Format

Send to

Choose Destination
Genetics. 2008 Sep;180(1):391-408. doi: 10.1534/genetics.108.087981. Epub 2008 Aug 24.

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

Author information

1
Department of Plant Breeding and Genetics, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, People's Republic of China.

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 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 approximately 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.

PMID:
18723883
PMCID:
PMC2535690
DOI:
10.1534/genetics.108.087981
[Indexed for MEDLINE]
Free PMC Article

Publication types, MeSH terms, Substance, Secondary source ID, Grant support

Publication types

MeSH terms

Substance

Secondary source ID

Grant support

Supplemental Content

Full text links

Icon for HighWire Icon for PubMed Central
Loading ...
Support Center