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

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

doi:10.1016/j.isci.2022.104092

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

iScience. 2022 Mar 17;25(4):104092. doi: 10.1016/j.isci.2022.104092. eCollection 2022 Apr 15.

Authors

Guoyong Yan^{1

2}, Yi Lan^{1

2}, Jin Sun³, Ting Xu^{1

2}, Tong Wei^{1

2}, Pei-Yuan Qian^{1

2}

Affiliations

¹ Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
² Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
³ Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.

Abstract

Precise gene expression reflects the molecular response of deep-sea organisms to their harsh living environments. However, changes in environmental factors during lifting samples from the deep sea to a research vessel can also affect gene expression. By using the transcriptomic approach, we compared the gene expression profiles of the onboard fixed with the in situ fixed samples of the deep-sea limpet Bathyacmaea lactea. Our results revealed that the concomitant stress during conventional deep-sea sampling without RNA in situ fixation greatly influenced the gene expression. Various biological activities, such as cell and tissue structure, lysosomal activity, fluid balance, and unsaturated fatty acid metabolism, were perturbed, suggesting that the sampling stress has exerted systemic impacts on the life of the limpets. These findings clearly illustrate that deep-sea samples without RNA in situ fixation can easily lead to biased results in gene expression analysis, which requires to be appropriately addressed in future studies.

Keywords: Biotehnology; Transcriptomics; marine biotechnology; omics.