The amphipod genome reveals population dynamics and adaptations to hadal environment

Haibin Zhang; Shuai Sun; Jun Liu; Qunfei Guo; Liang Meng; Jianwei Chen; Xueyan Xiang; Yang Zhou; Nannan Zhang; Helu Liu; Yalin Liu; Guoyong Yan; Qianyue Ji; Lisheng He; Shanya Cai; Chongyang Cai; Xin Huang; Shiyu Xu; Yunlu Xiao; Yangrui Zhang; Kun Wang; Yujing Liu; Haixin Chen; Zhen Yue; Shunping He; Jian Wang; Huanming Yang; Xin Liu; Inge Seim; Ying Gu; Qiye Li; Guojie Zhang; Simon Ming Yuen Lee; Karsten Kristiansen; Xun Xu; Shanshan Liu; Guangyi Fan

doi:10.1016/j.cell.2025.01.030

The amphipod genome reveals population dynamics and adaptations to hadal environment

Haibin Zhang^*, Shuai Sun, Jun Liu, Qunfei Guo, Liang Meng, Jianwei Chen, Xueyan Xiang, Yang Zhou, Nannan Zhang, Helu Liu, Yalin Liu, Guoyong Yan, Qianyue Ji, Lisheng He, Shanya Cai, Chongyang Cai, Xin Huang, Shiyu Xu, Yunlu Xiao, Yangrui ZhangKun Wang, Yujing Liu, Haixin Chen, Zhen Yue, Shunping He, Jian Wang, Huanming Yang, Xin Liu, Inge Seim, Ying Gu, Qiye Li, Guojie Zhang, Simon Ming Yuen Lee, Karsten Kristiansen, Xun Xu, Shanshan Liu, Guangyi Fan

^*Corresponding author af dette arbejde

Genomforskning og Molekylær Biomedicin

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

2 Citationer (Scopus)

Abstract

The amphipod Hirondellea gigas is a dominant species inhabiting the deepest part of the ocean (∼6,800–11,000 m), but little is known about its genetic adaptation and population dynamics. Here, we present a chromosome-level genome of H. gigas, characterized by a large genome size of 13.92 Gb. Whole-genome sequencing of 510 individuals from the Mariana Trench indicates no population differentiation across depths, suggesting its capacity to tolerate hydrostatic pressure across wide ranges. H. gigas in the West Philippine Basin is genetically divergent from the Mariana and Yap Trenches, suggesting genetic isolation attributed to the geographic separation of hadal features. A drastic reduction in effective population size potentially reflects glacial-interglacial changes. By integrating multi-omics analysis, we propose host-symbiotic microbial interactions may be crucial in the adaptation of H. gigas to the extremely high-pressure and food-limited environment. Our findings provide clues for adaptation to the hadal zone and population genetics.

Originalsprog	Engelsk
Tidsskrift	Cell
Vol/bind	188
Udgave nummer	5
Sider (fra-til)	1378-1392.e18
Antal sider	15
ISSN	0092-8674
DOI	https://doi.org/10.1016/j.cell.2025.01.030
Status	Udgivet - 2025

Bibliografisk note

Funding Information:
We are grateful to the captain, crew, scientific staff of the R/V Tansuo 1, and pilots of the manned submersible Fendouzhe. This study was supported by the Global Trench Exploration and Diving Program (Global TREnD), the National Key Research and Development Program of China (2022YFC2805400, 2023YFC2809300, 2016YFC0304905, and 2018YFC0309804), the Major Scientific and Technological Projects of Hainan Province (ZDKJ2019011), the Strategic Priority Research Program of the Chinese Academy of Sciences (CAS) (XDB06010104), Hainan Yazhou Bay Seed Lab (JBGS B23YQ2003), the Major Science and Technology Research Project of Sanya Yazhou Bay Science and Technology City (SKJC-2021-01-001), and the Joint Funds of the National Natural Science Foundation of China (U2106228). We would like to thank the Institutional Center for Shared Technologies and Facilities of IDSSE, Chinese Academy of Sciences, for the use of their computing resources. We thank Jun Chen and Jun Li from the Institute of Deep-sea Science and Engineering, CAS, for their help in sample collection and Shuchao Pang for sample preparation. We are grateful to Professor Xiang Xiao from Shanghai Jiao Tong University for providing insightful suggestions on the manuscript. We also appreciate the technical support from the China National GeneBank for the library construction and sequencing in whole-genome short reads.

Publisher Copyright:
© 2025 Elsevier Inc.

