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LegumeIP: An Integrative Platform to Study Gene Function and Genome Evolution in Legumes

Legumes play vital roles in maintaining nitrogen circle of biosphere and in agriculture for their unique ability to carry out symbiotic nitrogen fixation (SNF) through endosymbiotic interactions with bacteria in root nodules. This vital feature cannot be studied using the model plant, Arabidopsis thaliana. Aside from the root nodulation and nitrogen fixation symbiosis with rhizobia, legumes possess many unique features that are not found in A. 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, an integrative database platform for comparative genomics and transcriptomics of model legumes to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular-based breeding tools to improve crop legumes.

LegumeIP currently hosts large-scale genomics and transcriptomics data, including:

  • genomic sequences of three model legumes, i.e. Medicago truncatula, Glycine max (soybean) and Lotus japonicus, and two reference plant species, Arabidopsis thaliana and Poplar trichocarpa, with the annotation based on UniProt TrEMBL, InterProScan, Gene Ontology and KEGG databases, covering 222,217 protein-coding gene sequences;
  • large-scale gene expression data compiled from 104 array hybridizations from L. japonicas, 156 array hybridizations from M. truncatula gene atlas database, and 14 RNA-Seq-based gene expression profiles from G. max on different tissues including four common tissues: Nodule, Flower, Root and Leaf;
  • systematic synteny analysis among M. truncatula, G. max, L. japonicus and A. thaliana;
  • reconstruction of gene family and gene family-wide phylogenetic analysis across the five hosted species. LegumeIP features comprehensive search and visualization tools to enable the flexible query on gene annotation, gene family, synteny, relative abundance of gene expression.

» Visit the LegumeIP Server


Copyright © 2007 by The Samuel Roberts Noble Foundation, Inc.