Scripting Analyses of Genomes in Ensembl Plants [chapter]

Bruno Contreras-Moreira, Guy Naamati, Marc Rosello, James E. Allen, Sarah E. Hunt, Matthieu Muffato, Astrid Gall, Paul Flicek
2022 Msphere  
AbstractEnsembl Plants (http://plants.ensembl.org) offers genome-scale information for plants, with four releases per year. As of release 47 (April 2020) it features 79 species and includes genome sequence, gene models, and functional annotation. Comparative analyses help reconstruct the evolutionary history of gene families, genomes, and components of polyploid genomes. Some species have gene expression baseline reports or variation across genotypes. While the data can be accessed through the
more » ... nsembl genome browser, here we review specifically how our plant genomes can be interrogated programmatically and the data downloaded in bulk. These access routes are generally consistent across Ensembl for other non-plant species, including plant pathogens, pests, and pollinators.
doi:10.1007/978-1-0716-2067-0_2 pmid:35037199 pmcid:PMC7614177 fatcat:lx6odri4lvfrzkutlccjpuzgg4