Scientists Sequence Genome of Hydrothermal Vent-Dwelling Sea Cucumber


Researchers in China have mapped the entire genome of Chiridota heheva, a species of sea cucumber collected at a depth of 2,428 m during a submarine trip to a hydrothermal vent.

Chirodota heheva in the Gulf of Mexico. Image credit: Aquapix and Expedition to the Deep Slope 2007.

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 new work provides the first genome of a sea cucumber specimen — Chiridota heheva — collected at a hydrothermal vent.

First described in 2004, Chiridota heheva is known from deeper regions in the Western Atlantic Ocean, but has a cosmopolitan distribution.

It is one of the few echinoderms that occupy all three types of chemosynthetic ecosystems: hydrothermal vents, cold seeps, and organic fall. This suggests that the species is well adapted to deep-sea reducing environments.

Unlike most cold seep- and hydrothermal vent-dwelling species, Chiridota heheva does not host chemosynthetic bacteria.

It derives nutrients from a variety of sources, extracting organic components from sediment detritus, suspended material, and wood fragments when available.

“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,” said lead author Dr. Yujin Pu from the Sanya Institute of Deep-sea Science and Engineering and her colleagues.

“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 their research, the authors sequenced the genome of an individual of Chiridota heheva collected from the bottom of Indian Ocean at the Kairei vent field (depth of 2,428 m).

“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,” they said.

“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 — the 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.”

The results appear in the journal GigaScience.


Y. Pu et al. 2023. A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation. Gigascience, in press; doi: 10.1093/gigascience/giad107


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