@article{d28402c12eb3432fa8819e1ba1f09430,
title = "An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions",
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.",
author = "Annabelle Haudry and Platts, {Adrian E.} and Emilio Vello and Hoen, {Douglas R.} and Mickael Leclercq and Williamson, {Robert J.} and Ewa Forczek and Zo{\'e} Joly-Lopez and Steffen, {Joshua G.} and Hazzouri, {Khaled M.} and Ken Dewar and Stinchcombe, {John R.} and Schoen, {Daniel J.} and Xiaowu Wang and Jeremy Schmutz and Town, {Christopher D.} and Edger, {Patrick P.} and Pires, {J. Chris} and Schumaker, {Karen S.} and Jarvis, {David E.} and Terezie Mand{\'a}kov{\'a} and Lysak, {Martin A.} and {Van Den Bergh}, Erik and Schranz, {M. Eric} and Harrison, {Paul M.} and Moses, {Alan M.} and Bureau, {Thomas E.} and Wright, {Stephen I.} and Mathieu Blanchette",
note = "Funding Information: We would like to thank the US Department of Energy Joint Genome Institute (for the C. rubella genome sequence, produced under a Community Sequencing Program (CSP) proposal submitted by D. Weigel and colleagues, and the E. salsugineum genome sequence, produced under a CSP proposal submitted by K. Schumaker, R. Wing and T. Mitchell-Olds) and R. Clark (for A. lyrata mRNA sequencing). We also thank S.-C. Chantha for assistance with genome sequencing in L. alabamica, S. Joly for suggestions on the genomic DNA isolation protocol and D. Scofield for helpful discussions about intron-exon structure. We thank M. Freeling, D. Weigel, E. Harmsen and I. Lacroix for comments on the manuscript. This project was funded by a Genome Canada/G{\'e}nome Qu{\'e}bec grant to T.E.B., S.I.W., M.B., J.S., A.M.M., D.J.S. and P.M.H. In addition, T.M. and M.A.L. were supported by the European Regional Development Fund (CZ.1.05/1.1.00/02.0068) and by the Czech Science Foundation (excellence cluster P501/12/G090). J.G.S. was supported by National Science Foundation (NSF) award 0929262. M.E.S. and E.v.d.B. were supported by a Vidi grant from the Netherlands Organisation for Scientific Research.",
year = "2013",
month = aug,
doi = "10.1038/ng.2684",
language = "English (US)",
volume = "45",
pages = "891--898",
journal = "Nature Genetics",
issn = "1061-4036",
publisher = "Nature Publishing Group",
number = "8",
}