Transcriptome characterization and evolution in cultivated and wild tomato species

Project Summary

Solanum lycopersicum, more commonly known as the tomato, is one of our most important agricultural crop. Not only is the bright red and fleshy fruit of the tomato a good source of vitamins and antioxidants, it also provides an important model system for fruit development. Despite its importance in agriculture however, Solanum lycopersicum suffers from a severe lack of genetic variation. Due to a combination of bottleneck effects and centuries of inbreeding, individual tomato plants are nearly genetically identical to each other. As a consequence of the decreased variation, this cultivated plant becomes much more susceptible to disease and changes in climate. Wild tomato species on the other hand, are rich in genetic variability and contain many adaptations to less-than-ideal conditions, such as arid climates and high altitude. Such species may be vital in breeding programs to create a more evolutionarily fit tomato.

This summer we assembled the transcriptomes of the wild tomato species, Solanum pervianum andSolanum pimpinellifolium and annotated the genomes of Solanum chilense, Solanum habrochaites, and Solanum pennellii with tools such as Trinity and Maker respectively. We also completed de novo genome assembly of Solanum chilense, a species more heterozygous than tomato,with Platanus. With the data from these wild tomato species, we constructed a phylogeny using programs such as ClustalX, Dnaml, and PAML. While tomato phylogeny trees had already been constructed in previous efforts, they were based on a much smaller sample size than we have available to us now. Using a larger sample size can help resolve phylogenies for wild species and provide greater insight into the evolutionary divergence of these tomato species. Overall, the work we completed offered interesting insights within the wild tomato species and will aid further research in improving tomato crop.

My Experience

My summer at Boyce Thompson Institute and in Lukas Mueller’s lab has allowed my bioinformatics skills to grow exponentially. Not only am I much more comfortable with UNIX systems and a multitude of bioinformatics tools, I have gained a better appreciation for the broad potential of big data in supporting the growth of plant science research. Outside of bioinformatics, I was able to witness the diversity of plant research conducted by some of the best scientists in their field. I leave the summer much more experienced and am ready to apply my newly learned skills to my continuing immersion in bioinformatics