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Journal: Mitochondrial DNA

28

There are two subspecies of Rhinolophus ferrumequinum currently recognized in South Korea. The Korean greater horseshoe bat subspecies, Rhinolophus ferrumequinum quelpartis, is distributed only in Jeju Island. The complete mitochondrial genome of the island subspecies was determined and revealed 99.7% similarity to the mainland subspecies Rhinolophus ferrumequinum korai. If d-loop region is excluded, similarity of the two genomes was 99.9%.

Concepts: DNA, Genome, South Korea, Korean language, Jeju-do, Rhinolophus, Rhinolophidae, Greater Horseshoe Bat

28

Tandemly repeated sequences are a common feature of vertebrate mitochondrial DNA control regions. However, questions still remain about their mode of evolution and function. To better understand patterns of variation in length and to explore the existence of previously described domain, we have characterized the control region structure of the Amazonian ornamental fish Nannostomus eques and Nannostomus unifasciatus. The control region ranged from 1121 to 1142 bp in length and could be separated into three domains: the domain associated with the extended terminal associated sequences, the central conserved domain, and the conserved sequence blocks domain. In the first domain, we encountered a sequence repeated 10 times in tandem (variable number tandem repeat (VNTR)) that could adopt an “inverted repetitions” type structural conformation. The results suggest that the VNTR pattern encountered in both N. eques and N. unifasciatus is consistent with the prerequisites of the illegitimate elongation model in which the unequal pairing of the chains near the 5'-end of the control region favors the formation of repetitions.

Concepts: DNA, Bacteria, Evolution, Molecular biology, Mitochondrion, Amazon River, Variable number tandem repeat, Short tandem repeat

28

In this study, the 17,694-bp long complete mitochondrial genome (mitogenome) of the dwarf honeybee, Apis florea (Hymenoptera: Apidae), was described, and a noteworthy triplicated tRNA(ser)(AGN) region and an extraordinary long A+T-rich region with repeat regions were identified. The gene arrangement of A. florea mitogenome was identical to that of Apis mellifera, but it contained three tRNA(Ser)(AGN), each of which was preceded by a 44-bp-long repeat unit and followed by a 64-bp-long repeat unit plus one complete first repeat adjacent to tRNA(Met). A total of 1610-bp long two repeat regions in 1987-bp long A+T-rich region were composed of nearly identical 141-219-bp long 5 tandem repeats and 50-52-bp long 12 tandem repeats that were encompassed by three non-repeat sequences. One potential explanation for this repeat sequence is slipped-strand mispairing and unequal crossing-over events during DNA replication.

Concepts: DNA, Mitochondrion, Mitochondrial DNA, Insect, DNA replication, Honey bee, Apis florea, Apis andreniformis

27

Abstract The Chinese mandarin fish (Siniperca chuatsi) is currently one of the most important economic freshwater fish in China, whereas the wild resource has declined dramatically in recent years. In this study, we examined the genetic structure and diversity of five populations from the middle reach of the Yangtze River using mitochondrial cytochrome b sequences and microsatellite markers. This research revealed high genetic diversity and low genetic differentiation of S. chuatsi from these regions. The pairwise Fst values of the two markers showed low and no-significant differentiation among populations. AMOVA analysis of two markers and the haplotype genealogy of the Cytb gene confirmed these results. The STRUCTURE analysis of the microsatellite marker implied that the dam upon the tributary of the Yangtze River blocked the gene flow among those regions. This research will be useful in breeding programs and conservation management of this species.

Concepts: DNA, Genetics, Evolution, Biology, China, Population genetics, Shanghai, Mandarin fish

27

The correct detection of mitochondrial DNA (mtDNA) heteroplasmy by automated sequencing presents methodological constraints. The main goals of this study are to investigate the effect of sense and distance of primers in heteroplasmy detection and to test if there are differences in the accurate determination of heteroplasmy involving transitions or transversions. A gradient of the heteroplasmy levels was generated for mtDNA positions 9477 (transition G/A) and 15,452 (transversion C/A). Amplification and subsequent sequencing with forward and reverse primers, situated at 550 and 150 bp from the heteroplasmic positions, were performed. Our data provide evidence that there is a significant difference between the use of forward and reverse primers. The forward primer is the primer that seems to give a better approximation to the real proportion of the variants. No significant differences were found concerning the distance at which the sequencing primers were placed neither between the analysis of transitions and transversions. The data collected in this study are a starting point that allows to glimpse the importance of the sequencing primers in the accurate detection of point heteroplasmy, providing additional insight into the overall automated sequencing strategy.

