02528nas a2200445   4500000000100000000000100001008004100002260001300043100001900056700001700075700002000092700001500112700002700127700001800154700002400172700002100196700001900217700001800236700002100254700001700275700001700292700001600309700001500325700002100340700001600361700001800377700001600395700002200411700001400433700001600447700001600463700001800479700001900497700001600516245005600532300001200588490000700600520146100607022001402068       2014                            d  c2014 Jan1 aMarcela Monaco1 aJoshua Stein1 aSushma Naithani1 aSharon Wei1 aPalitha Dharmawardhana1 aSunita Kumari1 aVindhya Amarasinghe1 aKen Youens-Clark1 aJames Thomason1 aJustin Preece1 aShiran Pasternak1 aAndrew Olson1 aYinping Jiao1 aZhenyuan Lu1 aDan Bolser1 aArnaud Kerhornou1 aDan Staines1 aBrandon Walts1 aGuanming Wu1 aPeter D'Eustachio1 aRobin Haw1 aDavid Croft1 aPaul Kersey1 aLincoln Stein1 aPankaj Jaiswal1 aDoreen Ware00aGramene 2013: comparative plant genomics resources.  aD1193-90 v423 aGramene (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.  a1362-4962