Genetics. Published Articles Ahead of Print: August 24, 2008, Copyright © 2008
doi:10.1534/genetics.108.087981


A more recent version of this article appeared on September 1, 2008.

REGULAR RESEARCH PAPERS

Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae

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

1 Cornell University

* To whom correspondence should be addressed. E-mail: acs4{at}cornell.edu.

Submitted on February 11, 2008
Revised on June 23, 2008
Accepted on 23 June 2008


Abstract

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 105kb 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 >1/3 of short genomic segments (5-15bp) are under selection, and that >2/3 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.

Key Words: comparative genomics, molecular evolution, plant genomics