Mitochondrial DNA Genome Research Articles

The complete mitochondrial genome of the Spotted Greenshank Tringa guttifer (Charadriiforemes: Charadriidae)

The complete mitochondrial DNA genome of the Endangered Spotted Greenshank, Tringa guttifer, was detected using phenol–chloroform extraction procedure and polymerase chain reaction method. It is a circular molecule of 16,935 bp in size, exhibits the typical structure of mitochondrial genomes of Charadriiformes, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. Overall base composition of the complete mitochondrial DNA is A (31.7%), T (25.5%), C (29.5%), and G (13.3%), the percentage of A and T (57.2%) is higher than G and C. The phylogenetic relationships of 34 species were reconstructed using the maximum-likelihood and Bayesian inference, and unravel T. guttifer is close to T. semipalmata.

The complete mitochondrial genome sequence and gene organization of Istigobius campbelli (Perciformes, Gobiidae) with phylogenetic consideration

The complete mitochondrial genome DNA sequence of Istigobius campbelli was 16,527 bp in length. It consists of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. 28 of the 37 genes were encoded on the heavy strand, and 9 of them were encoded on the light strand. The overall base composition of the genome is 27.84% A, 25.81% T, 29.68% C, and 16.67% G. The phylogenetic tree suggested I. campbelli was genetically closest to Acentrogobius pflaumii and Oxyurichthys formosanus. This study could provide valuable information for further studies on I. campbelli.

Biodiversity lost: The phylogenetic relationships of a complete mitochondrial DNA genome sequenced from the extinct wolf population of Sicily

Using next-generation sequencing, we obtained for the first time a complete mitochondrial DNA genome from a museum specimen of the extinct wolf (Canis lupus) population of the island of Sicily (Italy). Phylogenetic analyses indicated that this genome, which was aligned with a number of historical and extant wolf and dog mitogenomes sampled worldwide, was closely related to an Italian wolf mtDNA genome (the observed proportion of nucleotide sites at which the two sequences are different was p = 0.0012), five to seven times shorter than divergence among Sicilian and any other known wolf mtDNA genomes (p range = 0.0050 – 0.0070). Sicilian and Italian mitogenomes joined a basal clade belonging to the mtDNA haplogroup-2 of ancient western European wolf populations (Pilot et al., 2010). Bayesian calibration of divergence times indicated that this clade coalesced at MRCA = 13.400 years (with 95% HPD = 4000 – 21.230 years). These findings suggest that wolves probably colonized Sicily from southern Italy towards the end of the last Pleistocene glacial maximum when the Strait of Messina was almost totally dry. Additional mtDNA and genomic data will further clarify the origin and population dynamics before the extinction of wolves in Sicily.

A Novel Pathogenic Variant in MT-CO2 Causes an Isolated Mitochondrial Complex IV Deficiency and Late-Onset Cerebellar Ataxia.

Both nuclear and mitochondrial DNA defects can cause isolated cytochrome c oxidase (COX; complex IV) deficiency, leading to the development of the mitochondrial disease. We report a 52-year-old female patient who presented with a late-onset, progressive cerebellar ataxia, tremor and axonal neuropathy. No family history of neurological disorder was reported. Although her muscle biopsy demonstrated a significant COX deficiency, there was no clinical and electromyographical evidence of myopathy. Electrophysiological studies identified low frequency sinusoidal postural tremor at 3 Hz, corroborating the clinical finding of cerebellar dysfunction. Complete sequencing of the mitochondrial DNA genome in muscle identified a novel MT-CO2 variant, m.8163A>G predicting p.(Tyr193Cys). We present several lines of evidence, in proving the pathogenicity of this heteroplasmic mitochondrial DNA variant, as the cause of her clinical presentation. Our findings serve as an important reminder that full mitochondrial DNA analysis should be included in the diagnostic pipeline for investigating individuals with spinocerebellar ataxia.

Analysis of Human Mitochondrial DNA Content by Southern Blotting and Nonradioactive Probe Hybridization.

