An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

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Authors

HAUNDRY Annabelle PLATTS Adrian E. VELLO Emilio HOEN Douglas R. LECLERCQ Mickael WILLIAMSON Robert J. FORCZEK Ewa JOLY-LOPEZ Zoé STEFFEN Joshua G. HAZZOURI Khaled M. DEWAR Ken STINCHCOMBE John R. SCHOEN Daniel J. WANG Xiaowu SCHMUTZ Jeremy TOWN Christopher D. EDGER Patrick P. PIRES J. Chris SCHUMAKER Karen S. JARVIS David E. MANDÁKOVÁ Terezie LYSÁK Martin VAN DEN BERGH Erik SCHRANZ M. Eric HARRISON Paul M. MOSES Alan M. BUREAU Thomas E. WRIGHT Stephen I. BLANCHETTE Mathieu

Year of publication 2013
Type Article in Periodical
Magazine / Source Nature Genetics
MU Faculty or unit

Central European Institute of Technology

Citation
Web http://www.nature.com/ng/journal/v45/n8/ng.2684/metrics/blogs
Doi http://dx.doi.org/10.1038/ng.2684
Field Genetics and molecular biology
Keywords ARABIDOPSIS-THALIANA; HUMAN GENOME; DNA ELEMENTS; ULTRACONSERVED ELEMENTS; BRASSICA-OLERACEA; GENE-EXPRESSION; EVOLUTION; DROSOPHILA; SIZE; ANNOTATION
Description Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum) and their joint analysis with six previously sequenced crucifer genomes. Conservation across orthologous bases suggests that at least 17% of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions. Much of this sequence can be localized to approximately 90,000 conserved noncoding sequences (CNSs) that show evidence of transcriptional and post-transcriptional regulation. Population genomics analyses of two crucifer species, A. thaliana and Capsella grandiflora, confirm that most of the identified CNSs are evolving under medium to strong purifying selection. Overall, these CNSs highlight both similarities and several key differences between the regulatory DNA of plants and other species.
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