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Nat Commun. 2017 Feb 6;8:14229. doi: 10.1038/ncomms14229.

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

Author information

1
Mammalian Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.
2
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama 6-3, Aoba-ku, Sendai 980-8578, Japan.
3
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
4
China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
5
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark.
6
Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, USA.
7
Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, Aobayama 6-3, Aoba-ku, Sendai 980-8578, Japan.
8
Norwegian University of Science and Technology, University Museum, N-7491 Trondheim, Norway.
9
Department of Integrative Biology University of California, Berkeley, California 94720, USA.
10
Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.
11
Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
12
Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, Copenhagen 2100, Denmark.

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.

PMID:
28165450
PMCID:
PMC5473641
DOI:
10.1038/ncomms14229
[Indexed for MEDLINE]
Free PMC Article

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