Concepts: DNA, Mutation, Mitochondrion, Mitochondrial DNA, Statistical significance, DNA polymerase, Paternal mtDNA transmission, Heteroplasmy

27

To investigate the spectrum of common mitochondrial mutations in Tunisia during the years of 2002-2012, 226 patients with mitochondrial disorders were clinically diagnosed with hearing loss, Leigh syndrome (LS), diabetes, cardiomyopathy, Kearns-Sayre syndrome (KSS), Pearson syndrome (PS), myopathy, mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes syndrome (MELAS) and Wolfram syndrome. Restriction fragment length polymorphism (PCR-RFLP), radioactive PCR, single specific primer-PCR (SSP-PCR) analysis and PCR-sequencing methods were used to identify the mutations. Two cases with m.1555A>G mutation and two families with the novel 12S rRNA m.735A>G transition were detected in patients with hearing loss. Three cases with m.8993T>G mutation, two patients with the novel m.5523T>G and m.5559A>G mutations in the tRNA(Trp) gene, and two individuals with the undescribed m.9478T>C mutation in the cytochrome c oxidase subunit III (COXIII) gene were found with LS. In addition, one case with hypertrophic cardiomyopathy and deafness presented the ND1 m.3395A>G mutation and the tRNA(Ile) m.4316A>G variation. Besides, multiple mitochondrial deletions were detected in patients with KSS, PS, and Wolfram syndrome. The m.14709T>C mutation in the tRNA(Glu) was reported in four maternally inherited diabetes and deafness patients and a novel tRNA(Val) m.1640A>G mutation was detected in a MELAS patient.

Concepts: DNA, Genetics, Mutation, Mitochondrion, DNA repair, Point mutation, Mitochondrial diseases, Cytochrome c oxidase subunit III

26

Abstract The violet-spotted reef lobster Enoplometopus debelius Holthuis, 1983 (Decapoda, Astacidea, Enoplometopidae) is found in the tropical reef areas of the Indo-Pacific region, and is a highly prized and very popular species in the aquarium trade industry. The complete mitochondrial genome of E. debelius has 15,641 base pairs consisting of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region of 746 bp. The base composition of E. debelius is 36.4% A, 35.3% T, 18.1% C, 10.3% G, and the species has an AT content of 71.7%. The E. debelius mitogenome was found to have a gene arrangement and transcriptional polarity identical to that of the Homarus americanus mitogenome, a representative of the arthropod ground pattern. Here, we present the complete mitogenome sequence of E. debelius, which is the first in the superfamily Enoplometopoidea. These data will provide a useful molecular resource for the phylogenetic study of the infraorder Astacidea/order Decapoda.

Concepts: DNA, Gene, Genetics, Genome, Species, Lobster, Astacidea, Reef lobster

26

Abstract The complete mitogenome sequence of Martes flavigula, which is an endangered and endemic species in South Korea, was determined. The genome is 16,533 bp in length and its gene arrangement pattern, gene content, and gene organization is identical to those of martens. The control region was located between the tRNAPro and tRNAPhe genes and is 1087 bp in length. This mitogenome sequence data might be an important role in the preservation of genetic resources by allowing researchers to conduct phylogenetic and systematic analyses of Mustelidae.

Concepts: DNA, Gene, Biology, Organism, Horizontal gene transfer, Mustelidae, Carnivora, Marten

26

Abstract The mitochondrial DNA (mtDNA) variant T16189C has been investigated in several metabolic diseases. In this study, we aimed to estimate the frequency of the T16189C variant in Tunisian and other Mediterranean populations and to evaluate the impact of this variant on the phylogeny of Mediterranean populations. Blood sample of 240 unrelated Tunisian subjects were recruited from several Tunisian localities. The hypervariable region 1 of the mtDNA were amplified and sequenced. Additional sequences (N = 4921) from Mediterranean populations were compiled from previous studies. The average frequency of T16189C variant in Tunisia (29%) is similar to that observed in North African and Near Eastern populations. Our findings showed positive correlation of the T16189C variant with Sub-Saharan and North African lineages, while a negative correlation was found with the Eurasian haplogroups, reaching its maximum with the Eurasian haplogroup H. The principal component analyses showed a high internal heterogeneity between Tunisian localities. At the Mediterranean scale, Tunisians are closer to North African (Algerian and Moroccan) and Near Eastern populations (Syrians and Palestinians) than to Europeans.

Concepts: DNA, Mitochondrion, Africa, Genetic genealogy, Tunisia, Algeria, Morocco, Human mitochondrial DNA haplogroup

26

Abstract The Metahomaloptera omeiensis is the only one species within the genus, Metahomaloptera. The complete mitochondrial genome of M. omeiensis was sequenced, which was 16,558 bp in length, including 13 protein-coding genes, 7 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 1 control region. It has the typical circular molecule structure of vertebrate’s mitochondrial genome. The whole base composition was estimated to be 29.44% A, 25.44% T, 28.28% C and 16.84% G with AT bias of 54.88%. The complete mitogenome of M. omeiensis provides the basis for genetic resources and phylogenetic analyses on this freshwater fish species.

Concepts: DNA, Gene, Genetics, Archaea, Organism, RNA, Ribosome, Transfer RNA