Gramene 2013: comparative plant genomics resources

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.

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

“…The pipeline was run on the MAKER-P 136 annotations for ten Oryza species and L. perrieri (Table 1). Also included were annotations of three outgroup species, Arabidopsis thaliana (version TAIR10) 137 , Sorghum bicolor (version Sbi1.4) 138 and B. distachyon (version Brachy1.2) 139 , loaded from Gramene v40 Ensembl core databases 140 . Tree reconciliation to classify duplication and speciation nodes, and the assignment of taxon levels to nodes, made use of the following input species tree, which was devised on the basis of results described here (Fig.…”

“…Putative falsely split gene models were detected by an automated pipeline that identifies adjacent 'paralogs' that do not overlap in multiple-sequence alignments 140 .…”

“…The integrated genetic/physical map (constructed using data from Harushima et al 147 and McCouch et al 148 ) for O. sativa vg. japonica was downloaded from Gramene (see URLs) 140 . Recombination rates were calculated as cM/Mb over 2-Mb windows across each chromosome.…”

A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses

“…Only genes with a 100% match to the same chromosome from the v2.1 genome assembly were used for the SNP comparison. EMS-induced SNPs were compared with two natural variation sets available from the Gramene database (Monaco et al, 2014): The first population consists of 265,000 SNPs from 971 worldwide accessions, assayed by genotyping-by-sequencing (Morris et al, 2013); the second population consists of six million SNPs, assayed by whole-genome sequencing of 45 S. bicolor and two S. propinquum lines (Mace et al, 2013). The coordination of SNPs within the mapped genes was converted from the v1.4 assembly to v2.1 using a script written in house.…”

Multiple functional polymorphisms in a single disease resistance gene in rice enhance durable resistance to blast

“…The use of resistance (R) genes is an effective way to control it. Extensive studies have identified more than 90 R genes for resistance to M. oryzae from diverse genetic resources 2 . Most of them are race specific, and all of those genes for race-specific resistance that have been cloned so far encode proteins containing a nucleotidebinding site (NBS) and leucine-rich repeats (LRRs), constituting a major class of R genes in plants 3,4 ; an exception is Pid2, which encodes a receptor-like kinase 5 .…”