Adgang til dokumentet

10.1016/j.cell.2025.01.030

Citationsformater

Zhang, H, Sun, S, Liu, J, Guo, Q, Meng, L, Chen, J, Xiang, X, Zhou, Y, Zhang, N, Liu, H, Liu, Y, Yan, G, Ji, Q, He, L, Cai, S, Cai, C, Huang, X, Xu, S, Xiao, Y, Zhang, Y, Wang, K, Liu, Y, Chen, H, Yue, Z, He, S, Wang, J, Yang, H, Liu, X, Seim, I, Gu, Y, Li, Q, Zhang, G, Lee, SMY, Kristiansen, K, Xu, X, Liu, S & Fan, G 2025, 'The amphipod genome reveals population dynamics and adaptations to hadal environment', Cell, bind 188, nr. 5, s. 1378-1392.e18. https://doi.org/10.1016/j.cell.2025.01.030

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abstract = "The amphipod Hirondellea gigas is a dominant species inhabiting the deepest part of the ocean (∼6,800–11,000 m), but little is known about its genetic adaptation and population dynamics. Here, we present a chromosome-level genome of H. gigas, characterized by a large genome size of 13.92 Gb. Whole-genome sequencing of 510 individuals from the Mariana Trench indicates no population differentiation across depths, suggesting its capacity to tolerate hydrostatic pressure across wide ranges. H. gigas in the West Philippine Basin is genetically divergent from the Mariana and Yap Trenches, suggesting genetic isolation attributed to the geographic separation of hadal features. A drastic reduction in effective population size potentially reflects glacial-interglacial changes. By integrating multi-omics analysis, we propose host-symbiotic microbial interactions may be crucial in the adaptation of H. gigas to the extremely high-pressure and food-limited environment. Our findings provide clues for adaptation to the hadal zone and population genetics.",

keywords = "amphipod genome, hadal adaptation, high pressure, Hirondellea gigas, host-symbiotic interactions, multi-omics, population structure and differentiation, Psychromonas, trimethylamine N-oxide, whole-genome sequencing",

author = "Haibin Zhang and Shuai Sun and Jun Liu and Qunfei Guo and Liang Meng and Jianwei Chen and Xueyan Xiang and Yang Zhou and Nannan Zhang and Helu Liu and Yalin Liu and Guoyong Yan and Qianyue Ji and Lisheng He and Shanya Cai and Chongyang Cai and Xin Huang and Shiyu Xu and Yunlu Xiao and Yangrui Zhang and Kun Wang and Yujing Liu and Haixin Chen and Zhen Yue and Shunping He and Jian Wang and Huanming Yang and Xin Liu and Inge Seim and Ying Gu and Qiye Li and Guojie Zhang and Lee, {Simon Ming Yuen} and Karsten Kristiansen and Xun Xu and Shanshan Liu and Guangyi Fan",

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year = "2025",

doi = "10.1016/j.cell.2025.01.030",

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AU - Chen, Jianwei

AU - Xiang, Xueyan

AU - Zhou, Yang

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AU - Liu, Helu

AU - Liu, Yalin

AU - Yan, Guoyong

AU - Ji, Qianyue

AU - He, Lisheng

AU - Cai, Shanya

AU - Cai, Chongyang

AU - Huang, Xin

AU - Xu, Shiyu

AU - Xiao, Yunlu

AU - Zhang, Yangrui

AU - Wang, Kun

AU - Liu, Yujing

AU - Chen, Haixin

AU - Yue, Zhen

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AU - Wang, Jian

AU - Yang, Huanming

AU - Liu, Xin

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AU - Gu, Ying

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N2 - The amphipod Hirondellea gigas is a dominant species inhabiting the deepest part of the ocean (∼6,800–11,000 m), but little is known about its genetic adaptation and population dynamics. Here, we present a chromosome-level genome of H. gigas, characterized by a large genome size of 13.92 Gb. Whole-genome sequencing of 510 individuals from the Mariana Trench indicates no population differentiation across depths, suggesting its capacity to tolerate hydrostatic pressure across wide ranges. H. gigas in the West Philippine Basin is genetically divergent from the Mariana and Yap Trenches, suggesting genetic isolation attributed to the geographic separation of hadal features. A drastic reduction in effective population size potentially reflects glacial-interglacial changes. By integrating multi-omics analysis, we propose host-symbiotic microbial interactions may be crucial in the adaptation of H. gigas to the extremely high-pressure and food-limited environment. Our findings provide clues for adaptation to the hadal zone and population genetics.

AB - The amphipod Hirondellea gigas is a dominant species inhabiting the deepest part of the ocean (∼6,800–11,000 m), but little is known about its genetic adaptation and population dynamics. Here, we present a chromosome-level genome of H. gigas, characterized by a large genome size of 13.92 Gb. Whole-genome sequencing of 510 individuals from the Mariana Trench indicates no population differentiation across depths, suggesting its capacity to tolerate hydrostatic pressure across wide ranges. H. gigas in the West Philippine Basin is genetically divergent from the Mariana and Yap Trenches, suggesting genetic isolation attributed to the geographic separation of hadal features. A drastic reduction in effective population size potentially reflects glacial-interglacial changes. By integrating multi-omics analysis, we propose host-symbiotic microbial interactions may be crucial in the adaptation of H. gigas to the extremely high-pressure and food-limited environment. Our findings provide clues for adaptation to the hadal zone and population genetics.

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KW - population structure and differentiation

KW - Psychromonas

KW - trimethylamine N-oxide

KW - whole-genome sequencing

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