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<p>Nuclear mitochondrial DNA sequences (NUMTs) are mitochondrial DNA sequences inserted into the nuclear genomes of almost all eukaryotic organisms. There is considerable variation among species in terms of abundance, size, and location of NUMTs. Notably, the number of NUMTs detected can vary significantly depending on the detection method employed. This study aimed to provide the first comprehensive description and annotated collection of NUMTs in domestic water buffalo (<i>Bubalus bubalis</i>). By aligning mtDNA sequence (NC_049568.1) of <i>Bubalus bubalis</i> with reference nuclear genome (GCA_019923935.1) using the BLASTn method, we identified 61 NUMTs. By merging NUMTs found in close proximity, 15 distinct NUMTs region were found across the buffalo genome. By merging NUMTs located in close proximity, we identified 15 distinct NUMT regions across the buffalo genome. These regions comprised a variety of mitochondrial sequences with differing sequence identities, rather than the entire mitochondrial genome, and included one nearly complete D-loop sequence (15,087–16,358&#xa0;bp) integrated into BBA 2 (spanning 9,990–16,358&#xa0;bp), exhibiting almost 100% sequence identity to the corresponding mitochondrial region. Fourteen genes (PMS1, ERBB4, USP37, AGBL3, CNOT4, MSRB3, CDH23, BNIP2, NEO1, CHDH, MYO7A, ADAMTS19, TGM3, and lncRNA) were found within the 61 NUMTs, many of which are related to cancer and disease. The findings of this study offer a valuable resource for curating genomic databases and will aid in preventing NUMT co-amplification in studies involving mtDNA, such as those in phylogenetics, population genetics, and evolutionary biology.</p>

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Genome wide mapping of nuclear mitochondrial DNA sequences (NUMTs) and their functionality in domestic water buffalo (Bubalus bubalis)

  • 期刊论文

  • 发表日期：

    2025年9月13日

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  • Rangasai Chandra Goli,
  • Karan Mahar,
  • Kiyevi G. Chishi,
  • Tanuj Gunturu,
  • Vikas Diwakar,
  • Amit Kumar,
  • Ganesh N. Aderao,
  • K. C. Nikhil,
  • Muralidhar Metta,
  • Nidhi Sukhija,
  • K. K. Kanaka

摘要

Nuclear mitochondrial DNA sequences (NUMTs) are mitochondrial DNA sequences inserted into the nuclear genomes of almost all eukaryotic organisms. There is considerable variation among species in terms of abundance, size, and location of NUMTs. Notably, the number of NUMTs detected can vary significantly depending on the detection method employed. This study aimed to provide the first comprehensive description and annotated collection of NUMTs in domestic water buffalo (Bubalus bubalis). By aligning mtDNA sequence (NC_049568.1) of Bubalus bubalis with reference nuclear genome (GCA_019923935.1) using the BLASTn method, we identified 61 NUMTs. By merging NUMTs found in close proximity, 15 distinct NUMTs region were found across the buffalo genome. By merging NUMTs located in close proximity, we identified 15 distinct NUMT regions across the buffalo genome. These regions comprised a variety of mitochondrial sequences with differing sequence identities, rather than the entire mitochondrial genome, and included one nearly complete D-loop sequence (15,087–16,358 bp) integrated into BBA 2 (spanning 9,990–16,358 bp), exhibiting almost 100% sequence identity to the corresponding mitochondrial region. Fourteen genes (PMS1, ERBB4, USP37, AGBL3, CNOT4, MSRB3, CDH23, BNIP2, NEO1, CHDH, MYO7A, ADAMTS19, TGM3, and lncRNA) were found within the 61 NUMTs, many of which are related to cancer and disease. The findings of this study offer a valuable resource for curating genomic databases and will aid in preventing NUMT co-amplification in studies involving mtDNA, such as those in phylogenetics, population genetics, and evolutionary biology.