ND2 Gene Research Articles

Expanding the clinical spectrum of the mitochondrial mutation A13084T in the ND5 gene.

Our group previously published about a patient with a LS/MELAS (Leigh syndrome/mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes) overlap phenotype associated with a novel mitochondrial mutation in the ND5 gene.1 At that time, his 38-year-old mother presented only migraine and asymptomatic bilateral optic atrophy, without other neurologic signs or symptoms. Headache attacks, occurring about twice a month, were localized mainly in the right frontoparietal region, sometimes associated with nausea or vomit or phonophotophobia, and were responsive to nonsteroidal anti-inflammatory drugs. She carried lower levels of heteroplasmy of the same A13084T mutation (57% in lymphocytes and 48% in fibroblasts) compared with her son (82% in blood and 72% in fibroblasts). The authors gratefully thank the Associazione Centro Dino Ferrari for its support.

Alternations in mitochondrial genome in carcinogenesis of HPV positive cervix

ObjectiveIt is well known that mitochondrial dysfunctions are involved in tumorigenesis. A special interest of scientists is mitochondrial ND1 gene (mtND1). Recently detected mutations in the mtND1 can disrupt the normal activity of complex I and affect oxidative phosphorylation, thus leading to increase reactive oxygen species production. This study was undertaken to determine the alternations in the mtND1 and evaluate their association with development of precancerous lesions and cervical cancer. MethodsIn the study 29 cervical cancer, 28 low grade squamous intraepithelial lesion (L-SIL) and 30 high grade squamous intraepithelial lesion (H-SIL) HPV positive fragments tissue were screened for the presence of mtND1 mutations. ResultsOur study showed that mutations in the mtND1 gene were detected in patients with precancerous stage, as well as cervical cancer. We have identified 12 point mutations in 116 analyzed precancerous and cancer samples HPV positive. Most detected missense mutations were previously described, except one (p. M156K) with Grantham value 95. The lower expression of mRNA ND1 was detected in cervical cancer cases and in all samples in which mtND1 mutations were identified. Our analyses revealed that level of ROS production was higher in cervical cancer tissues and all cases characterized by mtND1 mutations. ConclusionsWe hypothesize that mutations in MT-ND1 observed in H-SIL and cancer could activate cervical carcinogenesis by increased ROS production.

Crossing Lydekker's Line: Northern Water Dragons (Tropicagama temporalis) Colonized the Mollucan Islands of Indonesia from New Guinea

Wallace's and Lydekker's Lines both describe important biogeographic barriers in the Indo-Australian Archipelago, with Wallace's Line demarcating the boundary of the Greater Sunda Shelf and Lydekker's Line indicating the edge of the Sahul continental shelf. Despite their similarities, Wallace's Line has been much more heavily studied than has Lydekker's Line, yet provides an interesting system for testing the source of fauna into eastern Wallacea. New collections of Northern Water Dragons, Tropicagama temporalis, from several islands in Maluku, eastern Indonesia now allow for an assessment of the phylogeography of the species and the ability to test if New Guinean or Australian populations served as the source for over-water dispersal across Lydekker's Line into Maluku. We collected specimens from remote islands in eastern Indonesia, sequenced the mitochondrial ND2 gene, and aligned the data to previously sequenced specimens on GenBank. We conducted several phylogenetic and divergence time analyses to investigate the source population and timing of dispersal. We found low genetic diversity among the islands in Maluku, and these samples showed little genetic divergence from New Guinea samples. The New Guinea and Maluku populations diverged less than 1 million years ago (Ma) and together diverged from the Australian population between 2.3 and 4.7 Ma. These results, along with patterns in other taxa, illustrated that, despite Australia's close geographic proximity to many of the islands in southeastern Indonesia, New Guinea has been the more frequent source of Wallacean fauna from Sahul.

