Novel Algorithms Motivated by Sequencing the Solanum pennellii Genome

Solanum pennelliiis a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. A complete set of Introgression lines (ILs) in which large genomic regions of S. lycopersicum cv. M82are replaced with the corresponding segments from S. pennelliiwere developed in the Zamir lab during the 1990s. Here we present the high­quality de­novo genome assembly of the introgressed parent, S. pennellii, as well as the resequencing of the recurrent parent, S. lycopersicum cv. M82. The 1.2 gigabase S. pennellii genome was sequenced using in a pure next generation sequencing (NGS) approach using Illumina technology. The resulting 942Mbp assembly had an N50 of over 1.7Mbp, and 97.1% of this could be anchored to the 12 chromosomes using a combination of traditional and NGS derived markers. During this project, we identified several opportunities to develop improved genome assembly algorithms and tools. Our recently published tool for read trimming, Trimmomatic, has already seen wide adoption by the community. We have also created novel algorithms for genome and transcriptome assembly which combine the advantages of the Overlap­ Layout ­Consensus and De­ Bruijn ­Graph approaches. Prototype implementations have been developed and show promising potential for improving both the data­ efficiency and the quality of the resulting assemblies. Here we also outline these approaches and initial results.