The first chromosome-level genome for a marine mammal as a resource to study ecology and evolution
Fan, Guangyi1,2,3,4; Zhang, Yaolei1,5; Liu, Xiaochuan1; Wang, Jiahao1; Sun, Zeguo1,6; Sun, Shuai1; Zhang, He1; Chen, Jianwei1; Lv, Meiqi1; Han, Kai1; Tan, Xiaoxuan1; Hu, Jie1; Guan, Rui1; Fu, Yuanyuan1; Liu, Shanshan1; Chen, Xi7; Xu, Qiwu1; Qin, Yating1; Liu, Longqi2; Bai, Jie2; Wang, Ou2; Tang, Jingbo2,8; Lu, Haorong6; Shang, Zhouchun2; Wang, Bo6; Hu, Guohai6; Zhao, Xia6,8; Zou, Yan2; Chen, Ao2; Gong, Meihua2; Zhang, Wenwei2; Lee, Simon M. -Y.3,4; Li, Songhai9; Liu, Junnian1; Li, Zhen10; Lu, Yishan11; Sabir, Jamal S. M.12; Sabir, Mumdooh J.12; Khan, Muhummadh12; Hajrah, Nahid H.12; Yin, Ye2,13; Kristiansen, Karsten13; Yang, Huanming2,14; Wang, Jian2,14; Xu, Xun1,2,6; Liu, Xin1,2,6
2019-07-01
Source PublicationMOLECULAR ECOLOGY RESOURCES
ISSN1755-098X
Volume19Issue:4Pages:944-956
Abstract

Marine mammals are important models for studying convergent evolution and aquatic adaption, and thus reference genomes of marine mammals can provide evolutionary insights. Here, we present the first chromosome-level marine mammal genome assembly based on the data generated by the BGISEQ-500 platform, for a stranded female sperm whale (Physeter macrocephalus). Using this reference genome, we performed chromosome evolution analysis of the sperm whale, including constructing ancestral chromosomes, identifying chromosome rearrangement events and comparing with cattle chromosomes, which provides a resource for exploring marine mammal adaptation and speciation. We detected a high proportion of long interspersed nuclear elements and expanded gene families, and contraction of major histocompatibility complex region genes which were specific to sperm whale. Using comparisons with sheep and cattle, we analysed positively selected genes to identify gene pathways that may be related to adaptation to the marine environment. Further, we identified possible convergent evolution in aquatic mammals by testing for positively selected genes across three orders of marine mammals. In addition, we used publicly available resequencing data to confirm a rapid decline in global population size in the Pliocene to Pleistocene transition. This study sheds light on the chromosome evolution and genetic mechanisms underpinning sperm whale adaptations, providing valuable resources for future comparative genomics.

Keywordancestral chromosomes aquatic adaptations genome assembly genomics proteomics major histocompatibility complex mammals molecular evolution sperm whale
DOI10.1111/1755-0998.13003
Indexed BySCI
Funding OrganizationShenzhen Municipal Government of China Peacock Plan ; Guangdong Provincial Key Laboratory of Genome Read and Write
Language英语
Funding ProjectShenzhen Municipal Government of China Peacock Plan[KQTD20150330171505310] ; Guangdong Provincial Key Laboratory of Genome Read and Write[2017B030301011]
WOS KeywordMULTIPLE SEQUENCE ALIGNMENT ; PROTEIN FAMILIES ; LINE-1 ELEMENTS ; DATABASE ; ANNOTATION ; PREDICTION ; SELECTION ; IDENTIFICATION ; DUPLICATION ; RECOGNITION
WOS Research AreaBiochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology
WOS SubjectBiochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
WOS IDWOS:000471830200011
PublisherWILEY
Citation statistics
Cited Times:1[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Version出版稿
Identifierhttp://ir.idsse.ac.cn/handle/183446/6875
Collection深海科学研究部_深海生物学研究室_海洋哺乳动物与海洋生物声学研究组
Corresponding AuthorLiu, Xin
Affiliation1.BGI Shenzhen, BGI Qingdao, Qingdao 266555, Shandong, Peoples R China
2.BGI Shenzhen, Shenzhen, Peoples R China
3.Univ Macau, State Key Lab Qual Res Chinese Med, Macau, Peoples R China
4.Univ Macau, Inst Chinese Med Sci, Macau, Peoples R China
5.Tech Univ Denmark, Dept Biotechnol & Biomed, Lyngby, Denmark
6.BGI Shenzhen, China Natl GeneBank, Shenzhen, Peoples R China
7.Guangdong Pearl River Estuary Chinese White Dolph, Zhu Hai, Guangdong, Peoples R China
8.BGI Shenzhen, MGI, Shenzhen, Peoples R China
9.Chinese Acad Sci, Inst Deep Sea Sci & Engn, Marine Mammal & Marine Bioacoust Lab, Sanya, Peoples R China
10.Hlth & Family Planning Integrated Supervis Enforc, Qingdao, Shandong, Peoples R China
11.Guangdong Ocean Univ, Shenzhen, Peoples R China
12.KAU, Dept Biol Sci, Jeddah, Saudi Arabia
13.Univ Copenhagen, Dept Biol, Copenhagen, Denmark
14.James D Watson Inst Genome Sci, Hangzhou, Zhejiang, Peoples R China
Recommended Citation
GB/T 7714
Fan, Guangyi,Zhang, Yaolei,Liu, Xiaochuan,et al. The first chromosome-level genome for a marine mammal as a resource to study ecology and evolution[J]. MOLECULAR ECOLOGY RESOURCES,2019,19(4):944-956.
APA Fan, Guangyi.,Zhang, Yaolei.,Liu, Xiaochuan.,Wang, Jiahao.,Sun, Zeguo.,...&Liu, Xin.(2019).The first chromosome-level genome for a marine mammal as a resource to study ecology and evolution.MOLECULAR ECOLOGY RESOURCES,19(4),944-956.
MLA Fan, Guangyi,et al."The first chromosome-level genome for a marine mammal as a resource to study ecology and evolution".MOLECULAR ECOLOGY RESOURCES 19.4(2019):944-956.
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