LegumeIP - An Integrative Platform to Study Gene Function and Genome Evolution in Legumes: Year 3 Update

The LegumeIP (year 3 update) hosts large-scale integrative genomics, transcriptomics data and bioinformatics resources to study gene function as well as gene and genome evolution in legumes.

The expanded data resources include genomics sequences, gene models and annotations, protein sequences, Sanger sequencing- and RNA-seq-based EST sequences, and protein families, phylogenetics trees, predicted gene co-expression networks, etc., of six legume species and two outgroup reference species. Our year 3 update highlights the following new features/functions:

• Integration of genomic sequences of six model legumes including Medicago truncatula, Glycine max (soybean), Lotus japonicus, Phaseolus vulgaris (common bean), Cicer arietinumx (chickpea) and Cajanus cajan (pigeon pea), including two reference plant species, Arabidopsis thaliana and Poplar trichocarpa, with the annotation based on UniProt TrEMBL, InterProScan, Gene Ontology (GO) and the Kyoto Encyclopedia of Genes (KEGG) databases. LegumeIP (year 3 update) covers a total 391,107 protein-coding gene sequences.
• Integrating large-scale gene expression data including 238 array hybridizations from L. japonicas, 567 array hybridizations from M. truncatula, 972 gene expression profiles of G. max, and 4,164 microarray gene expression profiles of A. thaliana.

The key new functions in LegumeIP (year 3 update) include

• Integration of hierarchical tree-based GO, KEGG, Transporter Classification Database (TCDB) and Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis Tool (PlantTFcat) gene annotation explorers.
• Integration of gene expression atlas for three legumes species and A. thaliana and analytical functions for transcriptomics-based comparisons across multiple species, tissues, and treatment conditions.
• New sequence search and retrieval tools.

The LegumeIP (year 3 update) is freely and publically available at http://plantgrn.noble.org/LegumeIP/v2.