The legume information system and associated online genomic resources

Abstract

The Legume Information System (LIS; https://legumeinfo.org) houses genetic and genomic data, integrated in various online tools to allow comparative genomic analyses. The website and database maintain data for more than two dozen species, particularly focusing on crop and model species and holding data for other diverse species of taxonomic interest. Major analysis features include genome browsers, sequence‐search tools, legume‐focused gene families and a phylogenetic tree viewer, a gene annotation service (which places a submitted gene into a gene family and phylogenetic tree), an interactive microsynteny and pan‐genome viewer, a novel viewer of genetic variant data, genetic maps and viewers, a Data Store for data sets such as assemblies and annotations, InterMine instances for querying genetic and genomic data, and a tool for viewing geographic distributions of germplasm accessions. LIS also integrates with several other legume data resources and tools, including PeanutBase (https://peanutbase.org), SoyBase (https://soybase.org), Medicago Hapmap (https://medicagohapmap2.org), Alfalfa Breeder's Toolbox (https://alfalfatoolbox.org), and the Legume Federation (https://legumefederation.org).

Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.)

“…All genes within a 1000 kbp window around GWAS SNPs and SNP pair interactions were extracted. Enrichment analysis and the assignment of genes to functional categories was implemented in PeanutMine and BLUEGENES from InterMine (Smith et al 2012), on PeanutBase (Berendzen et al 2021;Dash et al 2016).…”

“…Upon filtering for redundancies, we retained a total 177 unique genes for enrichment analysis. Enrichment was performed using LegumeMine, PeanutMine, and BLUEGENES hosted on the Legume Information System database (Berendzen et al 2021;Dash et al 2016;Smith et al 2012).…”

Legumes: Embracing the genome era

“…The foundational genetic, genomic and phenomic resources available for more than a dozen legume crops are housed in the Legume Information System (LIS; https://legumeinfo.org), and are integrated into various comparative genomic tools found therein. Berendzen et al (2021) provide an overview of the LIS platform and discuss major data analysis features supported by the platform, including genome browsers, sequence‐search tools, phylogenetic tree viewer, an interactive microsynteny and pan‐genome viewer, and a novel genetic variant data viewer.…”

Genotypes to Phenotypes: Genomic attributes that impact Genome-wide Associations in peanut (Arachis hypogaea. L).

“…All genes within a 1000 kbp window around GWAS SNPs and SNP pair interactions were extracted. Enrichment analysis and the assignment of genes to functional categories was implemented in PeanutMine and BLUEGENES from InterMine (Smith et al 2012), on peanutbase.org (Sudhansu, et al 2016;Berendzen et al 2021). Significantly enriched gene ontology (GO) terms, gene families, and pathways in the gene list compared with background genes were defined with a hypergeometric test at p < 0.05.…”

“…Upon filtering for redundancies, we retained a total 177 unique genes for enrichment analysis. Enrichment was performed using LegumeMine, PeanutMine, and BLUEGENES hosted on the Legume Information System database (Sudhansu, et al 2016;Smith, et al 2012;Berendzen, et al 2021).…”