The first chromosome-level genome for a marine mammal as a resource to study ecology and evolution
文献类型:期刊论文
作者 | Liu, Xin9,13,14; Xu, Xun9,13,14; Wang, Jian1,13; Yang, Huanming1,13; Kristiansen, Karsten2; Yin, Ye2,13; Hajrah, Nahid H.3; Khan, Muhummadh3; Sabir, Mumdooh J.3; Sabir, Jamal S. M.3 |
刊名 | MOLECULAR ECOLOGY RESOURCES |
出版日期 | 2019-07-01 |
卷号 | 19期号:4页码:944-956 |
ISSN号 | 1755-098X |
关键词 | ancestral chromosomes aquatic adaptations genome assembly genomics proteomics major histocompatibility complex mammals molecular evolution sperm whale |
DOI | 10.1111/1755-0998.13003 |
英文摘要 | 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. |
WOS关键词 | MULTIPLE SEQUENCE ALIGNMENT ; PROTEIN FAMILIES ; LINE-1 ELEMENTS ; DATABASE ; ANNOTATION ; PREDICTION ; SELECTION ; IDENTIFICATION ; DUPLICATION ; RECOGNITION |
资助项目 | Shenzhen Municipal Government of China Peacock Plan[KQTD20150330171505310] ; Guangdong Provincial Key Laboratory of Genome Read and Write[2017B030301011] |
WOS研究方向 | Biochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology |
语种 | 英语 |
出版者 | WILEY |
WOS记录号 | WOS:000471830200011 |
资助机构 | Shenzhen Municipal Government of China Peacock Plan ; Guangdong Provincial Key Laboratory of Genome Read and Write |
版本 | 出版稿 |
源URL | [http://ir.idsse.ac.cn/handle/183446/6874] |
专题 | 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 |
通讯作者 | Liu, Xin |
作者单位 | 1.James D Watson Inst Genome Sci, Hangzhou, Zhejiang, Peoples R China 2.Univ Copenhagen, Dept Biol, Copenhagen, Denmark 3.KAU, Dept Biol Sci, Jeddah, Saudi Arabia 4.Guangdong Ocean Univ, Shenzhen, Peoples R China 5.Hlth & Family Planning Integrated Supervis Enforc, Qingdao, Shandong, Peoples R China 6.Chinese Acad Sci, Inst Deep Sea Sci & Engn, Marine Mammal & Marine Bioacoust Lab, Sanya, Peoples R China 7.BGI Shenzhen, MGI, Shenzhen, Peoples R China 8.Guangdong Pearl River Estuary Chinese White Dolph, Zhu Hai, Guangdong, Peoples R China 9.BGI Shenzhen, China Natl GeneBank, Shenzhen, Peoples R China 10.Tech Univ Denmark, Dept Biotechnol & Biomed, Lyngby, Denmark |
推荐引用方式 GB/T 7714 | Liu, Xin,Xu, Xun,Wang, Jian,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 | Liu, Xin.,Xu, Xun.,Wang, Jian.,Yang, Huanming.,Kristiansen, Karsten.,...&Fan, Guangyi.(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 | Liu, Xin,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. |
入库方式: OAI收割
来源:深海科学与工程研究所
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