Validating the relationships: which species of Myotis “nattereri” group (Chiroptera: Vespertilionidae) actually inhabits the Caucasus

Abstract Due to their conservative morphology, the complexity of the taxonomic composition of the Myotis “nattereri” species complex was highly underestimated until recently. In recent studies, the form inhabiting the Caucasus region was allocated to the species Myotis tschuliensis. However, no molecular data was available from its type territory in Turkmenistan. We successfully isolated DNA from two paratypes of M. tschuliensis stored in the Zoological museum of Moscow State University and obtained partial sequences of the mitochondrial gene ND1. The analysis of the DNA showed that the specimens from the Caucasus and Turkmenistan undoubtedly belong to the same genetic lineage. However, morphometric analysis of cranial and dental features showed that the Caucasus and Turkmenistan populations differ from each other approximately to the same extent as M. tschuliensis from M. nattereri. It is possible that there is a still undescribed geographical race in the Caucasus. However, final clarification of the taxonomic status of this population requires more extensive studies, both genetic and morphological.

Mitochondrial genomes of the Dorcus velutinus complex (Coleoptera: Lucanidae) with the large intergenic spacer showing unique short sequence repeats and their implications for systematics

• Mitochondrial genomes of Dorcus velutinus complex are assembled and described. • Validity of Dorcus tenuihirsutus as a distinct species is confirmed. • Sequence repeat pattern in intergenic spacer is found useful for lucanid systematics. Mitochondrial genomes of the three lucanid species in the Dorcus velutinus complex – Dorcus velutinus Thomson, D. ursulus Arrow and D. tenuihirsutus Kim and Kim – were assembled and analyzed through next generation sequencing. The mitogenome sequences were used to infer phylogenetic relationships among Dorcus species. Our analyses revealed that the newly sequenced mitogenomes are comparable in their size, content, and gene arrangement to other lucanid mitogenomes reported to date. However, we confirmed the presence of a large intergenic spacer (IGS) between trnS ( UCN ) and ND1 genes, whose length varied from 170 bp (in D. tenuihirsutus ) to 193 bp (in D. ursulus and D. velutinus ). Within this IGS region, a short sequence fragment (TACTAAATT) was found uniquely across the three species of Dorcus velutinus complex. Our phylogenetic analyses show that the D. velutinus complex constitutes a distinct clade with a significant divergence from other species of the genus Dorcus sensu stricto. Furthermore, we reaffirm the validity of D. tenuihirsutu s – a species originally described from Korea – as a distinct species, though the taxonomic status of D. ursulus remains to be studied further. Finally, we find the presence and location of large IGSs to be useful for studying evolutionary history and species delimitation in stag beetles.

A novel duplex SYBR Green real-time PCR with melting curve analysis method for beef adulteration detection

An efficient and reliable duplex SYBR Green real-time quantitative PCR (qPCR) method for beef products adulteration detection was developed based on bovine specific and vertebrate universal primers. By analyzing the numbers, positions (Tm value) of melting curve peaks of the duplex PCR products, we simultaneously identified bovine and preliminary screened non-bovine in samples, and also semi-quantified the bovine percentage according to the area ratios of peaks. All of these were necessary for adulteration determination. The specific and universal primers were designed based on mitochondrial genes ND4 and 16S rRNA respectively, their amplicons Tm values were 72.6 ± 0.5 °C and 79–81 °C. There might be some other peaks at 74–78 °C and above 81 °C if non-bovine components existed. Thelimit of detectionwas 1 pgforbovineDNA, and1 – 30 pg fornon-bovineDNAbasedon differentspecies.

Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast

The whole mitochondrial genome ofLateolabrax maculatus(Cuvier, 1828) was used to investigate the reasons for the observed patterns of genetic differentiation among 12 populations in northern and southern China. The haplotype diversity and nucleotide diversity ofL. maculatuswere 0.998 and 0.00169, respectively. Pairwise FSTvalues between populations ranged from 0.001 to 0.429, correlating positively with geographic distance. Genetic structure analysis and haplotype network analysis indicated that these populations were split into two groups, in agreement with geographic segregation and environment. Tajima’s D values, Fu’s Fs tests and Bayesian skyline plot (BSP) indicated that a demographic expansion event may have occurred in the history ofL. maculatus. Through selection pressure analysis, we found evidence of significant negative selection at the ATP6, ND3, Cytb, COX3, COX2 and COX1 genes. In our hypotheses, this study implied that demographic events and selection of local environmental conditions, including temperature, are responsible for population divergence. These findings are a step forward toward the understanding of the genetic basis of differentiation and adaptation, as well as conservation ofL. maculatus.

Taxonomic evaluation of two similar bent-toed geckos Squamata: Gekkonidae: Cyrtodactylus Gray, 1827) from East Java, Indonesia.

The bent-toed geckos of the genus Cyrtodactylus are the most speciose land vertebrates of Southeast Asia (about 300 species so far) and new species continue to be recognized at a rapid rate. Within the last decade three new species were described from Java, Indonesia, C. semiadii, C. petani, and C. klakahensis. The latter two are very similar, except for differences in the precloacal depression in adult males. These two species have relatively close type localities, separated from each other by only about 50 km, and with similar habitat type and elevation. Our study aimed to evaluate the taxonomic status of C. klakahensis and C. petani using both morphological and genetic evidence. These two species are genetically similar, with a genetic divergence of only 1.5 to 1.6%. This divergence is well below the level of typically characterizes sister species of Cyrtodactylus (approximately 4% in the mitochondrial ND2 gene), and is more in line with population variation due to geographic distance. Further examination of specimens, from both type localities, showed no diagnostic morphological characters between the two species. Thus, we conclude that C. klakahensis and C. petani are conspecific, and following article 23 of the ICZN, C. klakahensis is herein considered a junior synonym of C. petani.

Sequencing and characterization of complete mitogenome DNA of Rasbora tornieri (Cypriniformes: Cyprinidae: Rasbora) and its evolutionary significance

The yellowtail rasbora (Rasbora tornieri) is a miniature ray-finned fish categorized under the genus Rasbora in the family of Cyprinidae. In this study, a complete mitogenome sequence of R. tornieri was sequenced using four primers targeting two halves of the mitogenome with overlapping flanking regions. The size of mitogenome was 16,573 bp, housing 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organization was detected between this species and other members of Rasbora genus. The heavy strand encompassed 28 genes while the light strand accommodated the other nine genes. Most protein-coding genes execute ATG as start codon, excluding COI and ND3 genes, which utilized GTG instead. The central conserved sequence blocks (CSB-E, CSB-F and CSB-D), variable sequence blocks (CSB-1, CSB-3 and CSB-2) as well as the terminal associated sequence (TAS) were conserved within the control region. The maximum likelihood phylogenetic family tree revealed the divergence of R. tornieri from the basal region of the Rasbora clade, where its evolutionary relationships with other Rasbora members are poorly resolved as indicated by the low bootstrap values. This work acts as window for further population genetics and molecular evolution studies of Rasbora genus in future.

A new species of Hemiphyllodactylus (Squamata: Gekkonidae) from Tuyen Quang Province, Vietnam.

A new species of the gekkonid genus Hemiphyllodactylus is described from limestone karst forest of Tuyen Quang Province, northern Vietnam based on morphological differences and molecular divergence. Hemiphyllodactylus nahangensis sp. nov. is distinguished from the remaining congeners by having the unique combination of the following characters: a bisexual taxon; SVL of adults 41.4-43.6 mm; dorsal scale rows 18-23; ventral scale rows 9-13; chin scales bordering mental and first infralabial distinctly enlarged; 22-24 pore-bearing femoral and precloacal scales, in a continuous row, absent in females; digital lamella formula 3-4-5-4 (forefoot) and 4-5-5-5 (hindfoot); cloacal spur single, present in both sexes; dark lateral head stripe indistinct; postsacral mark cream and bearing anteriorly projecting arms. In phylogenetic analyses, the new species is placed in a clade that includes H. dushanensis, H. hongkongensis, H. huishuiensis, H. ngocsonensis and H. zugi. In terms of pairwise genetic distance, the new species is at least 5.9%-6.6% divergent from other congeners based on a fragment of the mitochondrial gene ND2.

