Mitochondrial Genetic Heterogeneity in Leber’s Hereditary Optic Neuropathy: Original Study with Meta-Analysis

Leber’s hereditary optic neuropathy (LHON) is a mitochondrial disorder that causes loss of central vision. Three primary variants (m.3460G>A, m.11778G>A, and m.14484T>C) and about 16 secondary variants are responsible for LHON in the majority of the cases. We investigated the complete mitochondrial DNA (mtDNA) sequences of 189 LHON patients and found a total of 54 disease-linked pathogenic variants. The primary variants m.11778G>A and m.14484T>C were accountable for only 14.81% and 2.64% cases, respectively. Patients with these two variants also possessed additional disease-associated variants. Among 156 patients who lacked the three primary variants, 16.02% harboured other LHON-associated variants either alone or in combination with other disease-associated variants. Furthermore, we observed that none of the haplogroups were explicitly associated with LHON. We performed a meta-analysis of m.4216T>C and m.13708G>A and found a significant association of these two variants with the LHON phenotype. Based on this study, we recommend the use of complete mtDNA sequencing to diagnose LHON, as we found disease-associated variants throughout the mitochondrial genome.

Mitochondrial Genome of Spirometra theileri Compared with Other Spirometra Species

This study was carried out to provide information on the taxonomic classification and analysis of mitochondrial genomes of <i>Spirometra theileri</i>. One strobila of <i>S. theileri</i> was collected from the intestine of an African leopard (<i>Panthera pardus</i>) in the Maswa Game Reserve, Tanzania. The complete mtDNA sequence of <i>S. theileri</i> was 13,685 bp encoding 36 genes including 12 protein genes, 22 tRNAs and 2 rRNAs with absence of <i>atp</i>8. Divergences of 12 protein-coding genes were as follow: 14.9% between <i>S. theileri</i> and <i>S. erinaceieuropaei</i>, 14.7% between <i>S. theileri</i> and <i>S. decipiens</i>, and 14.5% between <i>S. theileri</i> with <i>S. ranarum</i>. Divergences of 12 proteins of <i>S. theileri</i> and <i>S. erinaceieuropaei</i> ranged from 2.3% in <i>cox</i>1 to 15.7% in <i>nad</i>5, while <i>S. theileri</i> varied from <i>S. decipiens</i> and <i>S. ranarum</i> by 1.3% in <i>cox</i>1 to 15.7% in <i>nad</i>3. Phylogenetic relationship of <i>S. theileri</i> with eucestodes inferred using the maximum likelihood and Bayesian inferences exhibited identical tree topologies. A clade composed of <i>S. decipiens</i> and <i>S. ranarum</i> formed a sister species to <i>S. erinaceieuropaei</i>, and <i>S. theileri</i> formed a sister species to all species in this clade. Within the diphyllobothridean clade, <i>Dibothriocephalus, Diphyllobothrium</i> and <i>Spirometra</i> formed a monophyletic group, and sister genera were well supported.

Single-cell Individual Complete mtDNA Sequencing Uncovers Hidden Mitochondrial Heterogeneity in Human and Mouse Oocytes

The ontogeny and dynamics of mtDNA heteroplasmy remain unclear due to limitations of current mtDNA sequencing methods. We developed individual Mitochondrial Genome sequencing (iMiGseq) of full-length mtDNA for ultra-sensitive variant detection, complete haplotyping, and unbiased evaluation of heteroplasmy levels, all at the individual mtDNA molecule level. iMiGseq uncovers unappreciated levels of heteroplasmic variants in single healthy human oocytes well below the current 1% detection limit, of which numerous variants are detrimental and could contribute to late-onset mitochondrial disease and cancer. Extreme mtDNA heterogeneity among oocytes of the same mouse female, and a strong selection against deleterious mutations in human oocytes are observed. iMiGseq could comprehensively characterize and haplotype single-nucleotide and structural variants of mtDNA and their genetic linkage in NARP/Leigh syndrome patient-derived cells. Therefore, iMiGseq could not only elucidate the mitochondrial etiology of diseases, but also help diagnose and prevent mitochondrial diseases with unprecedented precision.