A single cell can contain several thousand copies of the mitochondrial DNA genome or mtDNA. Tools for assessing mtDNA content are necessary for clinical and toxicological research, as mtDNA depletion is linked to genetic disease and drug toxicity. For instance, mtDNA depletion syndromes are typically fatal childhood disorders that are characterized by severe declines in mtDNA content in affected tissues. Mitochondrial toxicity and mtDNA depletion have also been reported in human immunodeficiency virus-infected patients treated with certain nucleoside reverse transcriptase inhibitors. Further, cell culture studies have demonstrated that exposure to oxidative stress stimulates mtDNA degradation. Here we outline a Southern blot and nonradioactive digoxigenin-labeled probe hybridization method to estimate mtDNA content in human genomic DNA samples. © 2019 by John Wiley & Sons, Inc.

Using Machine Learning to Predict the Development of Diabetes and Potential Biomarkers Linked to Cardiac Risk

BackgroundDiabetes mellitus is a chronic, debilitating disease that continues to affect a greater percentage of people each year. Among its systemic comorbidities, diabetics are two to four times more likely to develop cardiovascular diseases. While glycosylated hemoglobin (HbA1c) remains the primary diagnostic for diabetes mellitus onset, predicting health outcomes through a single measure is difficult, with disparities existing between ethnic and demographic groups. The purpose of this study was to use machine learning algorithms to develop personalized prognostics in predicting the development and progression of diabetes mellitus in the heart.MethodsRight atrial appendages from 48 patients, 29 non‐diabetic and 19 type 2 diabetic, were procured from the WVU Ruby Memorial Hospital. Machine learning was applied to physiological (sex, BMI, HbA1c, comorbidities), biochemical (total methylation and mitochondrial bioenergetics functional parameters), and sequencing data (mitochondrial genomic DNA single nucleotide polymorphisms (SNPs) and nuclear genomic DNA CpG island methylation) for each patient. Supervised (including HbA1c) and unsupervised (without HbA1c) learning evaluated the efficiency of testing and training sets through classification and regression trees, logistic regression, support vector machines, and k nearest neighbors.ResultsNuclear 5‐methylcytosine content and s‐adenosyl methionine activity matched diagnostic accuracy of HbA1c (~91% testing) for all patients. Mitochondrial DNA SNPs found in the D‐Loop region (SNP‐152C, ‐16126C, and ‐16362C) were significantly associated with diabetes incidence. The CpG island for the mitochondrial transcription factor A (TFAM) revealed specific CpG sites (chr10:58384915 and 58385262) that showed high accuracy (~89% testing) in predicting diabetes incidence. Unsupervised learning, both binary (diabetic or non‐diabetic) and multi‐classification (diabetic, pre‐diabetic, or non‐diabetic), confirmed these results.ConclusionsUsing machine learning, we were able to predict health outcomes through the combination of multiple physiological, biochemical, and sequencing approaches, assessing the development and progression of diabetes. Linking mitochondrial and genomic/epigenomic data, we detail how learning algorithms can be applied to forwarding personalized medicine and developing novel, more advanced prognostics in the heart.Support or Funding InformationR01 HL‐128485 (JMH), AHA‐17PRE33660333 (QAH), WV‐INBRE support by NIH Grant P20GM103434, WVU Flow Cytometry & Single Cell Core supported by MBRCC CoBRE Grant GM103488 and Fortessa S10 Grant OD016165, and the Community Foundation for the Ohio Valley Whipkey Trust. We would like to acknowledge the WVU Genomics Core Facility, Morgantown WV for support provided to help make this work possible.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Mitochondrial DNA and genomic DNA ratio in embryo culture medium is not a reliable predictor for in vitro fertilization outcome

To investigate the ratio of mitochondrial DNA to genomic DNA (mt/gDNA) in embryo culture medium as a possible predictor for embryonic development and pregnancy outcome, we collected a total of 93 embryo biopsy specimens from 52 women at the corresponding Day 3 (D3) and Day 5 (D5) embryo culture medium of in vitro fertilization. With the multiple annealing and looping-based amplification cycles method of next-generation sequencing for whole genome amplification, we examined the karyotype of the biopsy samples and the mt/gDNA ratio in the culture medium. Results showed that the ratio of mt/gDNA had an upward trend with decreasing trophectoderm levels with no significant difference. At the same time, from D3 to D5, the mt/gDNA ratio in the medium of embryos that failed to become blastocysts showed an upward trend, and the mt/gDNA ratio of medium from embryos that reached blastulation with successful pregnancy showed a decreasing trend, but the differences were not statistically significant. We conclude that there is a certain correlation between mt/gDNA ratio and early embryonic development, but it does not reach a level that can be used as a clinical predictor.

