Draft genome sequence of the Tibetan antelope

被引：223

作者：

Ge, Ri-Li ^{[1
,2
]}

Cai, Qingle ^{[3
]}

Shen, Yong-Yi ^{[4
,5
]}

San, A. ^{[3
]}

Ma, Lan ^{[1
,2
]}

Zhang, Yong ^{[3
]}

Yi, Xin ^{[3
]}

Chen, Yan ^{[3
]}

Yang, Lingfeng ^{[3
]}

Huang, Ying ^{[3
]}

He, Rongjun ^{[3
]}

Hui, Yuanyuan ^{[3
]}

Hao, Meirong ^{[3
]}

Li, Yue ^{[3
]}

Wang, Bo ^{[3
]}

Ou, Xiaohua ^{[3
]}

Xu, Jiaohui ^{[3
]}

Zhang, Yongfen ^{[3
]}

Wu, Kui ^{[3
]}

Geng, Chunyu ^{[3
]}

Zhou, Weiping ^{[4
]}

Zhou, Taicheng ^{[4
]}

Irwin, David M. ^{[4
,6
]}

Yang, Yingzhong ^{[1
,2
]}

Ying, Liu ^{[7
]}

Bao, Haihua ^{[7
]}

Kim, Jaebum ^{[8
,9
]}

Larkin, Denis M. ^{[10
]}

Ma, Jian ^{[8
,11
]}

Lewin, Harris A. ^{[12
]}

Xing, Jinchuan ^{[13
]}

Platt, Roy N., II ^{[14
]}

Ray, David A. ^{[14
]}

Auvil, Loretta ^{[15
]}

Capitanu, Boris ^{[15
]}

Zhang, Xiufeng ^{[16
]}

Zhang, Guojie ^{[3
]}

Murphy, Robert W. ^{[17
]}

Wang, Jun ^{[3
,18
,19
]}

Zhang, Ya-Ping ^{[4
]}

Wang, Jian ^{[3
]}

机构：

[1] Qinghai Univ, Minist Chinese Educ, Key Lab High Altitude Med, Xining 810001, Peoples R China

[2] Qinghai Univ, Res Ctr High Altitude Med, Xining 810001, Peoples R China

[3] BGI Shenzhen, Shenzhen 518083, Peoples R China

[4] Chinese Acad Sci, State Key Lab Genet Resources & Evolut, Kunming Inst Zool, Kunming 650223, Peoples R China

[5] Xiamen Univ, Sch Life Sci, State Key Lab Cellular Stress Biol, Xiamen 361005, Peoples R China

[6] Univ Toronto, Dept Lab Med & Pathobiol, Toronto, ON M5S 1A8, Canada

[7] Qinghai Univ, Affiliated Hosp, Xining 810001, Qinghai, Peoples R China

[8] Univ Illinois, Inst Genom Biol, Urbana, IL 61801 USA

[9] Konkuk Univ, Dept Anim Biotechnol, Seoul 143701, South Korea

[10] Aberystwyth Univ, Inst Biol Environm & Rural Sci, Aberystwyth SY23 3DA, Ceredigion, Wales

[11] Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA

[12] Univ Calif Davis, Dept Ecol & Evolut, Davis, CA 95616 USA

[13] Univ Utah, Sch Med, Eccles Inst Human Genet, Salt Lake City, UT 84112 USA

[14] Mississippi State Univ, Dept Biochem Mol Biol Entomol & Plant Pathol, Starkville, MS 39762 USA

[15] Univ Illinois, Natl Ctr Supercomp Applicat, Urbana, IL 61801 USA

[16] Gerumud Hosp, Gerumud 816000, Qinghai, Peoples R China

[17] Royal Ontario Museum, Ctr Biodivers & Conservat Biol, Toronto, ON M5S 2C6, Canada

[18] Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark

[19] King Abdulaziz Univ, Jeddah 21589, Saudi Arabia

来源：

NATURE COMMUNICATIONS | 2013年 / 4卷

基金：

加拿大自然科学与工程研究理事会; 美国国家科学基金会;

关键词：

HIGH-ALTITUDE ADAPTATION; PHYLOGENETIC TREES; ALIGNMENT; EVOLUTION; MECHANISM; DATABASE; CELLS; ACID; DNA;

D O I：

10.1038/ncomms2860

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The Tibetan antelope (Pantholops hodgsonii) is endemic to the extremely inhospitable high-altitude environment of the Qinghai-Tibetan Plateau, a region that has a low partial pressure of oxygen and high ultraviolet radiation. Here we generate a draft genome of this artiodactyl and use it to detect the potential genetic bases of highland adaptation. Compared with other plain-dwelling mammals, the genome of the Tibetan antelope shows signals of adaptive evolution and gene-family expansion in genes associated with energy metabolism and oxygen transmission. Both the highland American pika, and the Tibetan antelope have signals of positive selection for genes involved in DNA repair and the production of ATPase. Genes associated with hypoxia seem to have experienced convergent evolution. Thus, our study suggests that common genetic mechanisms might have been utilized to enable high-altitude adaptation.