A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds

The commercialization of porgies or seabreams of the family Sparidae has greatly increased in the last decade, and some valuable species have become subject to seafood substitution. DNA regions currently used for fish species identification in fresh and processed products belong to the mitochondrial (mt) genes cytochrome b (Cytb), cytochrome c oxidase I (COI), 16S and 12S. However, these markers amplify for fragments with lower divergence within and between some species, failing to provide informative barcodes. We adopted comparative mitogenomics, through the analysis of complete mtDNA sequences, as a compatible approach toward studying new barcoding markers. The intent is to develop a specific and rapid assay for the identification of the common pandora Pagellus erythrinus, a sparid species frequently subject to fraudulent replacement. The genetic diversity analysis (Hamming distance, p-genetic distance, gene-by-gene sequence variability) between 16 sparid mtDNA genomes highlighted the discriminating potential of a 291 bp NAD2 gene fragment. A pair of species-specific primers were successfully designed and tested by end-point and real-time PCR, achieving amplification only in P. erythrinus among several fish species. The use of the NAD2 barcoding marker provides a rapid presence/absence method for the identification of P. erythrinus.

The mitochondrial genome of Angiostrongylus mackerrasae is distinct from A. cantonensis and A. malaysiensis

The native rat lungworm (Angiostrongylus mackerrasae) and the invasive rat lungworm (Angiostrongylus cantonensis) occur in eastern Australia. The species identity of A. mackerrasae remained unquestioned until relatively recently, when compilation of mtDNA data indicated that A. mackerrasae sensu Aghazadeh et al. (2015b) clusters within A. cantonensis based on their mitochondrial genomes (mtDNA). To re-evaluate the species identity of A. mackerrasae, we sought material that would be morphologically conspecific with A. mackerrasae. We combined morphological and molecular approaches to confirm or refute the specific status of A. mackerrasae. Nematodes conspecific with A. mackerrasae from Rattus fuscipes and Rattus rattus were collected in Queensland, Australia. Morphologically identified A. mackerrasae voucher specimens were characterized using amplification of cox1 followed by the generation of reference complete mtDNA. The morphologically distinct A. cantonensis, A. mackerrasae and A. malaysiensis are genetically distinguishable forming a monophyletic mtDNA lineage. We conclude that A. mackerrasae sensu Aghazadeh et al. (2015b) is a misidentified specimen of A. cantonensis. The availability of the mtDNA genome of A. mackerrasae enables its unequivocal genetic identification and differentiation from other Angiostrongylus species.

The paternal and maternal genetic history of Vietnamese populations

Vietnam exhibits great cultural and linguistic diversity, yet the genetic history of Vietnamese populations remains poorly understood. Previous studies focused mostly on the majority Kinh group, and thus the genetic diversity of the many other groups has not yet been investigated. Here we analyze complete mtDNA genome sequences and ~2.3 Mb sequences of the male-specific portion of the Y chromosome from the Kinh and 16 minority populations, encompassing all five language families present in Vietnam. We find highly variable levels of diversity within and between groups that do not correlate with either geography or language family. In particular, the Mang and Sila have undergone recent, independent bottlenecks, while the majority group, Kinh, exhibits low levels of differentiation with other groups. The two Austronesian-speaking groups, Giarai and Ede, show a potential impact of matrilocality on their patterns of variation. Overall, we find that isolation, coupled with limited contact involving some groups, has been the major factor influencing the genetic structure of Vietnamese populations, and that there is substantial genetic diversity that is not represented by the Kinh.

Phylogenetic Relationships of Russian Far-East Apis cerana with Other North Asian Populations

Apis cerana Fabricius, 1793 is the eastern honeybee species distributed throughout Asia from the tropical climate in the southern part to the temperate climate in the northern part. We sequenced and annotated the complete mitochondrial DNA (mtDNA) of A. cerana from Vladivostok, Primorsky Krai of the Russian Far East and uploaded it to the database GenBank (AP018450). MtDNA sequence has 15,919 bp length, AT-content 84% and GC-content 16% and contains 22 tRNA genes, 13 protein-coding genes, two ribosomal RNA genes, one AT-rich region and four non-coding intergenic regions (NC1-4). All proteincoding genes start with ATT and ATG codons, except for ATC, the start codon of the ATP8 gene, which and stop with the common stop codons TAA and TAG. A comparative analysis of complete mtDNA of A. cerana from China, Indonesia, Korea, Malaysia, Russia, Taiwan, Thailand, Vietnam, and Japan found that the Russian Far East Apis cerana differed from others on the subspecies level. Based on the comparative analysis of complete mtDNA (~16,000 bp), nuclear DNA (nDNA) gene Vitellogenin (VG) (~4,100 bp) and morphological measurements (six parameters), we assumed that the Russian Far-East A. cerana can be a distinct northern Asia population and can be described as a separate unique subspecies of A. c. ussuriensis subsp. nov. A. c. koreana subsp. nov. is also validated and described as a new subspecies.