Some sea cucumbers like it hot
The genome of a sea cucumber, collected at a depth of 2400 m during a submarine trip to a hydrothermal vent, sheds light on genetic features that help marine animals to survive in extreme conditions
IMAGE:
THE SAMPLING SITE FOR THE SEA CUCUMBER WAS AT THE KAIREI VENT FIELD AT THE BOTTOM OF INDIAN OCEAN. THE INSET SHOWS A PHOTO OF SAMPLING AT A DEPTH OF 2,428 M OF THE SEA CUCUMBER CHIRIDOTA HEHEVA USED FOR GENOME SEQUENCING.
view moreCREDIT: PU Y, ZHOU Y, LIU J, ZHANG H. A HIGH-QUALITY CHROMOSOMAL GENOME ASSEMBLY OF THE SEA CUCUMBER CHIRIDOTA HEHEVA AND ITS HYDROTHERMAL ADAPTATION. GIGASCIENCE 2023 GIAD107 HTTPS://DOI.ORG/10.1093/GIGASCIENCE/GIAD107
Hydrothermal vents are an unlikely environment for animals to flourish, characterized by rapid changes in temperature and a challenging chemistry: acidic pH, rich in sulfur and methane. Not to mention the high hydrostatic pressure and the darkness of the deep sea. A team of scientists at the Sanya Institute of Deep-sea Science and Engineering (China) have now sequenced the full genome of a particularly unusual inhabitant of the hydrothermal vent environment: the sea cucumber Chiridota heheva. The research has been published in the Open Science journal GigaScience.
Organisms found at hydrothermal vents are among the most unique life forms on the planet, as they evolved special adaptations to survive and procreate under these harsh conditions. For example, many microbes employ special metabolic functions to deal with the abundance of sulfur and iron, and to withstand the enormous heat near the vent. In addition to microbes, there are even multicellular and higher order organisms that have adapted to the hydrothermal vent conditions, including various species of worms, snails, crabs and shrimp.
In 2019, a Chinese deep sea expedition with the manned research submarine “Shenhaiyongshi” collected a specimen of the sea cucumber C. hehevae at the bottom of the Indian Ocean, at the Kairei vent field at a depth of 2,428 meters. The water around the Kairei vent is particularly enriched in dissolved iron, adding to the harsh conditions of high hydrostatic pressure, darkness and fluctuating temperatures.
Sea cucumbers are echinoderms, and as such related to sea urchins and sea stars - a group of animals with highly unusual body plans. They are found on sea floors all over the world, where they devour detritus and use their tentacle to explore the sediment. While other high-quality genomes of sea cucumbers are available, the work now presented in GigaScience is the first genome of a sea cucumber specimen collected at a hydrothermal vent.
Initial comparative genome analyses indicate that several gene families are expanded in this sea cucumber, meaning that the species has a higher repertoire of specific sets of genes than related species. These expanded and unique genes are involved in DNA repair and iron metabolism, among other processes - a first indication that the adaptations to the harsh, iron-rich environment are reflected in the species’ genome. The genomic data will provide a valuable resource for further studies on both, sea cucumbers and the unique vent fauna.
Further Reading:
Pu Y, Zhou Y, Liu J, Zhang H
A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation. Gigascience 2023 giad107 https://doi.org/10.1093/gigascience/giad107
URL: https://academic.oup.com/gigascience/article-lookup/doi/10.1093/gigascience/giad107
Data Availability:
Pu Y; Zhou Y; Liu J; Zhang H (2023): Supporting data for "A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation" GigaScience Database. http://dx.doi.org/10.5524/102481
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About GigaScience Press
GigaScience Press is BGI's Open Access Publishing division, which publishes scientific journals and data. Its publishing projects are carried out with international publishing partners and infrastructure providers, including Oxford University Press and River Valley Technologies. It currently publishes two award-winning data-centric journals: its premier journal GigaScience (launched in 2012), which won the 2018 American Publishers PROSE award for innovation in journal publishing, and its new journal GigaByte (launched 2020), which won the 2022 ALPSP Award for Innovation in Publishing. The press also publishes data, software, and other research objects via its GigaDB.org database. To encourage transparent reporting of scientific research and to enable future access and analyses, it is a requirement of manuscript submission to all GigaScience Press journals that all supporting data and source code be made openly available in GigaDB or in a community approved, publicly available repository.
About GigaScience
GigaScience is co-published by GigaScience Press and Oxford University Press. Winner of the 2018 PROSE award for Innovation in Journal Publishing (Multidisciplinary), the journal covers research that uses or produces 'big data' from the full spectrum of the biological and biomedical sciences. It also serves as a forum for discussing the difficulties of and unique needs for handling large-scale data from all areas of the life and medical sciences. The journal has a completely novel publication format -- one that integrates manuscript publication with complete data hosting, and analyses tool incorporation. To encourage transparent reporting of scientific research as well as enable future access and analyses, it is a requirement of manuscript submission to GigaScience that all supporting data and source code be made available in the GigaScience database, GigaDB, as well as in publicly available repositories. GigaScience will provide users access to associated online tools and workflows, and has integrated a data analysis platform, maximizing the potential utility and re-use of data.
About GigaDB:
GigaDB is a data repository supporting scientific publications in the Life/Biomedical Sciences domain. GigaDB organizes and curates data from individually publishable units into datasets, which are openly available as FAIR data. GigaDB primarily serves as a repository to host data, tools, and other research objects that underlie the research in the article, and also data from articles from other journals in approved cases. Through association with DataCite, each dataset in GigaDB is assigned a DOI that can be used as a standard citation for future use of these data in other articles by the authors and other researchers. To maximize utility for the research community, all datasets in GigaDB are placed under a CC0 waiver. However, for data that needs to be protected, GigaDB will include the contact information for access, the restrictions for use, and host the application form needed to gain permission for use. The protected databases must be persistent and internationally accessible.
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JOURNAL
GigaScience
METHOD OF RESEARCH
Experimental study
ARTICLE TITLE
A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation
ARTICLE PUBLICATION DATE
4-Jan-2024
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