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. 2012 Jan;40(Database issue):D1221-9.
doi: 10.1093/nar/gkr939. Epub 2011 Nov 21.

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

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Free PMC article

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

Jun Li et al. Nucleic Acids Res. .
Free PMC article

Abstract

Legumes play a vital role in maintaining the nitrogen cycle of the biosphere. They conduct symbiotic nitrogen fixation through endosymbiotic relationships with bacteria in root nodules. However, this and other characteristics of legumes, including mycorrhization, compound leaf development and profuse secondary metabolism, are absent in the typical model plant Arabidopsis thaliana. We present LegumeIP (http://plantgrn.noble.org/LegumeIP/), an integrative database for comparative genomics and transcriptomics of model legumes, for studying gene function and genome evolution in legumes. LegumeIP compiles gene and gene family information, syntenic and phylogenetic context and tissue-specific transcriptomic profiles. The database holds the genomic sequences of three model legumes, Medicago truncatula, Glycine max and Lotus japonicus plus two reference plant species, A. thaliana and Populus trichocarpa, with annotations based on UniProt, InterProScan, Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes databases. LegumeIP also contains large-scale microarray and RNA-Seq-based gene expression data. Our new database is capable of 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. Finally, LegumeIP provides comprehensive search and visualization tools that enable flexible queries based on gene annotation, gene family, synteny and relative gene expression.

Figures

Figure 1.
Figure 1.
Web interfaces for (A) searching, (B) exploring and (C) visualizing macrosyntenys and microsyntenys.
Figure 2.
Figure 2.
(A) Expression cluster displayed as heatmap for all expressed member genes in TribeMCL00867 and (B) OrthoMCL07722, which include SymRK genes.
Figure 3.
Figure 3.
Phylogenetic tree of the TribeMCL00867 gene family.
Figure 4.
Figure 4.
SymRK orthologous genes within a syntenic region common to L. japonicus, G. max and M. truncatula.
Figure 5.
Figure 5.
SymRK paralogous genes within a syntenic region in G. max.

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