Crops in the Brassicae family share much genomic variation and can relatively easily be crossed, yet show remarkable variation in form . Brassicae have undergone (an evolutionarily recent) genome triplication, followed by gradual gene loss. Resulting species include Brassica rapa, olacea and nigra. While these species differ substantially in many respects, they display the same range of forms. This begs the question what the mechanism underlying this form diversification is: is it random or directed?
In this project, the goal is to mine transcriptomics data available for various tissues in different Brassica species, as well as less relates Solanacea (tomato and potato). Transcripts can be clustered, pathway can be derived (e.g. based on co-expression) and annotated using protein function prediction tools. The desired outcome is an answer to the question whether the variation in form observed is caused by the same gene (modules) in each Brassica species, or whether the gene copy number plays an important role.
R.K. Basnet et al. (2013) Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes BMC Genomics 14:840.
Used skills: Programming, genomics
Requirements: INF-22306 Programming in Python, BIF-30806 Advanced bioinformatics, ABG-30306 Genomics