Chromosome-level genome assembly of the deep-sea snail Phymorhynchus buccinoides provides insights into the adaptation to the cold seep habitat

doi:10.1186/s12864-023-09760-0

	Chromosome-level genome assembly of the deep-sea snail Phymorhynchus buccinoides provides insights into the adaptation to the cold seep habitat
	Liu, Zhaoqun1,2,3,4 ; Huang, Yuting 5,6; Chen, Hao7,8 ; Liu, Chang 1,2,3,4; Wang, Minxiao 7,8; Bian, Chao 5; Wang, Lingling 1,2,3,4; Song, Linsheng 1,2,3,4
	2023-11-10
发表期刊	BMC GENOMICS
ISSN	1471-2164
卷号	24 期号:1 页码:16
通讯作者	Bian, Chao(bianchao@genomics.cn) ; Wang, Lingling(wanglingling@dlou.edu.cn) ; Song, Linsheng(lshsong@dlou.edu.cn)
摘要	Background The deep-sea snail Phymorhynchus buccinoides belongs to the genus Phymorhynchus (Neogastropoda: Raphitomidae), and it is a dominant specie in the cold seep habitat. As the environment of the cold seep is characterized by darkness, hypoxia and high concentrations of toxic substances such as hydrogen sulfide (H2S), exploration of the diverse fauna living around cold seeps will help to uncover the adaptive mechanisms to this unique habitat. In the present study, a chromosome-level genome of P. buccinoides was constructed and a series of genomic and transcriptomic analyses were conducted to explore its molecular adaptation mechanisms to the cold seep environments.Results The assembled genome size of the P. buccinoides was approximately 2.1 Gb, which is larger than most of the reported snail genomes, possibly due to the high proportion of repetitive elements. About 92.0% of the assembled base pairs of contigs were anchored to 34 pseudo-chromosomes with a scaffold N50 size of 60.0 Mb. Compared with relative specie in the shallow water, the glutamate regulative and related genes were expanded in P. buccinoides, which contributes to the acclimation to hypoxia and coldness. Besides, the relatively high mRNA expression levels of the olfactory/chemosensory genes in osphradium indicate that P. buccinoides might have evolved a highly developed and sensitive olfactory organ for its orientation and predation. Moreover, the genome and transcriptome analyses demonstrate that P. buccinoides has evolved a sulfite-tolerance mechanism by performing H2S detoxification. Many genes involved in H2S detoxification were highly expressed in ctenidium and hepatopancreas, suggesting that these tissues might be critical for H2S detoxification and sulfite tolerance.Conclusions In summary, our report of this chromosome-level deep-sea snail genome provides a comprehensive genomic basis for the understanding of the adaptation strategy of P. buccinoides to the extreme environment at the deep-sea cold seeps.
关键词	Cold seep Phymorhynchus buccinoides Chromosome-level genome Glutamate regulation Olfactory/chemosensory H2S detoxification
DOI	10.1186/s12864-023-09760-0
收录类别	SCI
语种	英语
资助项目	We are grateful to all the laboratory members for their technical advice and helpful discussions.
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:001103582400003
出版者	BMC
WOS关键词	POMPILIUS L. CEPHALOPODA ; GAMMA-AMINOBUTYRIC-ACID ; SULFIDE DETOXIFICATION ; ANAEROBIC OXIDATION ; HYDROTHERMAL-VENT ; PROTEIN ; SEQUENCE ; GLUTAMATE ; TOLERANCE ; STRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/184062
专题	海洋生态与环境科学重点实验室
通讯作者	Bian, Chao; Wang, Lingling; Song, Linsheng
作者单位	1.Dalian Ocean Univ, Liaoning Key Lab Marine Anim Immunol, Dalian 116023, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Funct Lab Marine Fisheries Sci & Food Prod Proc, Qingdao 266235, Peoples R China 3.Dalian Ocean Univ, Liaoning Key Lab Marine Anim Immunol & Dis Control, Dalian 116023, Peoples R China 4.Dalian Ocean Univ, Dalian Key Lab Aquat Anim Dis Prevent & Control, Dalian 116023, Peoples R China 5.Shenzhen Univ, Coll Life Sci & Oceanog, Lab Aquat Genom, Shenzhen 518060, Peoples R China 6.Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China 7.Chinese Acad Sci, Ctr Deep Sea Res, Qingdao, Peoples R China 8.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, Qingdao 266071, Peoples R China
推荐引用方式 GB/T 7714	Liu, Zhaoqun,Huang, Yuting,Chen, Hao,et al. Chromosome-level genome assembly of the deep-sea snail Phymorhynchus buccinoides provides insights into the adaptation to the cold seep habitat[J]. BMC GENOMICS,2023,24(1):16.
APA	Liu, Zhaoqun.,Huang, Yuting.,Chen, Hao.,Liu, Chang.,Wang, Minxiao.,...&Song, Linsheng.(2023).Chromosome-level genome assembly of the deep-sea snail Phymorhynchus buccinoides provides insights into the adaptation to the cold seep habitat.BMC GENOMICS,24(1),16.
MLA	Liu, Zhaoqun,et al."Chromosome-level genome assembly of the deep-sea snail Phymorhynchus buccinoides provides insights into the adaptation to the cold seep habitat".BMC GENOMICS 24.1(2023):16.

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