Investigation of human paternal mitochondrial DNA transmission in ART babies whose fathers with male infertility

ObjectiveTo investigate the paternal mitochondrial DNA’s effect on assisted reproductive technology (ART) applications and possible paternal mitochondrial DNA transmission in male factor infertility diagnosed fathers. Study designStudy group was designed according to the families all of which applied to assisted reproductive technologies as a result of male infertility. A total of 16 trios (48 mother-father-child samples) which contain 7 newborns and 9 infants born by in vitro fertilization method (IVF-ICSI) were studied using “Illumina, MiSeq” next-generation sequencing platform (Case-parent trio study). The study has been conducted between February 2017 and May 2018. Result(s)Sequencing analysis results were investigated on the basis of “mother-father-child”, “mother-child” and “father-child” mitochondrial DNA whole genome sequence data, respectively. In 14 “trios” of 16; maternal mitochondrial DNA haplotype were detected for children, the remaining 2 “trios” had different mitochondrial DNA haplotypes when compared to their mother and fathers. Also; “father-child” sharing same genetic variants (SNP (“Single nucleotide polymorphism”) / MNP (“Multiple nucleotide polymorphism”) / INDEL (“Insertion/Deletion”) were found in 8 “trios”. In 5 “trios” of 16; 98–99% paternal mitochondrial DNA genome sequence similarity were obtained by alignment of “father-child” mitochondrial DNA genome. Conclusion(s)This study is the first whole mitochondrial genome investigation for paternal mitochondrial DNA contribution in human IVF / ICSI applied trio cases. Our findings for paternally derived variants could be the result of intermolecular recombination between maternal and paternal mitochondrial DNA.

Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly

The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 380 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively “trivial” aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic.

Evidence of Austronesian Genetic Lineages in East Africa and South Arabia: Complex Dispersal from Madagascar and Southeast Asia

The Austronesian dispersal across the Indonesian Ocean to Madagascar and the Comoros has been well documented, but in an unexplained anomaly, few to no traces have been found of the Austronesian expansion in East Africa or the Arabian Peninsula. To revisit this peculiarity, we surveyed the Western Indian Ocean rim populations to identify potential Austronesian genetic ancestry. We generated full mitochondrial DNA genomes and genome-wide genotyping data for these individuals and compared them with the Banjar, the Indonesian source population of the westward Austronesian dispersal. We find strong support for Asian genetic contributions to maternal lineages and autosomal variation in modern day Somalia and Yemen. Surprisingly, this input reveals two apparently different geographic origins and timings of admixture for the Austronesian contact; one at a very early phase (likely associated with the early Austronesian dispersals), and a later movement dating to the end of nineteenth century. These Austronesian gene flows come, respectively, from Madagascar and directly from an unidentified location in Island Southeast Asia. This result reveals a far more complex dynamic of Austronesian dispersals through the Western Indian Ocean than has previously been understood and suggests that Austronesian movements within the Indian Ocean may have been part of a lengthy process, probably continuing well into the modern era.

Association of mitochondrial DNA mutations with Chinese esophageal squamous cell carcinomas (ESCC) by analyzing the whole mitochondrial DNA genomes

Mitochondrial DNA (mtDNA) mutations play crucial roles in the pathogenesis and progression of human malignancies. However, studies reporting associations between mitochondrial DNA mutations and risks of esophageal squamous cell carcinomas (ESCC) have seldom been reported. In this study, we sequenced 22 cancer tissues and the corresponding adjacent non-cancerous tissues collected from 11 ESCC patients. The mtDNA sequence length ranged from 16,568–16,579 bp. The results indicated that there are several sensitive sites in the 22 mtDNAs, especially in the control region (CR) and protein-coding genes (PCGs). The 22 mtDNA sequences were classified into haplogroups B, D, G, M, and Z; haplogroup D and haplogroup M were shared within a wider distribution, but haplotype G was found only in two samples and all the patients showed the southern of East Asia or Northern East Asian haplogroups, the number and ratio of patients showed the southern of East Asia or Southeast Asia characters are equal. Our findings suggest that mtDNA haplogroups D and M might be potential risks for ESCC. In addition, our results suggest that mtDNA haplogroups and some sensitive sites confer genetic susceptibility to ESCC and they can serve as potential biomarkers for clinical diagnosis.

