Comparison of Evolutionary Selection Acting on the Mitochondrial Protein-Coding Genes Between Intertidal and Deep-Sea Gastropods
Keywords:
Deep sea, Gastropods, Intertidal, Mitochondria, Selection pressureAbstract
Marine molluscs are ecologically and economically important group of organisms that survive in the challenging environments of different oceanic zones. Of all the classes of the phylum Mollusca, gastropods have radiated into marine, freshwater and terrestrial habitats, successfully adapting themselves to thrive in changing environmental conditions. Hence, marine gastropods can be considered as an ideal system to study stress adaptation. In order to withstand the constant fluctuations in temperature, salinity and shifts in oxygen concentration of the intertidal zone, the gastropods inhabiting here rely on a modified and adaptive energy metabolism. The same is applicable for gastropods living in the deep sea environment, which is characterized by high hydrostatic pressure, low oxygen concentrations and abundance of heavy metals. Therefore, survival of these organisms may be correlated to their adaptive mitochondrial genome which serves as the principal site for energy metabolism and production in the cell. Here, we estimated selection pressure acting on the mitochondrial protein-coding genes of 13 intertidal and 2 deep sea gastropods based on site and branch-site specific models. The results exhibited higher number of sites under diversifying selection for the mitochondrial protein-coding genes of intertidal gastropods compared to deep sea species. Overall, this study focusses on the adaptive mitogenome evolution of marine gastropods for survival in the dynamic environments of the intertidal zone as well as deep sea.
Downloads
References
Boore, J.L. (1999) Animal mitochondrial genomes. Nucleic Acids Research. 27 (8), 1767–1780.
Smith, D.R. and Snyder, M. (2007) Complete mitochondrial DNA sequence of the scallop Placopecten magellanicus: evidence of transposition leading to an uncharacteristically large mitochondrial genome. Journal of Molecular Evolution. 65 (4), 380–391.
Blier, P.U., Dufresne, F., and Burton, R.S. (2001) Natural selection and the evolution of mtDNA-encoded peptides: evidence for intergenomic co-adaptation. Trends in Genetics : TIG. 17 (7), 400–406.
Lartigue, L. and Faustin, B. (2013) Mitochondria: metabolic regulators of innate immune responses to pathogens and cell stress. The International Journal of Biochemistry & Cell Biology. 45 (9), 2052–2056.
Sokolova, I. (2018) Mitochondrial Adaptations to Variable Environments and Their Role in Animals’ Stress Tolerance. Integrative and Comparative Biology. 58 (3), 519–531.
da Fonseca, R.R., Johnson, W.E., O’Brien, S.J., Ramos, M.J., and Antunes, A. (2008) The adaptive evolution of the mammalian mitochondrial genome. BMC Genomics. 9 119.
Foote, A.D., Morin, P.A., Durban, J.W., Pitman, R.L., Wade, P., Willerslev, E., et al. (2011) Positive selection on the killer whale mitogenome. Biology Letters. 7 (1), 116–118.
Almeida, D., Maldonado, E., Vasconcelos, V., and Antunes, A. (2015) Adaptation of the Mitochondrial Genome in Cephalopods: Enhancing Proton Translocation Channels and the Subunit Interactions. PloS One. 10 (8), e0135405.
Dhar, D., Dey, D., Basu, S., and Fortunato, H. (2021) Insight into the adaptive evolution of mitochondrial genomes in intertidal chitons. Journal of Molluscan Studies. 87 (2),.
Kocot, K.M., Cannon, J.T., Todt, C., Citarella, M.R., Kohn, A.B., Meyer, A., et al. (2011) Phylogenomics reveals deep molluscan relationships. Nature. 477 (7365), 452–456.
Gomes-dos-Santos, A., Lopes-Lima, M., Castro, L.F.C., and Froufe, E. (2020) Molluscan genomics: the road so far and the way forward. Hydrobiologia. 847 (7), 1705–1726.
Parker, L.M., Ross, P.M., O’Connor, W.A., Pörtner, H.O., Scanes, E., and Wright, J.M. (2013) Predicting the response of molluscs to the impact of ocean acidification. Biology. 2 (2), 651–692.
Appeltans, W., Ahyong, S.T., Anderson, G., Angel, M.V., Artois, T., Bailly, N., et al. (2012) The Magnitude of Global Marine Species Diversity. Current Biology. 22 (23), 2189–2202.
Parkhaev, P. (2007) The Cambrian ‘basement’ of gastropod evolution. Geological Society London Special Publications. 286 415–421.
Jensen, M.M. and Denny, M.W. (2016) Life in an extreme environment: Characterizing wave-imposed forces in the rocky intertidal zone using high temporal resolution hydrodynamic measurements. Limnology and Oceanography. 61 (5), 1750–1761.
Chen, C., Linse, K., Copley, J.T., and Rogers, A.D. (2015) The ‘scaly-foot gastropod’: a new genus and species of hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae) from the Indian Ocean. Journal of Molluscan Studies. 81 (3), 322–334.
