Originally published as Genetics Published Articles Ahead of Print on August 24, 2008.

Genetics, Vol. 180, 391-408, September 2008, Copyright © 2008
doi:10.1534/genetics.108.087981

Sequencing and Comparative Analysis of a Conserved Syntenic Segment in the Solanaceae

Ying Wang^*,,1, Adam Diehl^,1, Feinan Wu^*, Julia Vrebalov^,**, James Giovannoni^,**, Adam Siepel^,2 and Steven D. Tanksley^*

^* Department of Plant Breeding and Genetics, Graduate Field of Genetics and Development, USDA–ARS Plant, Soil and Nutrition Laboratory, ^** Boyce Thompson Institute for Plant Research and Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853 and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, People's Republic of China

² Corresponding author: 101 Biotechnology Bldg., Cornell University, Ithaca, NY 14853.
E-mail: acs4{at}cornell.edu

Comparative genomics is a powerful tool for gaining insight into genomic function and evolution. However, in plants, sequence data that would enable detailed comparisons of both coding and noncoding regions have been limited in availability. Here we report the generation and analysis of sequences for an unduplicated conserved syntenic segment (CSS) in the genomes of five members of the agriculturally important plant family Solanaceae. This CSS includes a 105-kb region of tomato chromosome 2 and orthologous regions of the potato, eggplant, pepper, and petunia genomes. With a total neutral divergence of 0.73–0.78 substitutions/site, these sequences are similar enough that most noncoding regions can be aligned, yet divergent enough to be informative about evolutionary dynamics and selective pressures. The CSS contains 17 distinct genes with generally conserved order and orientation, but with numerous small-scale differences between species. Our analysis indicates that the last common ancestor of these species lived 27–36 million years ago, that more than one-third of short genomic segments (5–15 bp) are under selection, and that more than two-thirds of selected bases fall in noncoding regions. In addition, we identify genes under positive selection and analyze hundreds of conserved noncoding elements. This analysis provides a window into 30 million years of plant evolution in the absence of polyploidization.

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