![]() Today, next-generation sequencing (NGS) has revolutionized the field of mtDNA haplotyping. later used the terms “haplotypes” and “haplogroups” (haplotype clusters or lineages), in particular, “A” through “D,” for the defining mtDNA polymorphisms of Indigenous tribes who peopled the Americas. published their groundbreaking discovery on lineage tracing of modern human mtDNA that led to a single tribe or “mother” in Africa, colloquially named, “Mitochondrial Eve”. Consequently, the discriminative power of HV-polymorphisms has been exploited for maternal lineage tracing, population studies, and forensics. The hypervariable regions (HV-I, HV-II, and HV-III) within the CR have a higher mutation rate than coding regions. The non-coding region, or control region (CR), plays a crucial role in mitochondrial DNA replication and transcription. It contains 37 genes, including 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. ![]() The human mitogenome is a 16.6-kilobase (kb), double-stranded, circular DNA that is separate from the nuclear genome and matrilineally inherited. This widely accepted “Endosymbiotic Theory” is supported by the presence of DNA (mitogenome) and a distinct RNA translation system within the eukaryotic cell. Mitochondria presumably originated as ancestral bacteria that were engulfed and integrated within host cells over 1.5 billion years ago. Since then, the field of mitochondrial genomics has advanced rapidly and revolutionized matrilineal genetics, mitochondrial pathologies, and oncogenetics, providing insights into human evolution, population genetics, and disease mechanisms. However, it was not until 1981 that the first complete sequence of human mitochondrial DNA (mtDNA) was published and established as the mtDNA Cambridge Reference Sequence (CRS). Mitochondrial DNA was first discovered in chick embryos by electron microscopy in 1963. Today, mitochondria are recognized as dynamic, ubiquitous organelles involved in various biological functions, including ATP synthesis, calcium signaling, metabolism, and apoptosis. “Mitochondria” were named by Carl Benda in 1898 to describe the threadlike granules found within the cytoplasm of eukaryotic cells. ![]() ![]() The mtDNA workflow proved to be a rapid, efficient, and accurate means of sequence analysis for translational mitogenomics. The auto-generated read mapping, variants track, and table of haplotypes and geo-origins were completed in 15 min for 47 samples. The hMITO DB automated workflow was tested using mtDNA-NGS sequences derived from Pap smears and cervical cancer cell lines. The macro-haplogroup (A to Z) distribution and representative phylogenetic tree were found to be consistent with published literature. The database was constructed from 4286 mitogenomes. To address this, we developed a customized human mitogenome database (hMITO DB) embedded in a CLC Genomics workflow for read mapping, variant analysis, haplotyping, and geo-mapping. However, mtDNA next-generation sequencing (NGS) analysis for matrilineal haplotyping and phylogeographic inference remains hindered by the lack of a consolidated mitogenome database and an efficient bioinformatics pipeline. The field of mitochondrial genomics has advanced rapidly and has revolutionized disciplines such as molecular anthropology, population genetics, and medical genetics/oncogenetics.
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