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Nucleic Acids Res. 2014 Jan;42(Database issue):D1193-9. doi: 10.1093/nar/gkt1110. Epub 2013 Nov 11.

Gramene 2013: comparative plant genomics resources.

Author information

1
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto M5G 1L7, Canada, Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA and NAA Plant, Soil & Nutrition Laboratory Research Unit, USDA-ARS, Ithaca, NY 14853, USA.

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.

PMID:
24217918
PMCID:
PMC3964986
DOI:
10.1093/nar/gkt1110
[Indexed for MEDLINE]
Free PMC Article

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