STUDY ON MITOCHONDRIAL VARIATIONS OF  THE SANDIU ETHNIC GROUP LIVING IN THAI NGUYEN

Trần Hữu Định; Võ Thị Bích Thủy; Nguyễn Thùy Dương

doi:10.34238/tnu-jst.10545

STUDY ON MITOCHONDRIAL VARIATIONS OF THE SANDIU ETHNIC GROUP LIVING IN THAI NGUYEN

About this article

Received: 05/06/24 Revised: 11/07/24 Published: 17/07/24

Authors

1. Tran Huu Dinh , Institute of Genome Research - Vietnam Academy of Science and Technology; Graduate University of Science and Technology - Vietnam Academy of Science and Technology
2. Vo Thi Bich Thuy, Institute of Genome Research - Vietnam Academy of Science and Technology
3. Nguyen Thuy Duong, Institute of Genome Research - Vietnam Academy of Science and Technology; Graduate University of Science and Technology - Vietnam Academy of Science and Technology

Abstract

The mitochondrion is an organelle involved in cellular energy production. The human mitochondrial genome (mtDNA) is widely used in research on genetic diversities and mitochondrial genetic diseases in different populations. In this study, total DNA from 26 individuals of Sandiu ethnic living in Phu Luong district of Thai Nguyen province was used for whole mtDNA sequencing using next-generation sequencing. By comparing the obtained sequences with the reference mitochondrial genome rCRS (revised Cambridge Reference Sequence), an average of 40.2 ± 5.2 variants per sample was detected, of which 53.8% of Sandiu individuals possess the variant T489C in the hypervariable region III (HVS-III) specific for Southeast Asia ethnic groups. Further analysis of genetic distances between six Sino-Tibetan ethnics (Sandiu, Hanhi, Phula, Sila, Lahu, and Lolo) revealed that although these ethnics are living in the Northern part of Vietnam, the genetic distances varied among different populations (0.011 - 0.183). This is the first study on the mtDNA variation of the Sandiu ethnic in Vietnam. These results are valuable data, contributing to future studies on the population genetics and mitochondrial diseases of the Sandiu and ethnic minorities in Vietnam.

Keywords

Variant; San Diu; Population genetics; Mitochondrial genome; Vietnam

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References

[1] N. V. Dang, T. S. Chu, and H. Luu, Ethnic Minorities in Vietnam. The Gioi (in English), 2017.

[2] General Statistics Office of Vietnam, "Completed results of the 2019 Vietnam population and housing census.", Statistical Publishing House, 2019. [Online]. Available: https://www.gso.gov.vn/. [Accessed: Apr. 12, 2024].

[3] W. Chen, H. Zhao, and Y. Li, "Mitochondrial dynamics in health and disease: mechanisms and potential targets," Signal Transduction and Targeted Therapy, vol. 8, no. 1, p. 333, 2023.

[4] M. Habbane, J. Montoya, T. Rhouda et al., "Human Mitochondrial DNA: Particularities and Diseases," Biomedicines, vol. 9, no. 10, p. 1364, 2021.

[5] J. W. Taanman, "The mitochondrial genome: structure, transcription, translation and replication," Biochim Biophys Acta, vol. 1410, no. 2, pp. 103-123, 1999.

[6] S. Oliveira, A. Hubner, A. M. Fehn et al., "The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola," European Journal of Human Genetics, vol. 27, no. 3, pp. 475-483, 2019.

[7] N. T. Duong, E. Macholdt, N. D. Ton et al., "Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia," Scientific Reports, vol. 8, no. 1, p. 11651, 2018.

[8] J. Liu, L. D. Wang, Y. B. Sun et al., "Deciphering the signature of selective constraints on cancerous mitochondrial genome," Molecular Biology and Evolution, vol. 29, no. 4, pp. 1255-1261, 2012.

[9] Y. Wu, X. H. Wang, X. H. Li et al., "Common mtDNA variations at C5178a and A249d/T6392C/G10310A decrease the risk of severe COVID-19 in a Han Chinese population from Central China," Military Medical Research, vol. 8, no. 1, p. 57, 2021.

[10] M. Venter, C. Tomas, I. S. Pienaar et al., "MtDNA population variation in Myalgic encephalomyelitis/Chronic fatigue syndrome in two populations: a study of mildly deleterious variants," Scientific Reports, vol. 9, no. 1, p. 2914, 2019.

[11] T. N. Nguyen, B. T. Nguyen, Q. H. Nguyen et al., "Single Nucleotide Polymorphisms in the D-Loop Region of the Mitochondrial Genomes of Individuals from Two Ethnic Groups Kinh and Mang of Austro-Asiatic Language Family," Vietnam Journal of Biotechnology, vol. 16, no. 2, pp. 231-240, 2018.

[12] T. D. Nguyen, V. P. Nguyen, T. N. Nguyen, and V. H. Nong, "Study on genetic variations of the D-loop region in three Vietnamese ethnic groups Kinh, Lolo, and Lahu," Vietnam Journal of Biotechnology, vol. 18, no. 2, pp. 231-238, 2020.

[13] T. T. H. Tran, D. H. Nguyen, V. K. Tran et al., "Variation of Mitochondrial DNA HV1 AND HV2 of the Vietnamese Population," Advances in Experimental Medicine and Biology, vol. 1292, pp. 37-63, 2020.

