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. 2022 Dec 14;23(1):828.
doi: 10.1186/s12864-022-09064-9.

Transcriptome analysis of gene expression profiling from the deep sea in situ to the laboratory for the cold seep mussel Gigantidas haimaensis

Hua Zhang  1   2   3 , Gaoyou Yao  1   4   3 , Maoxian He  5   6   7
Affiliations

Transcriptome analysis of gene expression profiling from the deep sea in situ to the laboratory for the cold seep mussel Gigantidas haimaensis

Hua Zhang et al. BMC Genomics. .

Abstract

Background: The deep-sea mussel Gigantidas haimaensis is a representative species from the Haima cold seep ecosystem in the South China Sea that establishes endosymbiosis with chemotrophic bacteria. During long-term evolution, G. haimaensis has adapted well to the local environment of cold seeps. Until now, adaptive mechanisms responding to environmental stresses have remained poorly understood.

Results: In this study, transcriptomic analysis was performed for muscle tissue of G. haimaensis in the in situ environment (MH) and laboratory environment for 0 h (M0), 3 h (M3) and 9 h (M9), and 187,368 transcript sequences and 22,924 annotated differentially expressed genes (DEGs) were generated. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, these DEGs were enriched with a broad spectrum of biological processes and pathways, including those associated with antioxidants, apoptosis, chaperones, immunity and metabolism. Among these significantly enriched pathways, protein processing in the endoplasmic reticulum and metabolism were the most affected metabolic pathways. These results may imply that G. haimaensis struggles to support the life response to environmental change by changing gene expression profiles.

Conclusion: The present study provides a better understanding of the biological responses and survival strategies of the mussel G. haimaensis from deep sea in situ to the laboratory environment.

Keywords: Cold seep; Gene expression; Gigantidas haimaensis; Transcriptomic analysis.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Transcript and unigene length distribution
Fig. 2
Fig. 2
Expression analysis of DEGs. A Number of DEGs in comparison groups. B Heatmap cluster analysis of DEGs
Fig. 3
Fig. 3
KEGG enrichment analysis of DEGs in pairwise comparison of six groups
Fig. 4
Fig. 4
Analysis of the environmental information processing pathway genes. A Heatmap of DEGs related to molecular chaperones. B Heatmap analysis of sacsin. C. Phylogenetic tree of heat shock 70 kDa protein with 1000 bootstrap replications. D Conserved motifs of HSP70 protein in G. haimaensis
Fig. 5
Fig. 5
Expression analysis of the lipid metabolism pathway genes
Fig. 6
Fig. 6
Sequence analysis and gene expression of the C1q family. A Protein sequence alignment of the C1q family from G. haimaensis. B Phylogenetic tree of C1q family construction and C1q protein domain analysis from G. haimaensis. C Heatmap analysis of C1q family gene expression
Fig. 7
Fig. 7
RT‒qPCR results of the thirteen candidate genes. A The relative expression levels using RT‒qPCR; B The corresponding expression levels using RNA-seq
See this image and copyright information in PMC

References

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