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Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis

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https://www.readbyqxmd.com/read/30198386/a-mitochondrial-long-noncoding-rna-in-atlantic-cod-harbors-complex-heteroplasmic-tandem-repeat-motifs
#1
Tor Erik Jørgensen, Bård Ove Karlsen, Åse Emblem, Lars Martin Jakt, Jarle T Nordeide, Truls Moum, Steinar D Johansen
A heteroplasmic tandem repeat (HTR) array occupies 100 to 300 bp of the mitochondrial DNA control region in the Atlantic cod, and recently we noted that the repeat appeared integrated in a polyadenylated mitochondrial long noncoding RNA. Here we provide a more detailed analysis of the mitochondrial HTR in the mitochondrial genome of 134 Atlantic cod specimens. We report all specimens to harbor mitochondrial HTRs in the control region, and identified 26 distinct variants among the 402 repeat motifs assessed...
September 10, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/30196742/evidence-for-intra-mitochondrial-variation-in-population-genetic-structure-of-platycephalus-sp-1-in-the-northwestern-pacific
#2
Shengyong Xu, Zhiyang Wang, Yan Zhang, Tianxiang Gao, Jianwei Zou, Xiumei Zhang
Understanding evolutionary dynamics of population structure and genetic diversity of marine fish species is of great importance for fishery management and resource conservation. Platycephalus sp.1 is a commercially important marine fish in the Northwestern Pacific. Yet, current understanding of population genetic patterns of Platycephalus sp.1 remains limited. In this study, the Platycephalus sp.1 individuals from four populations in the Northwestern Pacific, which cover large geographic distances and latitudinal gradients, were sampled to examine genetic diversity and population structure by investigating the mitochondrial sequences of Cytochrome b (CYTB, 1141 bp) and control region (CR, 458 bp), and then to assess intra-mitochondrial genetic variability by using a combination of population- and individual-based analytical approaches...
September 8, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/30044161/late-pleistocene-genetic-diversification-and-demographic-expansion-in-the-widely-distributed-neotropical-ant-neoponera-villosa-ponerinae
#3
Marilyn Mendoza-Ramírez, Jorge Gutiérrez-Rodríguez, Chantal Poteaux, Patricia Ornelas-García, Alejandro Zaldívar-Riverón
Phylogeographic studies of continent-wide distributed species are key to understand population dynamics processes that occurred at large geographical scales. Here, we examined two mitochondrial (mt) DNA sequence (COI, Cyt b) and eight nuclear microsatellites markers to investigate the cohesiveness, genetic diversity and demographic history of Neoponera villosa (Fabricius), a ponerine ant species widely distributed along most part of the Neotropics and southern Nearctic. The reconstructed phylogeny and mt variation supported the cohesiveness of the examined populations of N...
July 25, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/30043666/evidence-for-a-duplicated-mitochondrial-region-in-audubon-s-shearwater-based-on-minion-sequencing
#4
Lucas Torres, Andreanna J Welch, Catherine Zanchetta, R Terry Chesser, Maxime Manno, Cécile Donnadieu, Vincent Bretagnolle, Eric Pante
Mitochondrial genetic markers have been extensively used to study the phylogenetics and phylogeography of many birds, including seabirds of the order Procellariiformes. Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated, but no DNA fragment covering the entire duplication has been sequenced. We sequenced the complete mitochondrial genome of a non-albatross species of Procellariiformes, Puffinus lherminieri (Audubon's shearwater) using the long-read MinION (ONT) technology...
July 25, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29991298/structure-evolution-and-phylogenetic-informativeness-of-eelpouts-cottoidei-zoarcales-mitochondrial-control-region-sequences
#5
Sergei V Turanov, Youn-Ho Lee, Yuri Ph Kartavtsev
Control region (CR) is a major non-coding domain of mitochondrial DNA in vertebrates which contains the promoters for replication and transcription of mitochondrial genome along with the binding sites for metabolic machinery and, hence, is a vital element for the integrity of mitochondrial genome as a biological replicator. The origin and diversity of structural elements within CR have been intensively studied in recent years with the involvement of new diverse taxa. In this paper, we provide new data on the nucleotide and structural patterns of CR evolution and phylogenetic suitability among eelpouts (Cottoidei: Zoarcales)...