引用

页数：7

共 35 条

[1] Recent segmental duplications in the human genome [J].

Bailey, JA ;

Gu, ZP ;

Clark, RA ;

Reinert, K ;

Samonte, RV ;

Schwartz, S ;

Adams, MD ;

Myers, EW ;

Li, PW ;

Eichler, EE .

SCIENCE, 2002, 297 (5583) :1003-1007

[2] DAVID: Database for annotation, visualization, and integrated discovery [J].

Dennis, G ;

Sherman, BT ;

Hosack, DA ;

Yang, J ;

Gao, W ;

Lane, HC ;

Lempicki, RA .

GENOME BIOLOGY, 2003, 4 (09)

[3] Activation of nitric oxide synthase in endothelial cells by Akt-dependent phosphorylation [J].

Dimmeler, S ;

Fleming, I ;

Fisslthaler, B ;

Hermann, C ;

Busse, R ;

Zeiher, AM .

NATURE, 1999, 399 (6736) :601-605

[4] MUSCLE: multiple sequence alignment with high accuracy and high throughput [J].

Edgar, RC .

NUCLEIC ACIDS RESEARCH, 2004, 32 (05) :1792-1797

[5] The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution [J].

Elsik, Christine G. ;

Tellam, Ross L. ;

Worley, Kim C. ;

Gibbs, Richard A. ;

Abatepaulo, Antonio R. R. ;

Abbey, Colette A. ;

Adelson, David L. ;

Aerts, Jan ;

Ahola, Virpi ;

Alexander, Lee ;

Alioto, Tyler ;

Almeida, Iassudara G. ;

Amadio, Ariel F. ;

Anatriello, Elen ;

Antonarakis, Stylianos E. ;

Anzola, Juan M. ;

Astashyn, Alex ;

Bahadue, Suria M. ;

Baldwin, Cynthia L. ;

Barris, Wes ;

Baxter, Rebecca ;

Bell, Stephanie Nicole ;

Bennett, Anna K. ;

Bennett, Gary L. ;

Biase, Fernando H. ;

Boldt, Clayton R. ;

Bradley, Daniel G. ;

Brinkman, Fiona S. L. ;

Brinkmeyer-Langford, Candice L. ;

Brown, Wendy C. ;

Brownstein, Michael J. ;

Buhay, Christian ;

Caetano, Alexandre R. ;

Camara, Francisco ;

Carroll, Jeffrey A. ;

Carvalho, Wanessa A. ;

Casey, Theresa ;

Cervelatti, Elaine P. ;

Chack, Joseph ;

Chacko, Elsa ;

Chandrabose, Mimi M. ;

Chapin, Jennifer E. ;

Chapple, Charles E. ;

Chen, Hsiu-Chuan ;

Chen, Lin ;

Cheng, Ye ;

Cheng, Ze ;

Childers, Christopher P. ;

Chitko-McKown, Carol G. ;

Chiu, Readman .

SCIENCE, 2009, 324 (5926) :522-528

[6] The role of folic acid and Vitamin B12 in genomic stability of human cells [J].

Fenech, M .

MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS, 2001, 475 (1-2) :57-67

[7] Blunted hypoxic pulmonary vasoconstrictive response in the rodent Ochotona curzoniae (pika) at high altitude [J].

Ge, RL ;

Kubo, K ;

Kobayashi, T ;

Sekiguchi, M ;

Honda, T .

AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY, 1998, 274 (05) :H1792-H1799

[8] Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources [J].

Huang, Da Wei ;

Sherman, Brad T. ;

Lempicki, Richard A. .

NATURE PROTOCOLS, 2009, 4 (01) :44-57

[9] ADAPTATION OF BIRD HEMOGLOBINS TO HIGH-ALTITUDES - DEMONSTRATION OF MOLECULAR MECHANISM BY PROTEIN ENGINEERING [J].

JESSEN, TH ;

WEBER, RE ;

FERMI, G ;

TAME, J ;

BRAUNITZER, G .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1991, 88 (15) :6519-6522

[10] Repbase update, a database of eukaryotic repetitive elements [J].

Jurka, J ;

Kapitonov, VV ;

Pavlicek, A ;

Klonowski, P ;

Kohany, O ;

Walichiewicz, J .

CYTOGENETIC AND GENOME RESEARCH, 2005, 110 (1-4) :462-467

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