Van Dover, C.L., German, C.R., Speer, K.G., Parson, L.M., and Vrijenhoek, R.C. (2002) Evolution and biogeography of deep-sea vent and seep invertebrates. Science (New York, N.Y.). 295 (5558), 1253–1257.
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research. 32 (5), 1792–1797.
Kumar, S., Stecher, G., Li, M., Knyaz, C., and Tamura, K. (2018) MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution. 35 (6), 1547–1549.
Gao, F., Chen, C., Arab, D.A., Du, Z., He, Y., and Ho, S.Y.W. (2019) EasyCodeML: A visual tool for analysis of selection using CodeML. Ecology and Evolution. 9 (7), 3891–3898.
Yang, Z. (2007) PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution. 24 (8), 1586–1591.
Anisimova, M., Bielawski, J.P., and Yang, Z. (2001) Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Molecular Biology and Evolution. 18 (8), 1585–1592.
Yang, Z., Nielsen, R., Goldman, N., and Pedersen, A.M. (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics. 155 (1), 431–449.
Yang, Z., Wong, W.S.W., and Nielsen, R. (2005) Bayes empirical bayes inference of amino acid sites under positive selection. Molecular Biology and Evolution. 22 (4), 1107–1118.
Zhang, J., Nielsen, R., and Yang, Z. (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular Biology and Evolution. 22 (12), 2472–2479.
Kosakovsky Pond, S.L., Poon, A.F.Y., Velazquez, R., Weaver, S., Hepler, N.L., Murrell, B., et al. (2020) HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies. Molecular Biology and Evolution. 37 (1), 295–299.
Kosakovsky Pond, S.L. and Frost, S.D.W. (2005) Not so different after all: a comparison of methods for detecting amino acid sites under selection. Molecular Biology and Evolution. 22 (5), 1208–1222.
Murrell, B., Wertheim, J.O., Moola, S., Weighill, T., Scheffler, K., and Kosakovsky Pond, S.L. (2012) Detecting individual sites subject to episodic diversifying selection. PLoS Genetics. 8 (7), e1002764.
Shen, Y.-Y., Liang, L., Zhu, Z.-H., Zhou, W.-P., Irwin, D.M., and Zhang, Y.-P. (2010) Adaptive evolution of energy metabolism genes and the origin of flight in bats. Proceedings of the National Academy of Sciences of the United States of America. 107 (19), 8666–8671.
Tomasco, I.H. and Lessa, E.P. (2011) The evolution of mitochondrial genomes in subterranean caviomorph rodents: adaptation against a background of purifying selection. Molecular Phylogenetics and Evolution. 61 (1), 64–70.
Yu, L., Wang, X., Ting, N., and Zhang, Y. (2011) Mitogenomic analysis of Chinese snub-nosed monkeys: Evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation. Mitochondrion. 11 (3), 497–503.
Ning, T., Xiao, H., Li, J., Hua, S., and Zhang, Y.P. (2010) Adaptive evolution of the mitochondrial ND6 gene in the domestic horse. Genetics and Molecular Research : GMR. 9 (1), 144–150.
Mathiesen, C. and Hägerhäll, C. (2002) Transmembrane topology of the NuoL, M and N subunits of NADH:quinone oxidoreductase and their homologues among membrane-bound hydrogenases and bona fide antiporters. Biochimica et Biophysica Acta. 1556 (2–3), 121–132.
Trumpower, B.L. (1990) The protonmotive Q cycle. Energy transduction by coupling of proton translocation to electron transfer by the cytochrome bc1 complex. The Journal of Biological Chemistry. 265 (20), 11409–11412.
Luo, Y., Gao, W., Gao, Y., Tang, S., Huang, Q., Tan, X., et al. (2008) Mitochondrial genome analysis of Ochotona curzoniae and implication of cytochrome c oxidase in hypoxic adaptation. Mitochondrion. 8 (5–6), 352–357.
Sun, S., Hui, M., Wang, M., and Sha, Z. (2018) The complete mitochondrial genome of the alvinocaridid shrimp Shinkaicaris leurokolos (Decapoda, Caridea): Insight into the mitochondrial genetic basis of deep-sea hydrothermal vent adaptation in the shrimp. Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics. 25 42–52.
Zhang, B., Zhang, Y.-H., Wang, X., Zhang, H.-X., and Lin, Q. (2017) The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep-sea environment. Ecology and Evolution. 7 (13), 4951–4962.
Rogers, A.D., Tyler, P.A., Connelly, D.P., Copley, J.T., James, R., Larter, R.D., et al. (2012) The discovery of new deep-sea hydrothermal vent communities in the southern ocean and implications for biogeography. PLoS Biology. 10 (1), e1001234.
Downloads
Published
How to Cite
Issue
Section
License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
editor@ijrasb.com 