LegumeIP: An Integrative Platform for Comparative Genomics and Transcriptomics of Model Legumes

In this chapter, we introduce the latest development of LegumeIP: a platform of comparative genomics and transcriptomics, and then describe some practical usages of the LegumeIP for studying gene functions, molecular mechanisms underpinning the plant-rhizobia interactions, and genome evolution with respect to nitrogen fixing in several agriculturally important model legume species. LegumeIP currently hosts large-scale genomics and transcriptomics data that include (i) genomic sequences of three model legumes, Medicago truncatula, Glycine max (soybean), Lotus japonicus, and two reference plant species, Arabidopsis thaliana and Poplar trichocarpa, with the annotation based on UniProt, InterProScan, Gene Ontology, and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases, comprising a total of 222,217 protein-coding gene sequences; (ii) large-scale compendium gene expression data sets compiled from various tissues of multiple species. These include 104 microarray data sets from L. japonicus, 156 microarray data sets from M. truncatula gene atlas database, and 14 RNA-seq data sets from G. max. These data are further compiled centering on four tissues: nodules, flowers, roots, and leaves being shared by all species; (iii) systematic synteny analysis among M. truncatula, G. max, L. japonicus, and A. thaliana; (iv) reconstruction of gene family and gene family-wide phylogenetic analysis across the five hosted species; and (v) genome-wide reconstruction of gene coexpression networks. The usefulness of this platform in facilitating molecular research of legume species is demonstrated by two case studies, in which SymRK (symbiosis receptor-like kinase) genes for symbiosis analysis and nitrogen-fixation-related genes in M. truncatula were identified through integrative analysis of gene expression and constructed coexpression networks provided by the LegumeIP platform. The LegumeIP is freely available at http://plantgrn.noble.org/LegumeIP/