Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features.
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.
Mammalian Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.|Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama 6-3, Aoba-ku, Sendai 980-8578, Japan.
Ryohei
R
Seki
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.|China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.|Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark.
Cai
C
Li
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.|China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Qi
Q
Fang
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama 6-3, Aoba-ku, Sendai 980-8578, Japan.|Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, USA.
Shinichi
S
Hayashi
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama 6-3, Aoba-ku, Sendai 980-8578, Japan.
Shiro
S
Egawa
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
Jiang
J
Hu
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
Luohao
L
Xu
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.|China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Hailin
H
Pan
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama 6-3, Aoba-ku, Sendai 980-8578, Japan.
Mao
M
Kondo
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama 6-3, Aoba-ku, Sendai 980-8578, Japan.
Tomohiko
T
Sato
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama 6-3, Aoba-ku, Sendai 980-8578, Japan.
Haruka
H
Matsubara
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama 6-3, Aoba-ku, Sendai 980-8578, Japan.
Namiko
N
Kamiyama
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama 6-3, Aoba-ku, Sendai 980-8578, Japan.
Keiichi
K
Kitajima
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama 6-3, Aoba-ku, Sendai 980-8578, Japan.|Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, Aobayama 6-3, Aoba-ku, Sendai 980-8578, Japan.
Daisuke
D
Saito
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
Yang
Y
Liu
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark.|Norwegian University of Science and Technology, University Museum, N-7491 Trondheim, Norway.
M Thomas P
MT
Gilbert
Department of Integrative Biology University of California, Berkeley, California 94720, USA.
Qi
Q
Zhou
Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.
Xing
X
Xu
Mammalian Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.
Toshihiko
T
Shiroishi
Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Naoki
N
Irie
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama 6-3, Aoba-ku, Sendai 980-8578, Japan.
Koji
K
Tamura
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.|China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.|Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, Copenhagen 2100, Denmark.
Guojie
G
Zhang
D000818:Animals; D005075:Biological Evolution; D001717:Birds / Q000502:physiology*; D066264:Datasets as Topic; D025061:Dinosaurs / Q000502:physiology; D005241:Feathers / Q000254:growth & development; D005426:Flight, Animal / Q000502:physiology*; D018507:Gene Expression Regulation, Developmental / Q000502:physiology; D016678:Genome; D006657:Histones / Q000502:physiology; D010802:Phylogeny; D012045:Regulatory Sequences, Nucleic Acid / Q000502:physiology*; D014157:Transcription Factors / Q000502:physiology; D014921:Wings, Animal / Q000254:growth & development*
D006657:Histones; D014157:Transcription Factors