(Front row, second from left) HKUST Professor Qian Peiyuan; (front row, third from left) HKBU Dr Qiu Jianwen; (back row) HKUST Dr Sun Jin and their team: (front row, left) HKBU Mu Huawei; (front row, right) HKUST Lan Yi; (back row from left) HKBU Zhang Yanjie and Xu Ting.


(前排左二)科大錢培元教授、(前排左三)浸大邱建文博士、(後排右一)科大孫進博士與他們的團隊﹕ (前排左) 浸大母華偉、(前排右)科大蘭奕、(後排左起)浸大張燕傑和徐婷。

(Left) Shell of the deep-sea mussel “Bathymodiolus platifrons” and (right) shallow-water mussel “Modiolus philippinarum”.


(左)深海貽貝Bathymodiolus platifrons 和 (右) 淺海貽貝 Modiolus philippinarum。

Deep-sea mussels viewed from Jiaolong’s exploration of a methane seep in the South China Sea.


從蛟龍號觀察窗看到的南海冷泉區深海貽貝群落。

Date: 23 May 2017 (Tuesday)

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Research jointly led by HKBU and HKUST decoding the first deep-sea mussel genome published in “Nature Ecology & Evolution”

浸大與科大共同主導合作研究 首次破譯深海青口的基因組 研究刊於《自然──生態學與進化》

A joint research led by Hong Kong Baptist University and the Hong Kong University of Science and Technology (HKUST) has assembled the 1.64 gigabytes genome of a deep-sea mussel, which is roughly equivalent to 50% of the size of human genome. This is the first decoded genome among all deep-sea macrobenthic animals, revealing a complete set of DNA. The discovery gives wider insights into future research on the mechanisms of symbiosis in other marine organisms such as giant tubeworms and giant clams.

The research team, led by HKUST’s Chair Professor of Division of Life Science Professor Qian Peiyuan and HKBU’s Associate Professor of Biology Dr Qiu Jianwen, has published the research findings in prestigious international academic journal Nature Ecology & Evolution in early April.

The team used a specimen collected in 2013 during Dr Qiu’s participation in China’s manned submersible Jiaolong’s expedition of the South China Sea for the research. Deep-sea organisms including mussels thrive in the extreme environments of hydrothermal vents and cold seeps which are characterised by high hydrostatic pressure, lack of photosynthesis-derived food, variable temperatures and high concentrations of toxic substances. Despite their ability to survive under stressful conditions, a lack of genomic resources has hindered the understanding of their molecular mechanisms of adaptation.

The study sequenced the genome of the deep-sea mussel Bathymodiolus platifrons as well as its shallow-water relative Modiolus philippinarum collected from a local softshore in Tingkok for comparison of genomic features. Through phylogenetic analysis, the research team discovered that modern deep-sea mussels are the descendants of shallow-water mussels, and their ancestors migrated to the deep sea approximately 110 million years ago, providing evidence to support a hypothesis that their ancestors survived through an extinction event during the global anoxia period associated with the Palaeocene–Eocene Thermal Maximum which occurred around 57 million years ago.

Genome comparison revealed that the great expansion of several gene families in the deep-sea mussel may be related to its adaptation to the deep sea. For instance, the expansion of the “heat shock protein 70 family”, a family of proteins that are produced by a cell in response to exposure to stressful conditions, may help the mussel stabilise protein structures. The expansion of the “ABC transporters family”, the unit of the transport system, may enhance the mussel’s ability to move toxic chemicals outside its gill epithelial cells.

The expansion of gene families related to immune recognition, endocytosis and caspase-mediated apoptosis indicates the mussel’s adaptation to the presence of chemoautotrophic endosymbionts in its gills. An additional proteomic analysis of the deep-sea mussel gill reveals nutritional and energetic dependency of the mussel on its methanotrophic symbionts.

Professor Qian said, “The study has provided genomic resources for understanding how the deep-sea mussel has adapted to the abiotic stresses and lack of photosynthesis-derived food in the deep-sea chemosynthetic environment. The general mechanisms of symbiosis revealed in the study are of relevance to other symbiotic organisms such as deep-sea tubeworms and giant clams.”

