GreenPhylDB v5: a comparative pangenomic database for plant genomes
| Autor: | Guignon Valentin, Rouard Mathieu, Conte Matthieu, Toure Abdel, Droc Gaëtan, Dufayard Jean-François |
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| Přispěvatelé: | Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), French Institute of Bioinformatics (ELIXIR-FR), Syngenta France, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Syngenta Seeds SAS, CGIAR |
| Rok vydání: | 2020 |
| Předmět: |
Crops
Agricultural 0106 biological sciences AcademicSubjects/SCI00010 Arabidopsis Genomics Biology computer.software_genre 01 natural sciences Genome 03 medical and health sciences Gene Expression Regulation Plant Databases Genetic Protein Interaction Mapping Genetics Database Issue Gene family [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology Amino Acid Sequence Gene Phylogeny Plant Proteins 030304 developmental biology Comparative genomics Internet 0303 health sciences Sequence Homology Amino Acid Database Phylogenetic tree Molecular Sequence Annotation Oryza F70 - Taxonomie végétale et phytogéographie Plants 15. Life on land Plant genomes Tree (data structure) Gene Ontology Multigene Family Corrigendum Sequence Alignment computer Genome Plant Software 010606 plant biology & botany |
| Zdroj: | Nucleic Acids Research Nucleic Acids Research, Oxford University Press, 2021, 49 (D1), pp.D1464-D1471. ⟨10.1093/nar/gkaa1068⟩ |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkaa1068 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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