W099 Comparative and Population Genomics in the Brassicaceae

Date: Saturday, January 14, 2012
Time: 11:20 AM
Room: Royal Palm Salon 1-2
Stephen I. Wright , University of Toronto, Toronto, ON, Canada
Adrian Platts , McGill University, Montreal, QC, Canada
Annabelle Haudry , University of Toronto, Toronto, ON, Canada
Robert Williamson , University of Toronto, Toronto, ON, Canada
Khaled Hazzouri , University of Toronto, Toronto, ON, Canada
Emilio Vello , McGill University, Montreal, QC, Canada
Ewa Forczek , McGill University, Montreal, QC, Canada
Sier-Ching Chantha , McGill University, Montreal, QC, Canada
Simon Joly , University of Montreal, Montreal, QC, Canada
Daniel Koenig , Max Planck Institute for Developmental Biology, Tübingen, Germany
Thomas Mitchell-Olds , Duke University, Dept. of Biology, Durham, NC
Rod A. Wing , University of Arizona, Tucson, AZ
Detlef Weigel , Max Planck Institute for Developmental Biology, Tübingen, Germany
Karen Schumaker , University of Arizona, Tucson, AZ
Chris Town , J. Craig Venter Institute, Rockville, MD
Xiaowu Wang , Institute of Vegetables and Flowers, Beijing, China
M. Eric Schranz , University of Amsterdam, Amsterdam, Netherlands
J. Chris Pires , University of Missouri, Columbia, MO
Richard Clark , University of Utah, Salt Lake City, UT
Joshua Steffen , University of Utah, Salt Lake City, UT
Chris Toomajian , Kansas State University, Manhattan, KS
Simon Prochnik , DOE Joint Genome Institute
Jerry Jenkins , Hudson Alpha Institute of Biotechnology
Jeremy Schmutz , Hudson Alpha Institute of Biotechnology
Dan Rokhsar , DOE Joint Genome Institute, Walnut Creek, CA
Eef Harmsen , McGill University, Montreal, QC, Canada
John Stinchcombe , University of Toronto, Toronto, ON, Canada
Paul Harrison , McGill University, Montreal, QC, Canada
Thomas Bureau , McGill University, Montreal, QC, Canada
Daniel Schoen , McGill University, Montreal, QC, Canada
Alan Moses , University of Toronto, Toronto, ON, Canada
Mathieu Blanchette , McGill University, Montreal, QC, Canada
Despite the central importance of noncoding DNA in gene regulation and evolution, our understanding of the genomic extent and nature of selection on plant noncoding regions remains limited. We are combining comparative genomics with population genomics approaches to characterize the functional importance of plant noncoding regions, using the Brassicaceae. We conducted whole genome alignments of nine Brassicaceae species, including two new genome assemblies from the DOE Joint Genome Institute (Capsella rubella and Eutrema halophila) and de novo Illumina assemblies of three additional species by the VEGI consortium (Aethionema arabicum, Sisymbrium irio, and Leavenworthia alabamica). Analysis of multispecies conservation resulted in the identification of more than 90,000 conserved noncoding sequences (CNCs), ranging in size from 12 to 2000bp. Comparisons of motif patterns inside and outside of conserved motifs reveal an enrichment of known transcription factor binding sites, as well as candidate novel sites. Analysis of polymorphism and divergence in CNCs in both Arabidopsis and Capsella confirm the action of purifying selection on CNCs, but also suggest a high rate of positive selection in these regions. Our analysis indicates the predominance of weak purifying selection and positive selection in plant noncoding regions, highlighting the likely importance of these regions for functional variation and adaptive evolution.