Please cite our paper: Jun Li,Xinbin Dai,Tingsong Liu and Patrick Xuechun Zhao. LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes. Nucleic Acids Research 2012 Jan ;40(Database issue):D1221-D1229.
Welcome to LegumeIP
An Integrative Platform to Study Gene Function and Genome Evolution in Legumes (Version 2.0)    
 
Location:   Home
 

Legumes play vital roles in maintaining nitrogen cycle of biosphere and in agriculture for nitrogen fixation by their unique ability to carry out symbiotic nitrogen fixation (SNF) through endosymbiotic interactions with bacteria in root nodules. This vital feature can't be studied by using the model plant Arabidopsis thaliana. In addition to the root nodulation and SNF with rhizobia, legumes possess several 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. Therefore, legumes are not only important crops but also important plant models for studying physiology, genomics, plant-microbe interaction, sustainable agriculture, food production, security and renewable bioenergy generation.

LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes,to understand mechanisms that are fundamental to the legume species, especially the process of nitrogen-fixing endosymbiosis, which will be of great value to healthy, low input sustainable agriculture by decreasing the use of fertilizers, and ultimately to develope molecular based breeding tools to improve yield and quality of crop legumes.

The LegumeIP 2.0 currently hosts large-scale genomics and transcriptomics data, including:

  • Genomic sequences of six legume species, i.e. Medicago truncatula, Glycine max (soybean), Lotus japonicus, Phaseolus vulgaris (common bean), Cicer arietinum (chickpea) and Cajanus cajan (pigeonpea), and two outgroup reference species, A. thaliana and Poplar trichocarpa. The LegumeIP 2.0 covers 391,107 protein-coding gene sequences in total. All sequences were annotated based on sequence similarities and domain features by referring to the UniProt TrEMBL, InterProScan, Gene Ontology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases.
  • Brand new built-in gene expression atlases for four model legumes 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. These data sets were manually curated and hierarchically organized based on Experimental Ontology (EO) and Plant Ontology (PO) so that users can browse, search, and retrieve data for select experiments.
  • Systematic synteny analysis among six hosted legume species and two outgroup species.
  • Reconstruction of gene family and gene family-wide phylogenetic analysis across the six hosted species.

The LegumeIP 2.0 provide comprehensive search and visualization tools to search, retrieve and visualize large-scale gene sequences, annotations, gene families, macro- and micro- synteny blocks, and transcriptome profiles. The original release of LegumeIP, referred to as the LegumeIP 1.0, can be accessed here.

 
Funding by the National Science Foundation to Dr. Patrick X. Zhao Data & bioinformatics resources were generated by Dr. Patrick X. Zhao Lab at the Samuel Roberts Noble Foundation and many national and international collaborators


  © 2015 by The Samuel Roberts Noble Foundation, Inc. Site by Zhao Lab