A novel m.11406 T > A mutation in mitochondrial ND4 gene causes MELAS syndrome

Pathogenic point mutations of mitochondrial DNA (mtDNA) are associated with a large number of heterogeneous diseases involving multiple systems with which patients may present with a wide range of clinical phenotypes. In this study, we describe a novel heteroplasmic missense mutation, m.11406 T > A, of the ND4 gene encoding the subunit 4 of mitochondrial complex I in a 32-year-old woman with recurrent epileptic seizure, headache and bilateral hearing loss. Skeletal muscle histochemistry demonstrated that approximately 20% of fibers were cytochrome C oxidase (COX) deficient with increased activity of succinate dehydrogenase (SDH). Further investigations in muscle specimens showed significantly reduced level of ND4 protein. It is interesting that the subunits of complex I (ND1 and NDFUB8) and complex IV(CO1) were also remarkably decreased. These findings indicate that ND1, NDFUB8 and CO1 are more susceptible than other subunits to mutations in the mitochondrial ND4 gene.

The complete mitochondrial genome of Aesop slipper lobster Scyllarides haanii (De Haan, 1841)

The complete mitochondrial genome of Scyllarides haanii from South China Sea was first determined and characterized. With a length of 15,666 bp, the circular mitogenome of S. haanii consists of 22 tRNA genes, two rRNA genes, 13 protein-coding genes (PCGs), and one control region. The nucleotide composition is significantly biased (A, G, T, and C was 32.05%, 12.45%, 33.97%, and 21.53%, respectively) with A + T contents of 66.02%. Two PCGs used an unusual initiation codon, and five PCGs were ended with an uncomplete or abnormal stop codon. One microsatellite was identified in the mitogenome located in ND4 gene. Phylogenetic analysis demonstrated that S. haanii was first clustered with Scyllarides squammosus, then together with Scyllarides latus.

The complete mitochondrial genome of the African leaf butterfly Kallimoides rumia (Insecta: Lepidoptera: Nymphalidae)

The African leaf butterfly Kallimoides rumia Doubleday, 1849 (Nymphalidae), lives in the understory of Afrotropical primary forests. Genome skimming with Illumina sequencing of K. rumia permitted assembly of a complete circular mitogenome of 15,234 bp consisting of 80.9% AT nucleotides, 22 tRNAs, 13 protein-coding genes, 2 rRNAs and a control region. Kallimoides rumia COX1 features an atypical start codon (CGA). Genes ATP6, COX1, COX2, ND2, ND4 and ND5 feature incomplete stop codons, completed by adding 3’ A residues to the mRNA. Phylogenetic reconstruction places K. rumia as a distinct lineage, not closely related to Kallima, consistent with previous phylogenetic hypotheses.

Complete mitochondrial genome of Tropidophorus hangnam (Squamata: Scincidae) with phylogenetic analysis

The complete mitochondrial genome (mitogenome) of Tropidophorus hangnam was sequenced from its paratype (GenBank accession no. MN977920). It was 16,777 bp in length with a base composition of 31.99% A, 29.49% C, 14.34% G, and 24.18% T, and a GC content of 43.83%. The genome includes 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region (D loop). Most T. hangnam genes are located on the H strand, except for the ND6 gene and eight tRNA genes, which are located on the L strand. Phylogenetic analyses based on 13 PCGs indicated that T. hangnam is sister to the clade composed of the genera Scincella and Sphenomorphus. The newly sequenced T. hangnam mitogenome will provide basic data for further studies on the genetic diversity and molecular phylogenetic relationships of the genus Tropidophorus.

