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De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps
Liu, Ruoyu1,2; Wang, Kun3; Liu, Jun1; Xu, Wenjie3; Zhou, Yang1,2; Zhu, Chenglong3; Wu, Baosheng1,2; Li, Yongxin3; Wang, Wen3; He, Shunping1,4; Feng, Chenguang3; Zhang, Haibin1
2020-06-01
Source PublicationGENOME BIOLOGY AND EVOLUTION
ISSN1759-6653
Volume12Issue:6Pages:905-910
AbstractCold seeps, characterized by the methane, hydrogen sulfide, and other hydrocarbon chemicals, foster one of the most widespread chemosynthetic ecosystems in deep sea that are densely populated by specialized benthos. However, scarce genomic resources severely limit our knowledge about the origin and adaptation of life in this unique ecosystem. Here, we present a genome of a deepsea limpet Bathyacmaea lactea, a common species associated with the dominant mussel beds in cold seeps. We yielded 54.6 gigabases (Gb) of Nanopore reads and 77.9-Gb BGI-seq raw reads, respectively. Assembly harvested a 754.3-Mb genome for B. lactea, with 3,720 contigs and a contig N50 of 1.57 Mb, covering 94.3% of metazoan Benchmarking Universal Single-Copy Orthologs. In total, 23,574 protein-coding genes and 463.4 Mb of repetitive elements were identified. We analyzed the phylogenetic position, substitution rate, demographic history, and TE activity of B. lactea. We also identified 80 expanded gene families and 87 rapidly evolving Gene Ontology categories in the B. lactea genome. Many of these genes were associated with heterocyclic compound metabolism, membrane-bounded organelle, metal ion binding, and nitrogen and phosphorus metabolism. The high-quality assembly and in-depth characterization suggest the B. lactea genome will serve as an essential resource for understanding the origin and adaptation of life in the cold seeps.
Keyworddeep-sea adaptation cold seeps limpet Bathyacmaea mollusk genome Nanopore
DOI10.1093/gbe/evaa100
Indexed BySCI ; SCI
Funding OrganizationNational Key Research and Development Program of China ; Major scientific and technological projects of Hainan Province ; 1000 Talent Project of Shaanxi Province ; Research Funds for Interdisciplinary subject, NWPU
Language英语
Funding ProjectNational Key Research and Development Program of China[2016YFC0304905] ; National Key Research and Development Program of China[2017YFC0306604] ; Major scientific and technological projects of Hainan Province[ZDKJ2019011] ; 1000 Talent Project of Shaanxi Province ; Research Funds for Interdisciplinary subject, NWPU[19SH030408]
WOS KeywordPHYLOGENETIC ANALYSIS ; READ ALIGNMENT ; EVOLUTION ; IMPACT ; TOOL
WOS Research AreaEvolutionary Biology ; Genetics & Heredity
WOS SubjectEvolutionary Biology ; Genetics & Heredity
WOS IDWOS:000552380600014
PublisherOXFORD UNIV PRESS
Citation statistics
Document Type期刊论文
Identifierhttp://ir.idsse.ac.cn/handle/183446/7831
Collection研究生部
深海科学研究部_深海生物学研究室_海洋生物生态与进化研究组
Corresponding AuthorFeng, Chenguang; Zhang, Haibin
Affiliation1.Chinese Acad Sci, Inst Deep Sea Sci & Engn, Sanya, Peoples R China
2.Univ Chinese Acad Sci, Beijing, Peoples R China
3.Northwestern Polytech Univ, Ctr Ecol & Environm Sci, Xian, Peoples R China
4.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China
First Author AffilicationInstitute of Deep-sea Science and Engineering,CAS
Corresponding Author AffilicationInstitute of Deep-sea Science and Engineering,CAS
Recommended Citation
GB/T 7714
Liu, Ruoyu,Wang, Kun,Liu, Jun,et al. De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps[J]. GENOME BIOLOGY AND EVOLUTION,2020,12(6):905-910.
APA Liu, Ruoyu.,Wang, Kun.,Liu, Jun.,Xu, Wenjie.,Zhou, Yang.,...&Zhang, Haibin.(2020).De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps.GENOME BIOLOGY AND EVOLUTION,12(6),905-910.
MLA Liu, Ruoyu,et al."De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps".GENOME BIOLOGY AND EVOLUTION 12.6(2020):905-910.
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