Sequencing the Solanum pennellii genome and algorithms inspired thereby

The genome of Solanum pennellii, a wild tomato species endemic to Andean regions in South America, was published in 2014. This hardy species is notable due to its extreme stress tolerance and unusual morphology, which have enabled it to succeed in extremely  harsh conditions. From a scientific and breeding perspective, this plant offers exotic germplasm which can be exploited by the domesticated tomato Solanum lycoperiscum.

Here we present the data from this sequencing project together with some novel tools and algorithms that were motivated during this endeavor. Our tool Trimmomatic provides precise adapter removal, flexible quality filtering and high performance. It has been massively embraced by not only the plant community, but by the larger sequencing community. We are currently working on a novel assembly framework which combines the best of the De-Bruijn Graph and Overlap-Layout-Consensus approaches, and will enable not just de-novo assembly but also variant analysis for highly divergent genomes. Here we describe these proposed approaches and initial results.