The complete mitochondrial genome of the maize weevil, Sitophilus zeamais (Coleoptera: Curculionidae)

The complete mitochondrial genome (mitogenome) of Sitophilus zeamais was determined by an Illumina platform. This mitogenome was 18,531 bp in length, containing 13 protein coding genes, 2 rRNA genes, 22 tRNA genes that is typical among curculionoidea. Stop codon was incomplete for ND4 gene and ND5. The non-coding intergenic regions have increased in size to 1033 bp due to expansion of tandem repeat arrays. Phylogenetic analysis on mitogenome of S. zeamais would further contribute to resolve phylogenetic position and interrelationships of Sitophilus.

Defect in Mitochondrial NADH-Dehydrogenase Genes in Canine Mast Cell Tumours

Abstract Recent studies have demonstrated a significant role of mitochondrial DNA (mtDNA) defects in the pathogenesis of many human and some canine tumours. The aim of this study was to identify mutations in the ND2 and ND4 mitochondrial genes in canine mast cell tumours and determine their association with the process of neoplastic transformation and the phenotypic traits of dogs. In total, 136 gene sequences from 68 biological samples, including blood and neoplastic tissue samples from 34 dogs with diagnosed MCTs, were analysed. The study consisted in DNA sequencing of the ND2 and ND4 genes as well as bioinformatics and statistical analyses. For the first time, mutations in NADH-dehydrogenase genes were detected in dogs with MCTs. In total, 22 polymorphic loci and 19 mutations in the ND2 and ND4 genes were identified. The majority of the identified mutations were homoplasmic, and tumour heteroplasmy was detected in eight nucleotide positions in three dogs. Seven of the ND2 mutations and two of the ND4 mutations caused an amino acid change. The changes in non-synonymous protein-coding SNPs did not exert an adverse effect on proteins. A statistically significant correlation of the presence of mutations/polymorphisms with the sex, age, and size of the dogs and the tumour location was demonstrated. Polymorphisms and mutations in NADH-dehydrogenase genes, including mastocyte-specific changes, in canine mast cell tumours that had not been reported earlier in the literature were identified. Some of these changes may imply that these are the hotspot mutations in canine mast cell tumours. It cannot be excluded that the molecular changes are directly associated with the development of mast cell tumours, and further investigations are needed to verify whether they can become molecular markers of MCTs in the future.

Mitochondrial genome diversity and population mitogenomics of polar cod (Boreogadus saida) and Arctic dwelling gadoids

High-latitude fish typically exhibit a narrow thermal tolerance window, which may pose challenges when coping with temperatures that shift outside of a species’ range of tolerance. Due to its role in aerobic metabolism and energy balance, the mitochondrial genome is likely critical for the acclimation and adaptation to differing temperature regimes in marine ectotherms. As oceans continue to warm, there is growing need to understand the ability of organisms to respond to changing environmental conditions given evidence that some species, in particular cold-water species, may already be experiencing difficulties. To assess how Arctic gadids in Alaska have responded to differential thermal preferences in the past and how regions are interconnected, we sequenced complete mitochondrial genomes for four Arctic gadids to determine the distribution of mitochondrial diversity and population-level structure as well as to detect signatures of selection acting on the mitochondrial genome. We found little population-level structure within all four species with the clear exception of Gulf of Alaska saffron cod (Eleginus gracilis). Northern localities exhibited higher levels of genetic diversity and primarily northern lineages were observed within polar cod (Boreogadus saida) and saffron cod, likely reflecting asymmetrical dispersal and potentially admixture of distinct lineages via ocean currents. The main evolutionary force shaping the evolution of the mitogenome appears to be purifying selection, but we also identified potential positive selection of candidate amino acid replacements primarily in complex I (ND genes) in polar cod. The high levels of mitochondrial diversity observed in our study and large population size may provide this species with the ability to respond evolutionarily (i.e. long-term) to a changing environment.

