The LegumeIP (2016 Release) - a Web-Based Comparative Genomics and Gene Expression Atlas Platform for the Study of Gene Function and Genome Evolution in Legumes

Legumes are one of the most evolutionarily well-adapted plant families that play vital roles in ecology and agriculture. They have the unique ability to carry out symbiotic nitrogen fixation (SNF) through endosymbiotic interactions with bacteria. Aside from the root nodulation and nitrogen fixation symbiosis with rhizobia, legumes possess many unique features that are not found in the model plant Arabidopsis thaliana, such as mycorrhization, compound leaf development, protein-rich physiology, a profuse secondary metabolism, glandular trichome development and border cells in roots.

We present LegumeIP (http://plantgrn.noble.org/LegumeIP/) - a web-based comparative genomics and gene expression atlas platform that integrates large-scale genomics, transcriptomics data and bioinformatics tools to study gene function and genome evolution in legumes. The LegumeIP database  (2016 release) hosts 1) large-scale genomic data such as genomics sequences, gene models and annotations that are cross-refereed to the UniProt TrEMBL, InterProScan, Gene Ontology (GO) and the Kyoto Encyclopedia of Genes (KEGG) reference database for six model and crop legumes: Medicago truncatula, Glycine max (soybean), Lotus japonicus, Phaseolus vulgaris (common bean), Cicer arietinum (chickpea) and Cajanus cajan (pigeon pea), and two reference model plants: A. thaliana and Poplar trichocarpa; 2) gene expression atlases that that include 550 array hybridizations from M. truncatula, 962 gene expression profiles of G. max, 276 array hybridizations from L. japonicas and 56 RNA-Seq-based gene expression profiles for C. arietinum; and 3) gene families, orthologous groups, gene family phylogenetic trees and syntenic regions across hosted species. LegumeIP (2016 release) also integrates a suite of bioinformatics tools for exploring and analyzing 1) whole-genome synteny and detailed syntenic gene alignments; 2) gene annotations, gene families and orthologous groups; and 3) gene expression patterns, clusters and co-expression networks.