Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets



Ren, Zhe, Qi, Da ORCID: 0000-0001-6079-9764, Pugh, Nina, Li, Kai, Wen, Bo, Zhou, Ruo, Xu, Shaohang, Liu, Siqi and Jones, Andrew R ORCID: 0000-0001-6118-9327
(2019) Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets. Molecular and Cellular Proteomics, 18 (1). 86 - 98.

Access the full-text of this item by clicking on the Open Access link.

Abstract

Rice (Oryza sativa) is one of the most important worldwide crops. The genome has been available for over 10 years and has undergone several rounds of annotation. We created a comprehensive database of transcripts from 29 public RNA sequencing data sets, officially predicted genes from Ensembl plants, and common contaminants in which to search for protein-level evidence. We re-analyzed nine publicly accessible rice proteomics data sets. In total, we identified 420K peptide spectrum matches from 47K peptides and 8,187 protein groups. 4168 peptides were initially classed as putative novel peptides (not matching official genes). Following a strict filtration scheme to rule out other possible explanations, we discovered 1,584 high confidence novel peptides. The novel peptides were clustered into 692 genomic loci where our results suggest annotation improvements. 80% of the novel peptides had an ortholog match in the curated protein sequence set from at least one other plant species. For the peptides clustering in intergenic regions (and thus potentially new genes), 101 loci were identified, for which 43 had a high-confidence hit for a protein domain. Our results can be displayed as tracks on the Ensembl genome or other browsers supporting Track Hubs, to support re-annotation of the rice genome.

Item Type: Article
Depositing User: Symplectic Admin
Date Deposited: 15 Feb 2019 15:36
Last Modified: 12 Jan 2021 23:11
DOI: 10.1074/mcp.RA118.000832
Open Access URL: https://doi.org/10.1074/mcp.RA118.000832
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3032926