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

Zhaoqun Liu; Yuting Huang; Hao Chen; Chang Liu; Minxiao Wang; Chao Bian; Lingling Wang; Linsheng Song

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

BMC Genomics. 2023 Nov 10;24(1):679. doi: 10.1186/s12864-023-09760-0.

Authors

Zhaoqun Liu^#^{1

2

3

4}, Yuting Huang^#^{5

6}, Hao Chen^#⁷, Chang Liu^{1

2

3

4}, Minxiao Wang⁷, Chao Bian⁸, Lingling Wang^{9

10

11

12}, Linsheng Song^{13

14

15

16}

Affiliations

¹ Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China.
² Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
³ Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
⁴ Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
⁵ Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
⁶ College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
⁷ Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
⁸ Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China. bianchao@genomics.cn.
⁹ Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China. wanglingling@dlou.edu.cn.
¹⁰ Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China. wanglingling@dlou.edu.cn.
¹¹ Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China. wanglingling@dlou.edu.cn.
¹² Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China. wanglingling@dlou.edu.cn.
¹³ Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China. lshsong@dlou.edu.cn.
¹⁴ Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China. lshsong@dlou.edu.cn.
¹⁵ Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China. lshsong@dlou.edu.cn.
¹⁶ Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China. lshsong@dlou.edu.cn.

^# Contributed equally.

Abstract

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.

Keywords: Chromosome-level genome; Cold seep; Glutamate regulation; H2S detoxification; Olfactory/chemosensory; Phymorhynchus buccinoides.

MeSH terms

Animals
Chromosomes
Ecosystem*
Hypoxia
Phylogeny
Snails* / genetics
Sulfites

Substances

Sulfites

Abstract

MeSH terms

Substances

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