July 10, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29989478/molecular-identification-and-phylogenetic-assessment-of-species-under-genus-parapenaeopsis-alcock-1901-from-indian-waters
#6
L Mog Chowdhury, Kathirvelpandian A, Divya Pr, Basheer Vs, Rajool Shanis, Mohitha Chelath, A Pavan-Kumar, Gopal Krishna
Genus Parapenaeopsis constitute an important fishery resource in Indian waters. Parapenaeopsis stylifera, being morphologically very similar to Parapenaeopsis coromandelica, mainly differentiated using telsonic armature and it is subject of controversy regarding the number of armature for the species. The present study was aimed to resolve the taxonomic ambiguity between P. stylifera and P. coromandelica and to study phylogenetic relationship among five species under the genus Parapenaeopsis using partial sequences of mitochondrial 16S ribosomal DNA (rDNA) and cytochrome c oxidase subunit I (COI) genes...
July 10, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29989460/population-structure-and-genetic-diversity-of-hatchery-stocks-as-revealed-by-combined-mtdna-fragment-sequences-in-indian-major-carp-catla-catla
#7
L Sahoo, M Mohanty, P K Meher, K Murmu, J K Sundaray, P Das
Catla catla is the second most important Indian major carp due to high growth rate and acceptance to consumers for food value. It is widely cultured in the Indian subcontinent as monoculture or polyculture. In the present study, genetic diversity among hatchery stocks (total 218 samples of catla) collected from different geographical regions of India was examined using mtDNA fragment sequence of Cyt b (306 bp) and D loop (710 bp). High numbers (57) of population specific haplotypes were observed in the present study...
July 10, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29956577/levels-and-patterns-of-genetic-variation-in-japanese-whiting-sillago-japonica-based-on-mitochondrial-dna-control-region
#8
Tian-Xiang Gao, Tian-Yan Yang, Takashi Yanagimoto, Yong-Shuang Xiao
Japanese whiting (Sillago japonica) is a commercially important demersal fish distributed along the coasts of East Asia and becomes recently an aquaculture species. Despite its commercial importance, the levels and patterns of population genetic variation remain poorly understood. In this study, 346 specimens were collected from 14 localities along the coastal waters of China, Korea and Japan and their genetic variation was analyzed with mtDNA control region (D-loop) sequences. A total of 131 polymorphic sites were detected which determined 294 haplotypes...
June 29, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29956555/phylogenetic-analysis-and-genetic-structure-of-the-seahorse-hippocampus-fuscus-from-the-arabian-and-red-sea-based-on-mitochondrial-dna-sequences
#9
Xin Wang, Xue Han, Yuan Zhang, Shuaishuai Liu, Qiang Lin
The unique body morphology and specialized life history traits make seahorses excellent flagship species for many issues in marine conservation and biological evolution. In this study, the complete mitochondrial genome of Hippocampus fuscus was determined. Phylogenetic analyses showed that H. fuscus had a close genetic relationship to Hippocampus reidi, which give us a new insight into the speciation and dispersal among seahorse genus. A total of 843 base pairs of cytochrome b (Cytb) gene and a 646 base pairs of cytochrome oxidase I (COI) gene were obtained from 36 H...
June 29, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29338473/phylogenomics-of-tomato-chloroplasts-using-assembly-and-alignment-free-method
#10
Raúl Martin Amado Cattáneo, Luis Diambra, Andrés Norman McCarthy
Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance...
October 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29280404/delineating-closely-related-species-of-tylostega-meyrick-lepidoptera-crambidae-spilomelinae-from-mainland-china-using-dna-barcodes
#11
Misbah Ullah, Yanling Dong, Pingping Qiao, Yalin Zhang, Zhaofu Yang
Integrative taxonomic study of three species of the genus Tylostega revealed that the genetic distances of the COI gene among the tested species was relatively large (3.27-7.60%). The Automatic Barcode Gap Discovery (ABGD) system performed better than the Barcode Index Number (BIN) in discriminating closely related species. This work provides a molecular baseline for future integrative taxonomic study of Crambidae.
