Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

Lei Chen; Qiang Qiu; Yu Jiang; Kun Wang; Zeshan Lin; Zhipeng Li; Faysal Bibi; Yongzhi Yang; Jinhuan Wang; Wenhui Nie; Weiting Su; Guichun Liu; Qiye Li; Weiwei Fu; Xiangyu Pan; Chang Liu; Jie Yang; Chenzhou Zhang; Yuan Yin; Yu Wang; Yue Zhao; Chen Zhang; Zhongkai Wang; Yanli Qin; Wei Liu; Bao Wang; Yandong Ren; Ru Zhang; Yan Zeng; Rute R. Da Fonseca; Bin Wei; Ran Li; Wenting Wan; Ruoping Zhao; Wenbo Zhu; Yutao Wang; Shengchang Duan; Yun Gao; Yong E. Zhang; Chunyan Chen; Christina Hvilsom; Clinton W. Epps; Leona G. Chemnick; Yang Dong; Siavash Mirarab; Hans Redlef Siegismund; Oliver A. Ryder; M. Thomas P. Gilbert; Harris A. Lewin; Guojie Zhang; Rasmus Heller; Wen Wang

doi:10.1126/science.aav6202

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

Lei Chen, Qiang Qiu, Yu Jiang, Kun Wang, Zeshan Lin, Zhipeng Li, Faysal Bibi, Yongzhi Yang, Jinhuan Wang, Wenhui Nie, Weiting Su, Guichun Liu, Qiye Li, Weiwei Fu, Xiangyu Pan, Chang Liu, Jie Yang, Chenzhou Zhang, Yuan Yin, Yu WangYue Zhao, Chen Zhang, Zhongkai Wang, Yanli Qin, Wei Liu, Bao Wang, Yandong Ren, Ru Zhang, Yan Zeng, Rute R. Da Fonseca, Bin Wei, Ran Li, Wenting Wan, Ruoping Zhao, Wenbo Zhu, Yutao Wang, Shengchang Duan, Yun Gao, Yong E. Zhang, Chunyan Chen, Christina Hvilsom, Clinton W. Epps, Leona G. Chemnick, Yang Dong, Siavash Mirarab, Hans Redlef Siegismund, Oliver A. Ryder, M. Thomas P. Gilbert, Harris A. Lewin, Guojie Zhang, Rasmus Heller, Wen Wang

School of Ecology and Environment

Research output: Contribution to journal › Article › peer-review

300 Scopus citations

Abstract

The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.

Original language	English
Article number	eaav6202
Journal	Science
Volume	364
Issue number	6446
DOIs	https://doi.org/10.1126/science.aav6202
State	Published - 2019

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Chen, L., Qiu, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Bibi, F., Yang, Y., Wang, J., Nie, W., Su, W., Liu, G., Li, Q., Fu, W., Pan, X., Liu, C., Yang, J., Zhang, C., Yin, Y., ... Wang, W. (2019). Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science, 364(6446), Article eaav6202. https://doi.org/10.1126/science.aav6202

@article{d62a0da0623240bebf237e392c387bb5,

title = "Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits",

abstract = "The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.",

author = "Lei Chen and Qiang Qiu and Yu Jiang and Kun Wang and Zeshan Lin and Zhipeng Li and Faysal Bibi and Yongzhi Yang and Jinhuan Wang and Wenhui Nie and Weiting Su and Guichun Liu and Qiye Li and Weiwei Fu and Xiangyu Pan and Chang Liu and Jie Yang and Chenzhou Zhang and Yuan Yin and Yu Wang and Yue Zhao and Chen Zhang and Zhongkai Wang and Yanli Qin and Wei Liu and Bao Wang and Yandong Ren and Ru Zhang and Yan Zeng and {Da Fonseca}, {Rute R.} and Bin Wei and Ran Li and Wenting Wan and Ruoping Zhao and Wenbo Zhu and Yutao Wang and Shengchang Duan and Yun Gao and Zhang, {Yong E.} and Chunyan Chen and Christina Hvilsom and Epps, {Clinton W.} and Chemnick, {Leona G.} and Yang Dong and Siavash Mirarab and Siegismund, {Hans Redlef} and Ryder, {Oliver A.} and Gilbert, {M. Thomas P.} and Lewin, {Harris A.} and Guojie Zhang and Rasmus Heller and Wen Wang",

year = "2019",

doi = "10.1126/science.aav6202",

language = "英语",

volume = "364",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "6446",

}

Chen, L, Qiu, Q, Jiang, Y, Wang, K, Lin, Z, Li, Z, Bibi, F, Yang, Y, Wang, J, Nie, W, Su, W, Liu, G, Li, Q, Fu, W, Pan, X, Liu, C, Yang, J, Zhang, C, Yin, Y, Wang, Y, Zhao, Y, Zhang, C, Wang, Z, Qin, Y, Liu, W, Wang, B, Ren, Y, Zhang, R, Zeng, Y, Da Fonseca, RR, Wei, B, Li, R, Wan, W, Zhao, R, Zhu, W, Wang, Y, Duan, S, Gao, Y, Zhang, YE, Chen, C, Hvilsom, C, Epps, CW, Chemnick, LG, Dong, Y, Mirarab, S, Siegismund, HR, Ryder, OA, Gilbert, MTP, Lewin, HA, Zhang, G, Heller, R & Wang, W 2019, 'Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits', Science, vol. 364, no. 6446, eaav6202. https://doi.org/10.1126/science.aav6202

TY - JOUR

T1 - Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

AU - Chen, Lei

AU - Qiu, Qiang

AU - Jiang, Yu

AU - Wang, Kun

AU - Lin, Zeshan

AU - Li, Zhipeng

AU - Bibi, Faysal

AU - Yang, Yongzhi

AU - Wang, Jinhuan

AU - Nie, Wenhui

AU - Su, Weiting

AU - Liu, Guichun

AU - Li, Qiye

AU - Fu, Weiwei

AU - Pan, Xiangyu

AU - Liu, Chang

AU - Yang, Jie

AU - Zhang, Chenzhou

AU - Yin, Yuan

AU - Wang, Yu

AU - Zhao, Yue

AU - Zhang, Chen

AU - Wang, Zhongkai

AU - Qin, Yanli

AU - Liu, Wei

AU - Wang, Bao

AU - Ren, Yandong

AU - Zhang, Ru

AU - Zeng, Yan

AU - Da Fonseca, Rute R.

AU - Wei, Bin

AU - Li, Ran

AU - Wan, Wenting

AU - Zhao, Ruoping

AU - Zhu, Wenbo

AU - Wang, Yutao

AU - Duan, Shengchang

AU - Gao, Yun

AU - Zhang, Yong E.

AU - Chen, Chunyan

AU - Hvilsom, Christina

AU - Epps, Clinton W.

AU - Chemnick, Leona G.

AU - Dong, Yang

AU - Mirarab, Siavash

AU - Siegismund, Hans Redlef

AU - Ryder, Oliver A.

AU - Gilbert, M. Thomas P.

AU - Lewin, Harris A.

AU - Zhang, Guojie

AU - Heller, Rasmus

AU - Wang, Wen

PY - 2019

Y1 - 2019

N2 - The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.

AB - The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.

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U2 - 10.1126/science.aav6202

DO - 10.1126/science.aav6202

M3 - 文章

C2 - 31221828

AN - SCOPUS:85068491565

SN - 0036-8075

VL - 364

JO - Science

JF - Science

IS - 6446

M1 - eaav6202

ER -

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

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