P2EP: Plant Pathways Elucidation Project - Orthologous Clustering of Brassica oleracea RNASeq to Define Putative Genes in KEGG Pathways

Teams comprised of researchers from industry and academia joined forces with the UNC System and private partners to craft an expansive new transdisciplinary project initiative – the Plant Pathways Elucidation Project, or P2EP - launched on the new North Carolina Research Campus - NCRC (http://www.ncresearchcampus.net/). The primary goal of P2EP is to integrate student learning with cutting edge research in plant genomics as it relates to nutrition. This effort includes genome mapping , assembly and gene annotation in order to identify key components in nutritionally related pathways. Student scholars are involved in each step of the research and are relied on for manual gene annotation.

Here, we describe our initial clustering strategy for identifying putative genes involved in key plant pathways in Brassica Oleracea. Using RNASeq transcripts de novo assembled via Oases (Hiseq), KEGG gene sequences and annotated CDS sequences from a closely related Brassica Oleracea genome, we perform an all versus all comparison in protein space, followed by clustering based on similarity. Sequence clusters that contain KEGG sequences from a desired pathway are identified for further alignment and manual annotation. This process is 1 step in providing evidence for the manual annotation step in P2EP. This is combined automated approaches such as Maker (Cantarel, 2008) and ENSEMBL  which also identify putative genes. As students extract relevant genes of interest within the model pathways, they will rebuild the pathways, learning how to evaluate evidence to support annotations. More information is available at http://p2ep.org/.