DharmawardhanaPalithaBotanyPlantPathologyGramene2013_SupplementaryData.pdf
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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