, Nicolette
Rijke, Jill de
Redman, Elizabeth M.
Avramenko, Russell W.
Wit, Janneke
Poissant, Jocelyn
Gilleard, John S.
author_sort Workentine, Matthew L.
collection PubMed
description BACKGROUND: Marker gene surveys have a wide variety of applications in species identification, population genetics, and molecular epidemiology. As these methods expand to new types of organisms and additional markers beyond 16S and 18S rRNA genes, comprehensive databases are a critical requirement for proper analysis of these data. RESULTS: Here we present an ITS2 rDNA database for marker gene surveys of both free-living and parasitic nematode populations and the software used to build the database. This is currently the most complete and up-to-date ITS2 database for nematodes and is able to reproduce previous analysis that used a smaller database. CONCLUSIONS: This database is an important resource for researchers working on nematodes and also provides a tool to create ITS2 databases for any given taxonomy.
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spelling pubmed-73506102020-07-14 A database for ITS2 sequences from nematodes Workentine, Matthew L. Chen, Rebecca Zhu, Shawna Gavriliuc, Stefan Shaw, Nicolette Rijke, Jill de Redman, Elizabeth M. Avramenko, Russell W. Wit, Janneke Poissant, Jocelyn Gilleard, John S. BMC Genet Database BACKGROUND: Marker gene surveys have a wide variety of applications in species identification, population genetics, and molecular epidemiology. As these methods expand to new types of organisms and additional markers beyond 16S and 18S rRNA genes, comprehensive databases are a critical requirement for proper analysis of these data. RESULTS: Here we present an ITS2 rDNA database for marker gene surveys of both free-living and parasitic nematode populations and the software used to build the database. This is currently the most complete and up-to-date ITS2 database for nematodes and is able to reproduce previous analysis that used a smaller database. CONCLUSIONS: This database is an important resource for researchers working on nematodes and also provides a tool to create ITS2 databases for any given taxonomy. BioMed Central 2020-07-10 /pmc/articles/PMC7350610/ /pubmed/32650716 http://dx.doi.org/10.1186/s12863-020-00880-0 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Database
Workentine, Matthew L.
Chen, Rebecca
Zhu, Shawna
Gavriliuc, Stefan
Shaw, Nicolette
Rijke, Jill de
Redman, Elizabeth M.
Avramenko, Russell W.
Wit, Janneke
Poissant, Jocelyn
Gilleard, John S.
A database for ITS2 sequences from nematodes
title A database for ITS2 sequences from nematodes
title_full A database for ITS2 sequences from nematodes
title_fullStr A database for ITS2 sequences from nematodes
title_full_unstemmed A database for ITS2 sequences from nematodes
title_short A database for ITS2 sequences from nematodes
title_sort database for its2 sequences from nematodes
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7350610/
https://www.ncbi.nlm.nih.gov/pubmed/32650716
http://dx.doi.org/10.1186/s12863-020-00880-0
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