Dr Qiu said, “The genomic resources will facilitate various studies, including genetic connectivity among deep-sea populations, which is relevant to the establishment of deep-sea marine reserves.”

The study was supported by the Strategic Priority Research Program of Chinese Academy of Sciences of China, HKUST, HKBU, Scientific and Technical Innovation Council of Shenzhen, and Guangdong Natural Science Foundation. Other main collaborators are HKUST post-doctoral fellows Dr Sun Jin and Dr Zhang Weipeng, Dr Jerome Hui of The Chinese University of Hong Kong and his team members Nong Wenyan and Fiona Cheung, Dr Li Runsheng of HKBU, Dr Zhang Yu of Shenzhen University, Dr Zhang Yang of The South China Sea Institute of Oceanography, and Christopher Fields of University of Illinois at Urbana-Champaign.

Please click here to view the paper online.

Click here to read a commentary by two independent researchers highlighting the results and significance of this research.

一項由香港浸會大學和香港科技大學共同主導的合作研究組裝和注釋了總長達16.4 億鹼基對的深海貽貝(俗稱青口)基因組(其大小約為人類基因組的一半)。這是首次發表的深海海底大生物的基因組,結果將有助瞭解其他深海生物如管蟲、蛤對深海極端環境的適應機制。

科大生命科學部講座教授錢培元教授及浸大生物系副教授邱建文博士的研究結果已於上月初在國際權威學術期刊《自然──生態學與進化》中刊登。

用於是項研究的深海貽貝是邱建文博士在2013年參與內地載人潛水器「蛟龍號」在中國南海深海冷泉區考察時取得的生物樣本。深海生物包括貽貝廣泛分佈在海底熱泉和冷泉區,該處水壓高、缺乏由光合作用產生的食物、溫度變化大,並有大量的有毒物質,是非常極端的生存環境。由於缺乏深海生物的基因組資料,很難瞭解牠們在極端的環境下的生存和適應機制。

研究比較了深海貽貝Bathymodiolus platifrons和從香港汀角區採集的淺水貽貝Modiolus philippinarum的基因特徵。通過進化分析,團隊發現現代的深海貽貝是淺海貽貝的後裔,牠們的祖先約於1億1千萬年前移居到深海,成功度過了約5,700萬年前因全球溫度上升而造成的海洋底部缺氧導致的大滅絕事件。

基因組比較顯示,深海貽貝基因家族有明顯的擴張,而這些擴張可能與其對深海環境的適應有關。例如,「熱休克蛋白70家族」有穩定蛋白結構的作用,它們的擴張有助於修補深海生物在深海極端環境下蛋白質結構的損傷。另外,負責傳送物質的「ABC 運輸蛋白家族」的擴張,有利於深海貽貝透過鰓表皮細胞排出有毒物質。

負責免疫識別、內吞作用和細胞凋亡的基因家族的分析顯示,深海貽貝有維持鰓內化學自養共生細菌的能力。研究團隊還通過對貽貝鰓進行蛋白質組學研究,證明深海貽貝依靠甲烷營養共生細菌所合成養分,得以在沒有光合作用產物的環境中大量繁衍。

錢培元教授說:「對深海貽貝共生生存機制的分析有助將來對其他海洋生物如管蟲、蛤甚至珊瑚的共生機制的研究。」

邱建文博士說:「基因組資源可促進深海生物的基因聯繫的研究,有助於在資源豐富地區設立深海海洋保護區。」

是項研究由中國科學院先導專項、香港科技大學、浸會大學、深圳市科技創新委員會和廣東省自然科學基金支持。其他主要合作者包括科大博士後研究員孫進博士以及張偉鵬博士、香港中文大學許浩霖博士以及其團隊成員農文燕和張嘉敏、浸會大學李潤生博士、深圳大學張煜博士、中國科學院南海海洋研究所張揚博士,以及美國伊利諾大學厄巴納-香檳分校Christopher Fields博士。

按此瀏覽有關研究。

《自然──生態學與進化》亦發表了一篇評論文章介紹是項研究的結果與科學意義。