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.

Figure 1.

Gramene’s Ensembl and Biomart interfaces. (A) The synteny map browser facilitates navigation from one genome to another across orthologous regions. In the left panel grapevine chr. 13 is represented in the center surrounded by mapped chromosomes of poplar. Duplicated regions of poplar are obvious in this view but more difficult to trace when using Arabidopsis (chr. 5) as the reference (right panel). (B) Compara gene trees help identify putative split-gene models, here showing fragmented alignments of consecutive banana genes, and absence of a conserved InterPro domain (green highlighting) in these fragments. (C) The genome browser allows uploading of private user data, here showing the Arabidopsis browser with variation data from a VCF file and transcriptome alignment data from a BAM file. The browser automatically predicted the effect of each SNP on overlapping annotated gene transcripts as indicated by color-coding (legend omitted). (D) GrameneMart includes five databases for gene, variation, marker, mapping and QTL-oriented searching. Here maize transcription factor genes were mined for the existence of possible detrimental alleles in HapMap2 data (17,25).

Figure 2.

Gramene’s Pathway Database module. A view of Gramene’s BioCyc-based Plant Metabolic Pathways (http://www.gramene.org/pathway) entry page listing species wise pathways databases (A), detail information (B) on the RiceCyc example including accessibility of various features such as summary (C), browse (D, E) and Omics-Viewer tool (F) allows visualization of user-defined expression data on cellular overview diagram. For example, in the cellular overview diagram rice genes that show high expression at 0 h during diurnal cycle are highlighted in red color (Data source: Filichkin et al., 2011).