Mitochondrial DNA insertions into nuclear genome (numts) in Vietnam sheep: Implications and caveats for the utility of the mitochondrial DNA markers in genetic diversity studies in sheep

Ngoc Luong Nguyen, Nhu Cuong Nguyen, Thi Thu Ha Huynh
Author affiliations

Authors

  • Ngoc Luong Nguyen Department of Biology, College of Sciences, Hue University, 77 Nguyen Hue Road, Phu Nhuan Ward, Hue City, Thua Thien Hue Province, Vietnam
  • Nhu Cuong Nguyen Chu Van An Secondary School, 36A Duong Van An Road, Xuan Phu Ward, Hue City, Thua Thien Hue Province, Vietnam
  • Thi Thu Ha Huynh Department of Biology, College of Sciences, Hue University, 77 Nguyen Hue Road, Phu Nhuan Ward, Hue City, Thua Thien Hue Province, Vietnam

DOI:

https://doi.org/10.15625/1811-4989/19651

Abstract

Nuclear insertions of mitochondrial DNA sequences (numts) can introduce errors in population genetic studies using mitochondrial DNA markers (mtDNA markers). Despite their prevalence in mammalian genomes and the potential risk of contamination with mtDNA markers, adequate precautions are often overlooked. When investigating the genetic diversity of Vietnam sheep, we found numt contamination in D-loop amplification. Consequentially, to continue, we conducted a comprehensive in silico survey of numts using the reference genomes from the NCBI database. We identified four so-called “mega-numts” that are not only highly similar in sequence to the mitogenome but also span a large part of it, thus posing a serious problem for amplifying authentic mtDNA markers. We demonstrated the existence of two numts in three randomly selected Vietnam sheep individuals. Based on the assumed mutation rate of the D-loop region, we proposed a sequence identity threshold to help distinguish authentic D-loop sequences from their corresponding numts when studying contemporary sheep populations. We hope this study can serve as a guideline for future research into Vietnam sheep using mtDNA markers.

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Published

30-12-2023

How to Cite

Nguyen, N. L., Nguyen, N. C., & Ha Huynh, T. T. (2023). Mitochondrial DNA insertions into nuclear genome (numts) in Vietnam sheep: Implications and caveats for the utility of the mitochondrial DNA markers in genetic diversity studies in sheep. Vietnam Journal of Biotechnology, 21(4), 655–667. https://doi.org/10.15625/1811-4989/19651

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Articles