The tomato genome sequence provides insight into fleshy fruit evolution

Authors: Ware, Doreen; Thannhauser, Theodore - Ted; White, Ruth; Giovannoni, James

Submitted to: Nature
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/3/2012
Publication Date: 5/30/2012
Citation: Ware, D., Thannhauser, T.W., White, R.A., Giovannoni, J.J. 2012. The tomato genome sequence provides insight into fleshy fruit evolution. Nature. 485:635-641. DOI: 10.1038/nature11119.

Interpretive Summary: Tomato is a major crop plant and a model system for fruit development. We generated and present a high quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, S. pimpinellifolium, and compare them to each other and to potato (S. tuberosum). The two tomato genomes show little divergence as expected, but show >8% divergence from tomatoe’s close relative potato, with nine large and several smaller inversions. The lineage that includes tomato has experienced two consecutive genome triplications: one that is ancient and a more recent one. We show that these triplications set the stage for the evolution of genes controlling important fruit crop characteristics, such as color and fleshiness.

Technical Abstract: The genome of the inbred tomato cultivar ‘Heinz 1706’ was sequenced and assembled using a combination of Sanger and “next generation” technologies. The predicted genome size is ~900 Mb, consistent with prior estimates, of which 760 Mb were assembled in 91 scaffolds aligned to the 12 tomato chromosomes,with most gaps restricted to pericentromeric regions. Base accuracy is approximately one substitution error per 29.4 kb and one indel error per 6.4 kb. Relative expression of all tomato genes was determined by replicated strand-specific Illumina RNA-Seq of root, leaf, flower (2 stages) and fruit (6 stages) in addition to leaf and fruit (3 stages) of S. pimpinellifolium. Comparison of the tomato and grape genomes supports the hypothesis that a whole genome triplication affecting the rosid lineage occurred in a common eudicot ancestor. Comparison to the grape genome also reveals a more recent triplication in tomato and potato. This triplication, also evident in potato is estimated at 71 (+/-19.4) mya based on Ks of paralogous genes, and therefore predates the ~7.3 mya tomato-potato divergence. Combined orthology and synteny analyses suggest that both genome triplications added new gene family members that mediate important fruit-specific functions. The genome sequences presented here will allow breeders to tap tomato’s rich trait reservoir and identify domestication genes, providing biological knowledge and empowering biodiversity-based breeding.