Sequencing and characterizing human mitochondrial genomes in the biobank-based genomic research paradigm

Lintao Luo; Mengge Wang; Yunhui Liu; Jianbo Li; Fengxiao Bu; Huijun Yuan; Renkuan Tang; Chao Liu; Guanglin He

doi:10.1007/s11427-024-2736-7

Sequencing and characterizing human mitochondrial genomes in the biobank-based genomic research paradigm

Sci China Life Sci. 2025 Jan 21. doi: 10.1007/s11427-024-2736-7. Online ahead of print.

Authors

Lintao Luo^#^{1

2}, Mengge Wang^#^{3

4

5}, Yunhui Liu^#^{1

2}, Jianbo Li², Fengxiao Bu^{1

6}, Huijun Yuan^{7

8}, Renkuan Tang⁹, Chao Liu^{10

11}, Guanglin He^#^{12

13

14}

Affiliations

¹ Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
² Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China.
³ Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China. [email protected].
⁴ Center for Archaeological Science, Sichuan University, Chengdu, 610000, China. [email protected].
⁵ Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China. [email protected].
⁶ Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
⁷ Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China. [email protected].
⁸ Center for Archaeological Science, Sichuan University, Chengdu, 610000, China. [email protected].
⁹ Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China. [email protected].
¹⁰ Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China. [email protected].
¹¹ Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China. [email protected].
¹² Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China. [email protected].
¹³ Center for Archaeological Science, Sichuan University, Chengdu, 610000, China. [email protected].
¹⁴ Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China. [email protected].

^# Contributed equally.

PMID: 39843848
DOI: 10.1007/s11427-024-2736-7

Abstract

Human mitochondrial DNA (mtDNA) harbors essential mutations linked to aging, neurodegenerative diseases, and complex muscle disorders. Due to its uniparental and haploid inheritance, mtDNA captures matrilineal evolutionary trajectories, playing a crucial role in population and medical genetics. However, critical questions about the genomic diversity patterns, inheritance models, and evolutionary and medical functions of mtDNA remain unresolved or underexplored, particularly in the transition from traditional genotyping to large-scale genomic analyses. This review summarizes recent advancements in data-driven genomic research and technological innovations that address these questions and clarify the biological impact of nuclear-mitochondrial segments (NUMTs) and mtDNA variants on human health, disease, and evolution. We propose a streamlined pipeline to comprehensively identify mtDNA and NUMT genomic diversity using advanced sequencing and computational technologies. Haplotype-resolved mtDNA sequencing and assembly can distinguish authentic mtDNA variants from NUMTs, reduce diagnostic inaccuracies, and provide clearer insights into heteroplasmy patterns and the authenticity of paternal inheritance. This review emphasizes the need for integrative multi-omics approaches and emerging long-read sequencing technologies to gain new insights into mutation mechanisms, the influence of heteroplasmy and paternal inheritance on mtDNA diversity and disease susceptibility, and the detailed functions of NUMTs.

Keywords: NUMT; evolutionary medicine; genomic database; heteroplasmy; mitochondrial DNA.

Publication types

Review