Abstract
Background
Marine mammals, which have evolved independently into three distinct lineages, share common physiological features that contribute to their adaptation to the marine environment.
Objective
To identify positively selected genes (PSGs) for adaptation to the marine environment using available genomic data from three taxonomic orders: cetaceans, pinnipeds, and sirenians.
Methods
Based on the genomes within each group of Artiodactyla, Carnivora and Afrotheria, we performed selection analysis using the branch-site model in CODEML.
Results
Based on the branch-site model, 460, 614, and 359 PSGs were predicted for the cetaceans, pinnipeds, and sirenians, respectively. Functional enrichment analysis indicated that genes associated with hemostasis were positively selected across all lineages of marine mammals. We observed positive selection signals for the hemostasis and coagulation-related genes plasminogen activator, urokinase (PLAU), multimerin 1 (MMRN1), gamma-glutamyl carboxylase (GGCX), and platelet endothelial aggregation receptor 1 (PEAR1). Additionally, we found out that the sodium voltage-gated channel alpha subunit 9 (SCN9A), serine/arginine repetitive matrix 4 (SRRM4), and Ki-ras-induced actin-interacting protein (KRAP) are under positive selection pressure and are associated with cognition, neurite outgrowth, and IP3-mediated Ca2 + release, respectively.
Conclusion
This study will contribute to our understanding of the adaptive evolution of marine mammals by providing information on a group of candidate genes that are predicted to influence adaptation to aquatic environments, as well as their functional characteristics.
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Data availability
The authors confirm that the data supporting the findings of this study are available within the article or its supplementary materials. The data that support the findings of this study are available from the corresponding author, Lee or Park, upon reasonable request.
Abbreviations
- PSGs:
-
Positively selected genes
- aPTT:
-
Activated partial thromboplastin time
- MSA:
-
Multiple sequence alignment
- CDSs:
-
Coding sequences
- CSB:
-
Clean Segment Block
- EPC:
-
Edge Percolated Component
- MNC:
-
Maximum Neighborhood Component
- DMNC:
-
Density of Maximum Neighborhood Component
- MCC:
-
Maximal Clique Centrality
- BN:
-
Bottleneck
- GO:
-
Gene ontology
- CREB:
-
CAMP response element-binding proteins
- CBP:
-
CREB-binding protein
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Acknowledgements
This research was part of the “Development of biomedical materials based on marine proteins” project (20170305) funded by the Ministry of Oceans and Fisheries, Korea, and an in-house program (EA0122) from the Korea Institute of Ocean Science & Technology (KIOST).
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Roh, YR., Yim, HS., Park, K. et al. Molecular characterization of positively selected genes contributing aquatic adaptation in marine mammals. Genes Genom (2024). https://doi.org/10.1007/s13258-023-01487-2
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DOI: https://doi.org/10.1007/s13258-023-01487-2