C18 LegumeIP: An Integrative Platform for Comparative Genomics and Transcriptomics of Model Legumes

Date: Monday, January 16, 2012
Time: 1:35 PM
Room: California
Jun Li , The Samuel Roberts Noble Foundation, Ardmore, OK
Xinbin Dai , The Samuel Roberts Noble Foundation, Ardmore, OK
Tingsong Liu , The Samuel Roberts Noble Foundation, Ardmore, OK
Patrick Xuechun Zhao , The Samuel Roberts Noble Foundation, Ardmore, OK
We present LegumeIP, an integrative database for comparative genomics and transcriptomics of model legumes, for studying gene function and genome evolution in legumes.

LegumeIP (The 2011 release) integrates large-scale genomics and transcriptomics data of three model legumes, Medicago truncatula, Glycine max, and Lotus japonicus, and two reference plant species, Arabidopsis thaliana and Populus trichocarpa, encompassing 1) 222,217 protein-coding gene sequences with annotations based on Uniprot, InterProScan, Gene Ontology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG), and 2) tissue-specific transcriptomic profiles compiled from 104 microarray hybridizations from L. japonicas, 156 microarray hybridizations from the M. truncatula, and 14 RNA-Seq runs from G. max, with the gene expression profiles on time-course experiments and different tissues including four common tissues namely the nodule, flower, root, and leaf. LegumeIP also integrates a series of bioinformatics tools for systematic synteny analysis across M. truncatula, G. max, L. japonicas, and A. thaliana, as well as construction and phylogenetic analysis of gene families across the five hosted species.

LegumeIP is freely and publically available at http://plantgrn.noble.org/LegumeIP/, on which provides comprehensive search and visualization tools that enable flexible queries based on gene annotation, gene family, synteny, and relative gene expression.