GreenPhylDB v5: a comparative pangenomic database for plant genomes
Comparative genomics is the analysis of genomic relationships among different species and serves as a significant base for evolutionary and functional genomic studies. GreenPhylDB (https://www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relatio...
| Main Authors: | , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Oxford University Press
2021
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/110466 |
| _version_ | 1855520987887435776 |
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| author | Guignon, Valentin Touré, Abdel Droc, Gaëtan Dufayard, Jean-François Conte, Matthieu Rouard, Mathieu |
| author_browse | Conte, Matthieu Droc, Gaëtan Dufayard, Jean-François Guignon, Valentin Rouard, Mathieu Touré, Abdel |
| author_facet | Guignon, Valentin Touré, Abdel Droc, Gaëtan Dufayard, Jean-François Conte, Matthieu Rouard, Mathieu |
| author_sort | Guignon, Valentin |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Comparative genomics is the analysis of genomic relationships among different species and serves as a significant base for evolutionary and functional genomic studies. GreenPhylDB (https://www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relationships among plant genomes, including staple crops critically important for global food security. GreenPhylDB is available since 2007, after the release of the Arabidopsis thaliana and Oryza sativa genomes and has undergone multiple releases. With the number of plant genomes currently available, it becomes challenging to select a single reference for comparative genomics studies but there is still a lack of databases taking advantage several genomes by species for orthology detection. GreenPhylDBv5 introduces the concept of comparative pangenomics by harnessing multiple genome sequences by species. We created 19 pangenes and processed them with other species still relying on one genome. In total, 46 plant species were considered to build gene families and predict their homologous relationships through phylogenetic-based analyses. In addition, since the previous publication, we rejuvenated the website and included a new set of original tools including protein-domain combination, tree topologies searches and a section for users to store their own results in order to support community curation efforts. |
| format | Journal Article |
| id | CGSpace110466 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1104662025-12-08T10:11:39Z GreenPhylDB v5: a comparative pangenomic database for plant genomes Guignon, Valentin Touré, Abdel Droc, Gaëtan Dufayard, Jean-François Conte, Matthieu Rouard, Mathieu comparative genomics databases genomes plants data analysis documentation Comparative genomics is the analysis of genomic relationships among different species and serves as a significant base for evolutionary and functional genomic studies. GreenPhylDB (https://www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relationships among plant genomes, including staple crops critically important for global food security. GreenPhylDB is available since 2007, after the release of the Arabidopsis thaliana and Oryza sativa genomes and has undergone multiple releases. With the number of plant genomes currently available, it becomes challenging to select a single reference for comparative genomics studies but there is still a lack of databases taking advantage several genomes by species for orthology detection. GreenPhylDBv5 introduces the concept of comparative pangenomics by harnessing multiple genome sequences by species. We created 19 pangenes and processed them with other species still relying on one genome. In total, 46 plant species were considered to build gene families and predict their homologous relationships through phylogenetic-based analyses. In addition, since the previous publication, we rejuvenated the website and included a new set of original tools including protein-domain combination, tree topologies searches and a section for users to store their own results in order to support community curation efforts. 2021-01-08 2020-12-11T13:26:21Z 2020-12-11T13:26:21Z Journal Article https://hdl.handle.net/10568/110466 en Open Access application/pdf Oxford University Press Guignon, V.; Toure, A.; Droc, G.; Dufayard, J-F.; Conte, M.; Rouard, M. (2020) GreenPhylDB v5: a comparative pangenomic database for plant genomes. Nucleic Acids Research 49(D1) p. D1464–D1471. ISSN: 1362-4962. |
| spellingShingle | comparative genomics databases genomes plants data analysis documentation Guignon, Valentin Touré, Abdel Droc, Gaëtan Dufayard, Jean-François Conte, Matthieu Rouard, Mathieu GreenPhylDB v5: a comparative pangenomic database for plant genomes |
| title | GreenPhylDB v5: a comparative pangenomic database for plant genomes |
| title_full | GreenPhylDB v5: a comparative pangenomic database for plant genomes |
| title_fullStr | GreenPhylDB v5: a comparative pangenomic database for plant genomes |
| title_full_unstemmed | GreenPhylDB v5: a comparative pangenomic database for plant genomes |
| title_short | GreenPhylDB v5: a comparative pangenomic database for plant genomes |
| title_sort | greenphyldb v5 a comparative pangenomic database for plant genomes |
| topic | comparative genomics databases genomes plants data analysis documentation |
| url | https://hdl.handle.net/10568/110466 |
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