Gramene 2013: comparative plant genomics resources

Title 
Gramene 2013: comparative plant genomics resources 
Publication Type 
Journal Article 
Authors 
Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D'Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D 
Year of Publication 
2014 
Volume 
42 
Journal 
Nucleic Acids Research 
Issue 
D1 
Pagination 
D1193 - D1199 
Date Published 
01/2014 
ISSN 
1362-4962 
URL 
https://www.researchgate.net/publication/258445080_Gramene_2013_comparative_plant_genomics_resources?ev=sim_pub 
Keywords 
Beans, Cassava, Chickpea, comparative functional genomics, Cowpea, Data mgmt, Gramene, Groundnut, Maize, metabolic pathways, orthologous relationships, phylogenetics, Rice, Sorghum, syntenic relationships, Wheat 
DOI 
10.1093/nar/gkt1110 
Abstract 

Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. Whole-genome alignments complemented by phylogenetic gene family trees help infer syntenic and orthologous relationships. Genetic variation data, sequences and genome mappings available for 10 species, including Arabidopsis, rice and maize, help infer putative variant effects on genes and transcripts. The pathways section also hosts 10 species-specific metabolic pathways databases developed in-house or by our collaborators using Pathway Tools software, which facilitates searches for pathway, reaction and metabolite annotations, and allows analyses of user-defined expression datasets. Recently, we released a Plant Reactome portal featuring 133 curated rice pathways. This portal will be expanded for Arabidopsis, maize and other plant species. We continue to provide genetic and QTL maps and marker datasets developed by crop researchers. The project provides a unique community platform to support scientific research in plant genomics including studies in evolution, genetics, plant breeding, molecular biology, biochemistry and systems biology.

 
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