October 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29228836/complete-mtdna-sequencing-reveals-mutations-m-9185t-c-and-m-13513g-a-in-three-patients-with-leigh-syndrome
#12
Dita Pelnena, Birute Burnyte, Eriks Jankevics, Baiba Lace, Evelina Dagyte, Kristina Grigalioniene, Algirdas Utkus, Zita Krumina, Jolanta Rozentale, Irina Adomaitiene, Janis Stavusis, Liana Pliss, Inna Inashkina
The most common mitochondrial disorder in children is Leigh syndrome, which is a progressive and genetically heterogeneous neurodegenerative disorder caused by mutations in nuclear genes or mitochondrial DNA (mtDNA). In the present study, a novel and robust method of complete mtDNA sequencing, which allows amplification of the whole mitochondrial genome, was tested. Complete mtDNA sequencing was performed in a cohort of patients with suspected mitochondrial mutations. Patients from Latvia and Lithuania (n = 92 and n = 57, respectively) referred by clinical geneticists were included...
October 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29224405/phylogeography-and-genetic-population-structure-of-the-spadenose-shark-scoliodon-macrorhynchos-from-the-chinese-coast
#13
Xiao Chen, Jun-Jie Wang, Wei-Ming Ai, Hao Chen, Hung-Du Lin
The population structure of Scoliodon macrorhynchos from the Chinese coast was investigated using the mitochondrial control region. All 19 mtDNA haplotypes from 219 sequences were identified. Relatively high average haplotype diversity (0.797) and relatively low average nucleotide diversity (0.0013) were found together with a recent and sudden population expansion. Analysis of the mismatch distributions, neutrality tests and Bayesian skyline plot showed a pattern consistent with a recent population expansion event that may have taken place during the last glacial maximum (LGM)...
October 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29216781/comparative-analyses-of-species-delimitation-methods-with-molecular-data-in-snappers-perciformes-lutjaninae
#14
Raimundo da Silva, Pedro L V Peloso, Marcelo José Sturaro, Ivana Veneza, Iracilda Sampaio, Horacio Schneider, Grazielle Gomes
The integration of approaches that allow the incorporation of stochasticity of gene histories with phylogenetic methods resulted in new approaches for the old issue of species delimitation. Nevertheless, coalescent methods seem problematic for taxa with large effective population size and shallow temporal diversification (like marine fishes). Here, we investigate the performance of single-locus (cytochrome oxidase 1, commonly used in DNA barcoding initiatives) methods for molecular species delimitation in snappers of Lutjaninae from the Western Atlantic and Pacific Eastern...
October 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29191077/reconstruction-of-mitogenomes-by-ngs-and-phylogenetic-implications-for-leaf-beetles
#15
Nan Song, Xinming Yin, Xincheng Zhao, Junhua Chen, Jian Yin
Mitochondrial genome (mitogenome) sequences are frequently used to infer phylogenetic relationships of insects at different taxonomic levels. Next-generation sequencing (NGS) techniques are revolutionizing many fields of biology, and allow for acquisition of insect mitogenomes for large number of species simultaneously. In this study, 20 full or partial mitogenomes were sequenced from pooled genomic DNA samples by NGS for leaf beetles (Chrysomelidae). Combined with published mitogenome sequences, a higher level phylogeny of Chrysomelidae was reconstructed under maximum likelihood and Bayesian inference with different models and various data treatments...