A first record of complete mitochondrial genome of Cryptalaus Ohira (Insecta: Coleoptera: Elateridae) based on C. yamato (Nakane)

A complete mitochondrial DNA genome of a rare click beetle, Cryptalaus yamato (Nakane), is the first reported. The genome consists of 15,882 base pairs including 13 protein-coding genes (PCGs), 20 tRNAs, two rRNAs, and a 1279 bp long AT-rich region. The overall base composition is 69.4% AT and 30.6% GC. The maximum likelihood analysis based on nucleotide sequence data of 13 PCGs supported that C. yamato is involved in monophyletic group of Elateridae.

The complete mitochondrial genome of Tatia intermedia (Siluriformes, Auchenipteridae)

The complete mitochondrial DNA genome of Tatia intermedia was first reported using next-generation sequencing method. The entire length of mitochondrial genome is 16,582 bp and the nucleotide composition was made up of 31.4% A, 26.7% T, 26.2% C, and 15.7% G, respectively, indicating an A + T (58.1%)-rich feature. With the exception of eight tRNA genes and NADH6, mitochondrial genes are encoded on the heavy strand, which was similar to that in other vertebrates. The phylogenetic relationship of T. intermedia and other Auchenipteridae species showed that the species of Auchenipteridae were gathered in the same branch.

Draft mitochondrial DNA genome of a 1920 Barbados cryptic Bemisia tabaci ‘New World’ species (Hemiptera: Aleyrodidae)

Identification of invasive whitefly Bemisia tabaci cryptic species is best achieved by an integrated approach combining mating and genomic studies including complete mitochondrial DNA genomes (mitogenomes) characterization. We present the draft mitogenome of a 1920 historical B. tabaci specimen obtained using High Throughput Sequencing (HTS) technology. Our B. tabaci partial mtCOI gene best matched the B. tabaci ‘NW’ (New World) cryptic species (e.g. to AY057133; nucleotide identity: 99.85%). It has a circular genome of ca. 15,325bp with 13 protein-coding genes (PCGs), 22 tRNA’s, and two rRNA genes. A total of 43 amino acid residues differed between a Sanger-sequenced ‘NW’ mitogenome (AY521259.2) and this HTS-generated ‘NW’ mitogenome. High intra-specific amino acid conservation was observed across the partial 657 bp mitochondrial DNA COI (mtCOI) gene region used in species identification (i.e. from nucleotides 782 to 1438) when compared between both ‘NW’ (MK386668, AY521259.2) species.

Complete mitochondrial genome and phylogenetic analysis of Anabarilius brevianalis (Teleostei, Cyprinidae, Cultrinae)

The complete mitochondrial DNA genome of Anabarilius brevianalis was determined. The entire mitochondrial genome is 16,610 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 control region (CR). The gene arrangement, gene numbers, base composition, and codon usage pattern of this species were similar to the typical Cultrinae fish mitochondrial genomes. Maximum likelihood phylogenetic analysis based on the complete mitochondrial sequence shows the A. brevianalis clustered with A. grahami are closely related to Hemiculter branch within the subfamily Cultrinae.

The complete mitochondrial genome of Cyprinus Carpio Var. Guilin rice flower carp and its phylogeny in Cyprinidae

The complete mitochondrial genomic DNA of Cyprinus carpio var. Guilin was 16,582 bp in length, including 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes, and a D-loop region. Phylogenetic analysis indicated that it was most closely related to Cyprinus carpio isolate Oujiang. The results will provide a reference for further studies on the genetic relationships and evolution process of Cyprinus carpio variants in Cyprinidae.

Kajian Genetika untuk Konservasi Badak Sumatera (Dicerorhinus sumatrensis Gloger, 1841)

