User guide for the Gramene Oryza PanGenome site available

Is it sometimes hard to know where to start? If you are an old or new user of Gramene resources, we recommend you review our new quick user guide for exploring the Oryza PanGenome. The site is available at https://oryza.gramene.org/guides.

To support the user experience, the guide takes you on a tour of the site using the GW8 gene as the exemplar model.  GW8 is the gene symbol for Grain Width on chromosome 8, OsSPL16 or Os08g0531600, a transcription factor containing an SBP-domain that promotes cell division and grain filling by regulating grain width, size, shape and quality (Wang et al, 2012). It was identified as a domestication gene among 55 known selective domestication sweeps or signatures (Chen et al, 2019).

The guide demonstrates how to search for a gene in the site’s search interface and describes various views of the gene structure and associated data such as gene family trees with color-coded protein domains, amino acid alignments across a tree, and gene neighborhood views. Other data cross-linked from collaborators are Plant Reactome pathways and EBI-Atlas gene expression. In addition, users are taken through the oryza pangenomes installation on the Ensembl browser including comparative analysis data such as gene family trees, whole-genome alignments, and synteny maps. Other data also available in the browser are genetic and structural variation, QTL data and gene expression.

Literature References

Chen Erwang, Xuehui Huang, Zhixi Tian, Rod A.Wing, and Bin Han. 2019. The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis. Annu. Rev. Plant Biol. 70:639–65 doi: 10.1146/annurev-arplant-050718-100320.

Wang S,Wu K, Yuan Q, Liu X, Liu Z, et al. 2012. Control of grain size, shape and quality by OsSPL16 in rice. Nat. Genet. 44:950–54.