LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes
| Autor: | Tingsong Liu, Xinbin Dai, Jun Li, Patrick X. Zhao |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2011 |
| Předmět: |
0106 biological sciences
Genome evolution Genomics Biology computer.software_genre Genes Plant 01 natural sciences 03 medical and health sciences Cytochrome P-450 Enzyme System Databases Genetic Medicago truncatula Genetics Gene family Symbiosis 030304 developmental biology Synteny 2. Zero hunger Comparative genomics 0303 health sciences Database Models Genetic Gene Expression Profiling fungi food and beverages Glycosyltransferases Fabaceae Gene Annotation Articles 15. Life on land Gene expression profiling Systems Integration Lotus Soybeans UniProt computer Genome Plant Software 010606 plant biology & botany |
| Zdroj: | Nucleic Acids Research Biological Nitrogen Fixation |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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