ABSTRACT The Sumatran rhinoceros is one of the most critically endangered species of large mammals due to habitat loss, fragmentation and illegal hunting so that the population of this species drastically decreased. At present, reproductive problems with a limited population are also a threat and require an appropriate solution. Therefore, data on molecular genetic information is very important as a basis for conservation management in maintaining long-term persistence of this species. Phylogenetic analysis based on sequences of CO1, 12SrRNA, and Cytochrome b gen from mitochondrial DNA genomes using neighbor-joining and genetic distance matrix calculations with the Kimura 2-parameter model (K2P) were implemented in pairwise distance calculations in the Mega (Molecular Evolutionary Genetics Analysis) program version 6.05. The study results show the genetic distance of Sumatran Rhinos from Sumatra and Kalimantan respectively 0.2 ± 0.00%, 0.8 ± 0.4%, and 0%. These results were reconfirmed that the Sumatran Rhino species in Sumatra and Kalimantan were taxonomy is no different. The study of genetic diversity based on D-loop of mitochondrial DNA contained 5 haplotypes, namely haplotypes 1 and 2 originating from the island of Sumatra and haplotypes 3, 4, and 5 originating from the island of Borneo. The genetic distance between individuals in this study ranged from 2.54 ± 1.4%, haplotype diversity (Hd) was 0.8 ± 0.172, nucleotide diversity (Pi) was 0.02269, Fu’s Fs value was 2.523, and Tajima’s test was 0.69497. The positive value (Fu’s Fs and Tajima’s test) indicated low genetic diversity and population expansion in the Sumatran rhino. In the study using 10 microsatellite loci, where the average number of allel/loci in Kalimantan (1.68) was higher than in Sumatra (1.22). Data from this study show that genetic variation between Sumatran rhinoceros from Sumatra and Kalimantan can be used as a basis for alternative that the populations of Sumatra and Borneo be considered as a single management unit. Keywords: Sumateran Rhinoceros, Mitochondrial DNA, Microsatellite

Complete mitochondrial genome of Leptaulax koreanus (Coleoptera: Passalidae), a Korean endemic bess beetle

In the present paper, we make a first report on the complete mitochondrial DNA genome of Leptaulax koreanus, a Korean endemic species, in Passalidae. The mitogenome is 18,730 base pairs with 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a 4240 bp long AT-rich region. The overall base composition is 78.4% AT and 21.6% GC. The maximum likelihood analysis suggested that L. koreanus is a sister to other Scarabaeoidea species.

SINGLE NUCLEOTIDE POLYMORPHISMS IN THE D-LOOP REGION OF THE MITOCHONDRIAL GENOMES OF INDIVIDUALS FROM TWO ETHNIC GROUPS KINH AND MANG OF AUSTRO-ASIATIC LANGUAGE FAMILY

The two hypervariable regions HV-I and HV-II in the D-loop region are the most diverse region in the mitochondrial human genome. These DNA regions have an important role in population genetics and human evolution research. In this study, we identified single nucleotide polymorphisms (SNPs) in the D-loop region of the human mitochondrial DNA genomes of individuals in two Vietnamese ethnic groups: Kinh and Mang. 81 blood samples from 50 Kinh and 31 Mang unrelated individuals were collected for genomic DNA extraction. Using PCR and specific primers, we successfully amplified the two HV-I and HV-II regions with respective sizes of 693 bp and 689 bp. The PCR products then were purified and sequenced. After alignment to the reference mitochondrial genome rCRS (NC_012920.1), 96 SNPs were detected in the Kinh ethnic group, of which many polymorphisms were firstly found in this ethnic and 36 SNPs in the Mang ethnic group. Of the identified 132 SNPs, 16 SNPs were significantly different between the two ethnic groups (p < 0.05). Eight out of the 16 SNPs (T146C, T199C, A16182C, T16217C, T16297C, T16140C, A16183C, T16189C) were frequently found in the Kinh ethnic group but not or only rarely in the Mang ethnic group. On the other hand, 4 SNPs (C151T, A16162G, A16269G, T16271C) were commonly found in the Mang population but rarely in the Kinh population. These findings suggest that although Kinh and Mang belong to one language family (Austro-Asiatic), there is a noticeable diversity in the mitochondrial genomes between these two Vietnamese ethnic groups.

Whole sequence of the mitochondrial DNA genome of Kearns Sayre Syndrome patients: Identification of deletions and variants

Mitochondria both produce the energy of the cell as ATP via respiration and regulate cellular metabolism. Accordingly, any deletion or mutation in the mitochondrial DNA (mtDNA) may result in a disease. One of these diseases is Kearns Sayre syndrome (KSS), described for the first time in 1958, where different large-scale deletions of different sizes and at different positions have been reported in the mitochondrial genome of patients with similar clinical symptoms. In this study, sequences of the mitochondrial genome of three patients with clinic features of KSS were analyzed. Our results revealed the position, heteroplasmy percentage, size of deletions, and their haplogroups. Two patients contained deletions reported previously and one patient showed a new deletion not reported previously. These results display for the first time a systematic analysis of mtDNA variants in the whole mtDNA genome of patients with KSS to help to understand their association with the disease.