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

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.

Does urban agriculture contribute to food security, and how might this be achieved?

OBJECTIVE: Food system challenges exacerbate inequalities in access to fresh healthy food and threaten food security. Lack of food security, referred to as food insecurity, is associated with poorer physical and mental health outcomes and has been identified as a key challenge to address by calls for food system transformation. Increasing food production through urban agriculture, the production of fruit and vegetables in urban areas, has been identified as a potentially effective contributor to food system transformation, but the effect of this on household or UK-level food security is unclear. This paper reviews international evidence of urban agriculture's impact on food security. DESIGN: Narrative review. SETTING: This paper reviews international evidence of urban agriculture's impact on food security. PARTICIPANTS: Previously published international research. RESULTS: Whilst findings are mixed, available evidence suggests that urban agriculture makes a modest, yet positive, contribution to food security by facilitating the availability of and access to fresh fruit and vegetables to food insecure households. CONCLUSIONS: Capitalising on the potential for urban agriculture to benefit food security requires government investment and support at both the national and local levels; therefore, increasing access to land for food growing, reducing costs of related resources and collaboration with existing community groups to enhance sharing of skills and expertise are identified as avenues for exploration that may help to achieve this. This review also highlights opportunities for future research in this field that may strengthen the quality of the evidence supporting urban agriculture's impact on food security.