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Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources
The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genom...
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/PMC4653866/ https://www.ncbi.nlm.nih.gov/pubmed/26589635 http://dx.doi.org/10.1093/database/bav093 |
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author | Wang, Xiaobo Wu, Jian Liang, Jianli Cheng, Feng Wang, Xiaowu |
author_facet | Wang, Xiaobo Wu, Jian Liang, Jianli Cheng, Feng Wang, Xiaowu |
author_sort | Wang, Xiaobo |
collection | PubMed |
description | The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/ |
format | Online Article Text |
id | pubmed-4653866 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-46538662015-11-26 Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources Wang, Xiaobo Wu, Jian Liang, Jianli Cheng, Feng Wang, Xiaowu Database (Oxford) Database Update The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/ Oxford University Press 2015-11-20 /pmc/articles/PMC4653866/ /pubmed/26589635 http://dx.doi.org/10.1093/database/bav093 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 | Database Update Wang, Xiaobo Wu, Jian Liang, Jianli Cheng, Feng Wang, Xiaowu Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources |
title | Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources |
title_full | Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources |
title_fullStr | Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources |
title_full_unstemmed | Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources |
title_short | Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources |
title_sort | brassica database (brad) version 2.0: integrating and mining brassicaceae species genomic resources |
topic | Database Update |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653866/ https://www.ncbi.nlm.nih.gov/pubmed/26589635 http://dx.doi.org/10.1093/database/bav093 |
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