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

Wang, Y., Diehl, A., Wu, F., Vrebalov, J., Giovannoni, J., Siepel, A., Tanksley, S. D. (2008) Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics, 180 (1). pp. 391-408. ISSN 0016-6731 (Print)0016-6731

URL: http://www.ncbi.nlm.nih.gov/pubmed/18723883
DOI: 10.1534/genetics.108.087981

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.

Item Type: Paper
Uncontrolled Keywords: Base Sequence Binding Sites Chromosomes, Artificial, Bacterial Conserved Sequence Evolution, Molecular Genetic Variation Genomics Models, Genetic Models, Statistical Molecular Sequence Data Oligonucleotide Probes Phylogeny Sequence Homology, Nucleic Acid Solanaceae/*genetics Species Specificity
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > comparative genomics
organism description > plant
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Siepel lab
Depositing User: Matt Covey
Date Deposited: 12 Jan 2015 15:39
Last Modified: 12 Jan 2015 15:39
PMCID: PMC2535690
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31113

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