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PTGBase: an integrated database to study tandem duplicated genes in plants
Tandem duplication is a wide-spread phenomenon in plant genomes and plays significant roles in evolution and adaptation to changing environments. Tandem duplicated genes related to certain functions will lead to the expansion of gene families and bring increase of gene dosage in the form of gene clu...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4369376/ https://www.ncbi.nlm.nih.gov/pubmed/25797062 http://dx.doi.org/10.1093/database/bav017 |
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author | Yu, Jingyin Ke, Tao Tehrim, Sadia Sun, Fengming Liao, Boshou Hua, Wei |
author_facet | Yu, Jingyin Ke, Tao Tehrim, Sadia Sun, Fengming Liao, Boshou Hua, Wei |
author_sort | Yu, Jingyin |
collection | PubMed |
description | Tandem duplication is a wide-spread phenomenon in plant genomes and plays significant roles in evolution and adaptation to changing environments. Tandem duplicated genes related to certain functions will lead to the expansion of gene families and bring increase of gene dosage in the form of gene cluster arrays. Many tandem duplication events have been studied in plant genomes; yet, there is a surprising shortage of efforts to systematically present the integration of large amounts of information about publicly deposited tandem duplicated gene data across the plant kingdom. To address this shortcoming, we developed the first plant tandem duplicated genes database, PTGBase. It delivers the most comprehensive resource available to date, spanning 39 plant genomes, including model species and newly sequenced species alike. Across these genomes, 54 130 tandem duplicated gene clusters (129 652 genes) are presented in the database. Each tandem array, as well as its member genes, is characterized in complete detail. Tandem duplicated genes in PTGBase can be explored through browsing or searching by identifiers or keywords of functional annotation and sequence similarity. Users can download tandem duplicated gene arrays easily to any scale, up to the complete annotation data set for an entire plant genome. PTGBase will be updated regularly with newly sequenced plant species as they become available. Database URL: http://ocri-genomics.org/PTGBase/. |
format | Online Article Text |
id | pubmed-4369376 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-43693762015-04-17 PTGBase: an integrated database to study tandem duplicated genes in plants Yu, Jingyin Ke, Tao Tehrim, Sadia Sun, Fengming Liao, Boshou Hua, Wei Database (Oxford) Original Article Tandem duplication is a wide-spread phenomenon in plant genomes and plays significant roles in evolution and adaptation to changing environments. Tandem duplicated genes related to certain functions will lead to the expansion of gene families and bring increase of gene dosage in the form of gene cluster arrays. Many tandem duplication events have been studied in plant genomes; yet, there is a surprising shortage of efforts to systematically present the integration of large amounts of information about publicly deposited tandem duplicated gene data across the plant kingdom. To address this shortcoming, we developed the first plant tandem duplicated genes database, PTGBase. It delivers the most comprehensive resource available to date, spanning 39 plant genomes, including model species and newly sequenced species alike. Across these genomes, 54 130 tandem duplicated gene clusters (129 652 genes) are presented in the database. Each tandem array, as well as its member genes, is characterized in complete detail. Tandem duplicated genes in PTGBase can be explored through browsing or searching by identifiers or keywords of functional annotation and sequence similarity. Users can download tandem duplicated gene arrays easily to any scale, up to the complete annotation data set for an entire plant genome. PTGBase will be updated regularly with newly sequenced plant species as they become available. Database URL: http://ocri-genomics.org/PTGBase/. Oxford University Press 2015-03-22 /pmc/articles/PMC4369376/ /pubmed/25797062 http://dx.doi.org/10.1093/database/bav017 Text en © The Author(s) 2015. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Article Yu, Jingyin Ke, Tao Tehrim, Sadia Sun, Fengming Liao, Boshou Hua, Wei PTGBase: an integrated database to study tandem duplicated genes in plants |
title | PTGBase: an integrated database to study tandem duplicated genes in plants |
title_full | PTGBase: an integrated database to study tandem duplicated genes in plants |
title_fullStr | PTGBase: an integrated database to study tandem duplicated genes in plants |
title_full_unstemmed | PTGBase: an integrated database to study tandem duplicated genes in plants |
title_short | PTGBase: an integrated database to study tandem duplicated genes in plants |
title_sort | ptgbase: an integrated database to study tandem duplicated genes in plants |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4369376/ https://www.ncbi.nlm.nih.gov/pubmed/25797062 http://dx.doi.org/10.1093/database/bav017 |
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