Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features

Ryohei Seki, Cai Li, Qi Fang, Shinichi Hayashi, Shiro Egawa, Jiang Hu, Luohao Xu, Hailin Pan, Mao Kondo, Tomohiko Sato, Haruka Matsubara, Namiko Kamiyama, Keiichi Kitajima, Daisuke Saito, Yang Liu, M. Thomas P. Gilbert, Qi Zhou, Xing Xu, Toshihiko Shiroishi, Naoki Irie (), Koji Tamura () and Guojie Zhang ()
Additional contact information
Ryohei Seki: Mammalian Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics
Cai Li: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Qi Fang: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Shinichi Hayashi: Graduate School of Life Sciences, Tohoku University
Shiro Egawa: Graduate School of Life Sciences, Tohoku University
Jiang Hu: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Luohao Xu: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Hailin Pan: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Mao Kondo: Graduate School of Life Sciences, Tohoku University
Tomohiko Sato: Graduate School of Life Sciences, Tohoku University
Haruka Matsubara: Graduate School of Life Sciences, Tohoku University
Namiko Kamiyama: Graduate School of Life Sciences, Tohoku University
Keiichi Kitajima: Graduate School of Life Sciences, Tohoku University
Daisuke Saito: Graduate School of Life Sciences, Tohoku University
Yang Liu: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
M. Thomas P. Gilbert: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
Qi Zhou: Department of Integrative Biology University of California
Xing Xu: Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences
Toshihiko Shiroishi: Mammalian Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics
Naoki Irie: Graduate School of Science, University of Tokyo
Koji Tamura: Graduate School of Life Sciences, Tohoku University
Guojie Zhang: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences

Nature Communications, 2017, vol. 8, issue 1, 1-14

Abstract: Abstract Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous evolutionary innovations such as self-powered flight and its associated wings with flight feathers. By analysing 48 bird genomes, we identified millions of avian-specific highly conserved elements (ASHCEs) that predominantly (>99%) reside in non-coding regions. Many ASHCEs show differential histone modifications that may participate in regulation of limb development. Comparative embryonic gene expression analyses across tetrapod species suggest ASHCE-associated genes have unique roles in developing avian limbs. In particular, we demonstrate how the ASHCE driven avian-specific expression of gene Sim1 driven by ASHCE may be associated with the evolution and development of flight feathers. Together, these findings demonstrate regulatory roles of ASHCEs in the creation of avian-specific traits, and further highlight the importance of cis-regulatory rewiring during macroevolutionary changes.

Date: 2017
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DOI: 10.1038/ncomms14229

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