Transcriptome Assembly, Gene Annotation and Variation Discovery in Cultivated Chia

Chia (Salvia hispanica L.), is a plant in the mint family, Lamiaceae. Chia was consumed by many native people from the Americas for its rich source of nutrients, protein and oil. However, in the developed world, recent consumption of Chia seeds has grown in popularity as super food for its nutritional content, such as high omega-3-acids and dietary fiber. In order to understand the genetic and environmental impacts its rich nutritional quality, we need to develop genomic and genetic resources that are almost non-existent. Therefore, Salba, a cultivated variety, was chosen to develop genomic resources. We estimated its genome size by flow cytometry and generated a de novo transcriptome assembly and gene annotation derived from mRNA samples extracted from different tissue types and developmental stages. The transcriptome data was further investigated for gene homology, species phylogeny and scoring differentially expressed genes across different tissue types and developmental stages thus creating an expression atlas. Additional analysis include SNP and indel variations by comparing the white and black varieties against the Salba transcriptome. Downstream analysis include curation of omega-3-acid biosynthesis and regulatory pathways.