Correction to: Genetic characteristics of the Iranian honey bee, Apis mellifera meda, based on mitochondrial genes of ND4, ND4L and ND6 and their internal transcribed spacers

Honey bees are one of the most important social insects in the world. Genetic markers are powerful tools for differentiating honey bee subspecies. The purpose of the present research was the introduction of a new barcoding marker and assessment of the accuracy and discriminatory abilities of ND4, ND4L, ND6 genes and related intergenic spacers for the phylogenetic study of Iranian honey bees. Sampling was conducted throughout Iran (30 locations). ND4–ND4L–ND6 (with their ITS regions) demonstrated the most accurate analysis for the phylogenetic study of Iranian honey bees compared with ND4–ND4L (with ITS1) and ND4L–ND6 (with ITS2, ITS3, ITS4 and ITS5 regions). Additionally, the findings illustrated that all the collected honey bee samples were A. m. meda except those collected from the Kolachay area which were classified as A. m. carnica. Ten haplotypes were identified in the Iranian honey bee populations using the mitochondrial sequences of ND4–ND4L–ND6. Two main haplogroups were identified in the distribution range of the sampled areas. The samples of haplotype 1 containing the shortest sequence length (1580 bp), found in the Qazvin, Marand, Najafabad, Firuzkuh, Gonabad, Ilam, Birjand, Dehdasht, Sarpole-Zahab, Sanandaj, Borojerd, Sari, Zahedan and Shahrekurd samples, were grouped with A. m. meda KY464957. Moreover, the samples of haplotype 3 containing the longest sequence length (1588 bp) and found in the Kerman samples, was grouped with Bileh Savar and Soltaniyeh.

Two new species of Hemiphyllodactylus (Squamata: Gekkonidae) from Hoa Binh Province, Vietnam.

We describe two new species of the genus Hemiphyllodactylus on the basis of a new collection of geckos from limestone karst forest of Hoa Binh Province, northwestern Vietnam. Hemiphyllodactylus bonkowskii sp. nov. from Hang Kia-Pa Co Nature Reserve and Hemiphyllodactylus ngocsonensis sp. nov. from Ngoc Son-Ngo Luong Nature Reserve can be distinguished from each other and from their congeners by genetic distinction and morphological differences in circumnasal scales, chin scales, precloacal and femoral pores, cloacal spurs, dorsal scales, ventral scales, digital lamellae formula, and color pattern. In phylogenetic analyses, both new species are nested in a clade that includes H. dushanensis, H. flaviventris, H. hongkongensis, H. huishuiensis, H. kiziriani, H. serpispecus, and H. zugi. In terms of pairwise genetic distance, the two new species are at least 7.5%-8.5% divergent from other described species based on a fragment of the ND2 gene.

Late-onset MELAS syndrome with mtDNA 14453G\u2192A mutation masquerading as an acute encephalitis: a case report

BackgroundA unique patient with MELAS syndrome, who initially masqueraded as having acute encephalitis and was eventually diagnosed with MELAS syndrome harboring a mtDNA 14453G → A mutation, is described.Case presentationA 74-year-old Japanese man was admitted to another hospital due to acute onset of cognitive impairment and psychosis. After 7 days he was transferred to our hospital with seizures and deteriorating psychosis. The results of primary ancillary tests that included EEG, CSF findings, and brain MRI supported the diagnosis of an acute encephalitis. HSV-DNA and antibodies against neuronal surface antigens in the CSF were all negative. With the assistance of the lactate peak on the brain lesions in the magnetic resonance spectroscopy image and genetic analysis of the biopsied muscle, he was eventually diagnosed with MELAS syndrome harboring mtDNA 14453G → A mutation in the ND6 gene.ConclusionsThis case provides a caveat that MELAS syndrome can manifest in the symptoms and ancillary tests masquerading as an acute encephalitis caused by infection or autoimmunity. This is the first adult patient seen to harbor the mtDNA14453G → A with a unique onset, which broadens the phenotypic spectrum of MELAS syndrome associated with ND6 gene mutation.