BBSRC-NSF/BIO PanOryza: Globally coordinated genomes, proteomes and pathways for rice

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This project will create the pan gene set for cultivated Asian rice (Oryza sativa) and its wild Oryza relatives, using newly developed software to produce consistent gene models across all varieties and species. At the outset, we will have access to 16 "platinum standard" reference sequence (PSRefSeq) genomes for Asian rice, that represent the genetic diversity of O. sativa, as well as 25 wild rice genomes. At present, gene models are being annotated independently across different projects, leading to inconsistencies that cause confusion and challenges in fundamental and applied rice research. We will release consistent, aligned gene models for all Oryza genus reference genomes, through internationally recognised platforms Ensembl Plants and Gramene. We will develop capabilities within the Planteome knowledgebase for annotating rice genes with functional information, through semi-automated literature extraction, and provide a community platform for gene symbol assignment and manual gene model revisions. The PSRefSeqs will be fully aligned at the chromosomal level to define synteny, and enable users to view syntenic relationships between PSRefSeqs and their gene model sets. Genetic variant data coming from >3000 re-sequenced rice accessions will be mapped onto the aligned PSRefSeqs, and released via the European Variant Archive and linked to trait data on the varieties in the SNP-Seek platform.

Consistently annotated coding gene products i.e. proteomes, will be released via the world-leading protein knowledge-base UniProt, for all 16 O. sativa PSRefSeqs and 25 proteomes for wild rice. UniProt will add functional annotations, coordinated with Planteome, as well as defining the pan-proteome i.e. the full set of proteins present in all varieties of O. sativa and at the genus level. Large scale mass spectrometry data sets will be mined to provide protein-level evidence for coding genes, and to find and annotate sites of Post-Translational Modifications.

The PanOryza proposal encompasses and brings together the most widely used international databases for rice research and development. The planned objectives will improve data sharing between these resources, and greatly improve the quality of the data on rice genes, variants, proteins and post-translational modifications.

Beyond academic beneficiaries, the following groups will directly benefit:

- Seed companies and breeders will benefit through improved linkage of traits data e.g. held in SNP-Seek to improved gene models across the pan gene set for allele mining


There is potential for indirect benefits in breeders of other crops, via adoption of software and approaches developed in PanOryza improving capabilities for understanding the pan gene set within other species.

Staff will benefit through exposure to an international network of bioinformaticians, working in a key area of food security