[14] M. T. Nguyen, V. B. Nguyen, and D. T. Nguyen, "Mitochondrial NADH dehydrogenase subunit 5 and subunit 6 gene polymorphisms in Giarai and Ede ethnic people living in the central highlands," Vietnam Medical Journal, vol. 504, no. 1, pp. 20-25, 2021.

[15] B. K. Phung, V. M. Nguyen, T. H. L. Nguyen et al., "Detection and quantitation of mitochondrial G11778A mutation of LHON syndrome in a Vietnamese patient with tentatively diagnosed mitochondrial disease," VNU Journal of Science: Natural Sciences and Technology, vol. 33, no. 2S, pp. 20-25, 2017.

[16] D. H. Thao, T. H. Dinh, S. Mitsunaga et al., "Investigating demic versus cultural diffusion and sex bias in the spread of Austronesian languages in Vietnam," PLoS One, vol. 19, no. 6, 2024, Art. no. e0304964.

[17] T. Maricic, M. Whitten, and S. Paabo, "Multiplexed DNA sequence capture of mitochondrial genomes using PCR products," PLoS One, vol. 5, no. 11, 2010, Art. no. e14004.

[18] M. Meyer and M. Kircher, "Illumina sequencing library preparation for highly multiplexed target capture and sequencing," Cold Spring Harbor Protocols, vol. 2010, no. 6, 2010, Art. no. pdbprot5448.

[19] L. Arias, C. Barbieri, G. Barreto et al., "High-resolution mitochondrial DNA analysis sheds light on human diversity, cultural interactions, and population mobility in Northwestern Amazonia," American Journal of Physical Anthropology, vol. 165, no. 2, pp. 238-255, 2018.

[20] H. Weissensteiner, D. Pacher, A. Kloss-Brandstatter et al., "HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing," Nucleic Acids Research, vol. 44, no. W1, pp. W58-63, 2016.

[21] M. van Oven and M. Kayser, "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation," Human Mutation, vol. 30, no. 2, pp. E386-394, 2009.

[22] N. L. Sim, P. Kumar, J. Hu, S. Henikoff et al., "SIFT web server: predicting effects of amino acid substitutions on proteins," Nucleic Acids Res, vol. 40, no. Web Server, pp. W452-457, 2012.

[23] I. A. Adzhubei, S. Schmidt, L. Peshkin et al., "A method and server for predicting damaging missense mutations," Nat Methods, vol. 7, no. 4, pp. 248-249, 2010.

[24] M. Kircher, D. M. Witten, P. Jain, B. J. O'Roak et al., "A general framework for estimating the relative pathogenicity of human genetic variants," Nat Genet, vol. 46, no. 3, pp. 310-315, 2014.

[25] V. Pejaver, J. Urresti, J. Lugo-Martinez et al., "Inferring the molecular and phenotypic impact of amino acid variants with MutPred2," Nat Commun, vol. 11, no. 1, p. 5918, 2020.

[26] S. Castellana, J. Ronai, and T. Mazza, "MitImpact: an exhaustive collection of pre-computed pathogenicity predictions of human mitochondrial non-synonymous variants," Hum Mutat, vol. 36, no. 2, pp. E2413-22, 2015.

[27] R Core Team, "R: A Language and Environment for Statistical Computing," R Foundation for Statistical Computing, 2022. [Online]. Availabe: https://www.R-project.org/. [Accessed Apr. 12, 2024].

[28] W. Hadley, "ggplot2: Elegant Graphics for Data Analysis," Springer-Verlag New York, 2016. [Online]. Availabe: https://ggplot2.tidyverse.org. [Accessed Apr. 12, 2024].

[29] L. Excoffier and H. E. Lischer, "Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows," Molecular Ecology Resources, vol. 10, no. 3, pp. 564-567, 2010.

[30] W. Kutanan, J. Kampuansai, M. Srikummool et al., "Complete mitochondrial genomes of Thai and Lao populations indicate an ancient origin of Austroasiatic groups and demic diffusion in the spread of Tai-Kadai languages," Human Genetics, vol. 136, no. 1, pp. 85-98, 2017.

[31] J. Vanichanukulyakit, S. Khacha-Ananda, T. Monum et al., "The Analysis of Genetic Polymorphism on Mitochondrial Hypervariable Region III in Thai Population," Genes (Basel), vol. 14, no. 3, p. 682, 2023.

[32] A. Piotrowska-Nowak, E. Kosior-Jarecka, A. Schab et al., "Investigation of whole mitochondrial genome variation in normal tension glaucoma," Experimental Eye Research, vol. 178, pp. 186-197, 2019.

[33] S. Sharma, S. Singh, R. K. Gupta et al., "Mitochondrial DNA sequencing reveals association of variants and haplogroup M33a2'3 with High altitude pulmonary edema susceptibility in Indian male lowlanders," Scientific Reports, vol. 9, no. 1, p. 10975, 2019.

[34] F. Chen, S. Y. Wang, R. Z. Zhang et al., "Analysis of mitochondrial DNA polymorphisms in Guangdong Han Chinese," Forensic Science International: Genetics, vol. 2, no. 2, pp. 150-153, 2008.

[35] Y. C. Li, W. J. Ye, C. G. Jiang et al., "River Valleys Shaped the Maternal Genetic Landscape of Han Chinese," Molecular Biology and Evolution, vol. 36, no. 8, pp. 1643-1652, 2019.

DOI: https://doi.org/10.34238/tnu-jst.10545

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