Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences

Yan, Guoyong; Lan, Yi; Sun, Jin; Xu, Ting; Tong, Wei; Qian, Pei‐Yuan

doi:10.1016/j.isci.2022.104092

Cited by 9 publications

(8 citation statements)

References 56 publications

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“…This phenomenon was also observed in tubeworms recovered at atmosphere pressure (Dixon et al, 2002). Yan et al (2022) confirmed the extensive transcriptomic variations in response to pressure during unpressurized sampling. These studies suggest the necessity of pressurized sampling in deep-sea biology studies.…”

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confidence: 74%

Isobaric sampling apparatus and key techniques for deep sea macro-organisms: A brief review

et al. 2022

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The study of deep-sea fauna is one of the essential themes of marine scientific research. For all that, the biology of deep animals remains largely unknown, such as their behaviors, metabolic characteristics, and mechanisms of adaptation to the deep-sea environment. Obtaining samples in good condition is an essential prerequisite for these investigations. The isobaric samplers were created to keep the organisms as much as possible in the in-situ environment during recovery. This report reviews the history and the application of isobaric samplers for deep-sea animals established by researchers worldwide over the past hundred years. Also, the crucial technologies of isobaric samplers are analyzed and summarized, including pressure compensation, insulation, sealing, etc. Finally, prospects for the future development of isobaric sampling technologies from the aspects of high fidelity, function integration, and real-time communication and integration operation. This review can provide a reference for future design and optimization of fidelity samplers for deep-sea animals.

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confidence: 74%

Isobaric sampling apparatus and key techniques for deep sea macro-organisms: A brief review

et al. 2022

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“…Before the RAD, only two other methods had been developed for robotic deep-sea collection of delicate midwater species ( 22 ). Using those methods, deep-sea animals are captured and brought to the surface accompanied with: (i) complexities in keeping the animal alive ( 54 ), (ii) preservatives, such as formalin or ethanol, harden and alter tissue components ( 55 ), and (iii) there is an overexpression of stress genes as the animal has undergone a marked change in pressure and temperature before tissue preservation ( 56 ). Because of those issues, when a soft-bodied animal, such as a jellyfish, is preserved with alcohol or formalin after collection, it is no longer possible to obtain detailed and nuanced information regarding gene expression from the animal at depth or of tissue volume, structure, or dynamics.…”

Section: Discussionmentioning

confidence: 99%

An in situ digital synthesis strategy for the discovery and description of ocean life

Burns,

Becker,

Casagrande

et al. 2024

Sci. Adv.

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Revolutionary advancements in underwater imaging, robotics, and genomic sequencing have reshaped marine exploration. We present and demonstrate an interdisciplinary approach that uses emerging quantitative imaging technologies, an innovative robotic encapsulation system with in situ RNA preservation and next-generation genomic sequencing to gain comprehensive biological, biophysical, and genomic data from deep-sea organisms. The synthesis of these data provides rich morphological and genetic information for species description, surpassing traditional passive observation methods and preserved specimens, particularly for gelatinous zooplankton. Our approach enhances our ability to study delicate mid-water animals, improving research in the world’s oceans.

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“…Similar experimental approaches in model polychaete species are needed to assess if DNA methylation exerts direct epigenetic control on gene expression in this group. Since deep-sea worms have not been successfully reared in the laboratory, it will be very hard to conduct in vitro experiments, although the animals can be fixed in situ ( Yan et al 2022 ).…”

Section: Discussionmentioning

confidence: 99%

“…Likewise, the ubiquitin–proteasome pathway, which is responsible for degrading misfolded or damaged proteins and plays an important role in cold water–adapted species ( Todgham et al 2017 ), was overrepresented amongst genes with hypomethylated promoters in all three worms. Our samples were not fixed in situ, and thus, we cannot exclude that the methylation profiles of the worms partly reflect the decompression stress they suffered during their recovery to the ship ( Yan et al 2022 ). However, methylomes tend to be much more stable in time than transcriptomes ( Strader et al 2020 ), and thus, environmental stress during the short timeframe of samples recovery (a few hours at most) is unlikely to have had substantial consequences on worms’ methylomes.…”

Section: Discussionmentioning

confidence: 99%

Third-Generation Sequencing Reveals the Adaptive Role of the Epigenome in Three Deep-Sea Polychaetes

Perez

Aroh

Sun

et al. 2023

Molecular Biology and Evolution

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The roles of DNA methylation in invertebrates are poorly characterised, and critical data are missing for the phylum Annelida. We fill this knowledge gap by conducting the first genome-wide survey of DNA methylation in the deep-sea polychaetes dominant in deep-sea vents and seeps: Paraescarpia echinospica, Ridgeia piscesae and Paralvinella palmiformis. DNA methylation calls were inferred from Oxford Nanopore sequencing after assembling high-quality genomes of these animals. The genomes of these worms encode all the key enzymes of the DNA methylation metabolism and possess a mosaic methylome similar to that of other invertebrates. Transcriptomic data of these polychaetes support the hypotheses that gene body methylation strengthens the expression of housekeeping genes and that promoter methylation acts as a silencing mechanism but not the hypothesis that DNA methylation suppress the activity of transposable elements. The conserved epigenetic profiles of genes responsible for maintaining homeostasis under extreme hydrostatic pressure suggest DNA methylation plays an important adaptive role in these worms.

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Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences

Cited by 9 publications

References 56 publications

Isobaric sampling apparatus and key techniques for deep sea macro-organisms: A brief review

Isobaric sampling apparatus and key techniques for deep sea macro-organisms: A brief review

An in situ digital synthesis strategy for the discovery and description of ocean life

Third-Generation Sequencing Reveals the Adaptive Role of the Epigenome in Three Deep-Sea Polychaetes

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