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

Annabelle Haudry, Adrian E. Platts, Emilio Vello, Douglas R. Hoen, Mickael Leclercq, Robert J. Williamson, Ewa Forczek, Zoé Joly-Lopez, Joshua G. Steffen, Khaled M. Hazzouri, Ken Dewar, John R. Stinchcombe, Daniel J. Schoen, Xiaowu Wang, Jeremy Schmutz, Christopher D. Town, Patrick P. Edger, J. Chris Pires, Karen S. Schumaker, David E. JarvisTerezie Mandáková, Martin A. Lysak, Erik Van Den Bergh, M. Eric Schranz, Paul M. Harrison, Alan M. Moses, Thomas E. Bureau, Stephen I. Wright, Mathieu Blanchette

Research output: Contribution to journalArticle

180 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)891-898
Number of pages8
JournalNature Genetics
Volume45
Issue number8
DOIs
StatePublished - Aug 1 2013

ASJC Scopus subject areas

  • Genetics

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    Haudry, A., Platts, A. E., Vello, E., Hoen, D. R., Leclercq, M., Williamson, R. J., Forczek, E., Joly-Lopez, Z., Steffen, J. G., Hazzouri, K. M., Dewar, K., Stinchcombe, J. R., Schoen, D. J., Wang, X., Schmutz, J., Town, C. D., Edger, P. P., Pires, J. C., Schumaker, K. S., ... Blanchette, M. (2013). An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nature Genetics, 45(8), 891-898. https://doi.org/10.1038/ng.2684