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 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.
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dig-cirad-fr-6017212024-04-25T14:26:20Z http://agritrop.cirad.fr/601721/ http://agritrop.cirad.fr/601721/ GreenPhylDB v5: A comparative pangenomic database for plant genomes. Guignon Valentin, Toure Abdel, Droc Gaëtan, Dufayard Jean François, Conte Matthieu, Rouard Mathieu. 2021. Nucleic Acids Research, 49 (D1) : D1464-D1471.https://doi.org/10.1093/nar/gkaa1068 <https://doi.org/10.1093/nar/gkaa1068> GreenPhylDB v5: A comparative pangenomic database for plant genomes Guignon, Valentin Toure, Abdel Droc, Gaëtan Dufayard, Jean François Conte, Matthieu Rouard, Mathieu eng 2021 Nucleic Acids Research F70 - Taxonomie végétale et phytogéographie génome Oryza sativa banque de données Arabidopsis thaliana séquence nucléotidique génie génétique génomique Musa acuminata phylogénie logiciel ressource génétique végétale gène système basé sur la connaissance système d'information http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_33292 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_4994 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_24008 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_34276 http://aims.fao.org/aos/agrovoc/c_11769 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/601721/1/greenphyl.pdf text cc_by info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ https://doi.org/10.1093/nar/gkaa1068 10.1093/nar/gkaa1068 info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkaa1068 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1093/nar/gkaa1068 info:eu-repo/semantics/dataset/purl/https://www.greenphyl.org/cgi-bin/downloads.cgi |
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F70 - Taxonomie végétale et phytogéographie génome Oryza sativa banque de données Arabidopsis thaliana séquence nucléotidique génie génétique génomique Musa acuminata phylogénie logiciel ressource génétique végétale gène système basé sur la connaissance système d'information http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_33292 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_4994 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_24008 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_34276 http://aims.fao.org/aos/agrovoc/c_11769 F70 - Taxonomie végétale et phytogéographie génome Oryza sativa banque de données Arabidopsis thaliana séquence nucléotidique génie génétique génomique Musa acuminata phylogénie logiciel ressource génétique végétale gène système basé sur la connaissance système d'information http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_33292 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_4994 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_24008 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_34276 http://aims.fao.org/aos/agrovoc/c_11769 |
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F70 - Taxonomie végétale et phytogéographie génome Oryza sativa banque de données Arabidopsis thaliana séquence nucléotidique génie génétique génomique Musa acuminata phylogénie logiciel ressource génétique végétale gène système basé sur la connaissance système d'information http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_33292 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_4994 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_24008 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_34276 http://aims.fao.org/aos/agrovoc/c_11769 F70 - Taxonomie végétale et phytogéographie génome Oryza sativa banque de données Arabidopsis thaliana séquence nucléotidique génie génétique génomique Musa acuminata phylogénie logiciel ressource génétique végétale gène système basé sur la connaissance système d'information http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_33292 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_4994 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_24008 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_34276 http://aims.fao.org/aos/agrovoc/c_11769 Guignon, Valentin Toure, Abdel Droc, Gaëtan Dufayard, Jean François Conte, Matthieu Rouard, Mathieu GreenPhylDB v5: A comparative pangenomic database for plant genomes |
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 |
article |
topic_facet |
F70 - Taxonomie végétale et phytogéographie génome Oryza sativa banque de données Arabidopsis thaliana séquence nucléotidique génie génétique génomique Musa acuminata phylogénie logiciel ressource génétique végétale gène système basé sur la connaissance système d'information http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_33292 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_4994 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_24008 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_34276 http://aims.fao.org/aos/agrovoc/c_11769 |
author |
Guignon, Valentin Toure, Abdel Droc, Gaëtan Dufayard, Jean François Conte, Matthieu Rouard, Mathieu |
author_facet |
Guignon, Valentin Toure, Abdel Droc, Gaëtan Dufayard, Jean François Conte, Matthieu Rouard, Mathieu |
author_sort |
Guignon, Valentin |
title |
GreenPhylDB v5: A comparative pangenomic database for plant genomes |
title_short |
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_sort |
greenphyldb v5: a comparative pangenomic database for plant genomes |
url |
http://agritrop.cirad.fr/601721/ http://agritrop.cirad.fr/601721/1/greenphyl.pdf |
work_keys_str_mv |
AT guignonvalentin greenphyldbv5acomparativepangenomicdatabaseforplantgenomes AT toureabdel greenphyldbv5acomparativepangenomicdatabaseforplantgenomes AT drocgaetan greenphyldbv5acomparativepangenomicdatabaseforplantgenomes AT dufayardjeanfrancois greenphyldbv5acomparativepangenomicdatabaseforplantgenomes AT contematthieu greenphyldbv5acomparativepangenomicdatabaseforplantgenomes AT rouardmathieu greenphyldbv5acomparativepangenomicdatabaseforplantgenomes |
_version_ |
1798165084407595008 |