October 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29172898/mitochondrial-genome-mutations-in-13-subunits-of-respiratory-chain-complexes-in-chinese-han-and-mongolian-hypertensive-individuals
#16
Ying Zhao, Xi Chen, Haide Li, Chao Zhu, Yang Li, Yuqi Liu
Mitochondrial DNA (mtDNA) mutations are associated with cardiovascular disease, including hypertension (HTN). Here we performed a genetic and molecular analysis of 13 mtDNA-encoded subunits of respiratory chain complexes in 100 Chinese Han and 80 Mongolian HTN cases, and 100 Han and 42 Mongolian normotension subjects. The total cholesterol of the Mongolian normotensive subjects was higher than that of the Han normotensive group (p < .05). Sequence analysis identified 636 point mutations in the 13 mtDNA-encoded subunits in the Han and Mongolian hypertensive individuals, including 66 in NADH dehydrogenase subunit 1(ND1), 62 in ND2, 71 in COI, 29 in COII, 17 in ATP8, one in ATP6/8, 49 in ATP6, 27 in COIII, 27 in ND3, 14 in ND4L, 74 in ND4, 97 in ND5, 24 in ND6, and 78 in CYTB...
October 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29166850/fishes-in-the-desert-mitochondrial-variation-and-phylogeography-of-danakilia-actinopterygii-cichlidae-and-aphanius-actinopterygii-cyprinodontidae-in-the-danakil-depression-of-northeastern-africa
#17
Giorgio Chiozzi, Melanie L J Stiassny, S Elizabeth Alter, Giuseppe De Marchi, Yohannes Mebrahtu, Misikire Tessema, Berhan Asmamaw, Mauro Fasola, Adriana Bellati
The Danakil Depression in northeastern Africa represents one of the harshest arid environments on Earth, yet two genera of fishes, Danakilia (Cichlidae) and Aphanius (Cyprinodontidae), share its sparse aquatic habitats. The evolutionary history of these fishes is investigated here in the context of genetic, geological and paleoenvironmental information. We collected samples from seven sites and assessed phylogeographic relationships using concatenated COI and cytb mtDNA genes. Danakilia morphospecies show low differentiation at mitochondrial markers, but variation is partitioned between a northern cluster containing D...
October 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29166817/ambiguities-in-the-taxonomic-assignment-and-species-delineation-of-botryllid-ascidians-from-the-israeli-mediterranean-and-other-coastlines
#18
Eitan Reem, Jacob Douek, Baruch Rinkevich
Based on mtCOI sequences comparisons, recent studies reassigned the 'dwarf Botrylloides leachii' from the Levant as Botrylloides nigrum. Here we conducted a survey of the literature and of deposited mtCOI sequences of botryllid ascidians, elucidating ambiguities in their taxonomy. We found that the species, dwarf morph of Botrylloides leachii, Botrylloides nigrum, Botryllus aster and Botryllus arenaceus are grouped together on a single molecular taxon. Then, results of three additional markers (18S, 28S, H3) contradicted literature suggestions, revealing minute distances between Botrylloides leachii and the 'dwarf Botrylloides leachii'...
October 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29161943/analysis-of-sequence-divergence-in-redfin-cypriniformes-cyprinidae-tribolodon-based-on-mtdna-and-ndna-markers-with-inferences-in-systematics-and-genetics-of-speciation
#19
Anna O Zolotova, Yuri Ph Kartavtsev
To clarify relationship of species of the genus Tribolodon in the Russian part of their distribution ranges, two mitochondrial markers (Co-1 and Cyt-b), a nuclear marker (Rho), and a gene marker of rDNA internal transcribed spacer (ITS-1,2) were used. Depending on the marker, different numbers of species groups were detected by the ABGD method, but in combination with the analysis of phylograms, these data generally support the known species clusters and regional intraspecies groups. A complex analysis of sequences from three redfin species within the area of the study, based on four marker genes and using the methods of molecular phylogenetics, ordination of genetic distances, recombinant analysis, and population genetic approaches, has revealed clusters of three commonly recognized species, regional intraspecific groups or individuals of local populations, and few hybrid individuals...
October 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29157065/small-spotted-bodies-with-multiple-specific-mitochondrial-dnas-existence-of-diverse-and-differentiated-tigrina-lineages-or-species-leopardus-spp-felidae-mammalia-throughout-latin-america
#20
Manuel Ruiz-García, Myreya Pinedo-Castro, Joseph Mark Shostell
We analysed two sets of mitochondrial (mt) DNA data from tigrinas (traditionally, Leopardus tigrinus) we sampled in Costa Rica, Venezuela, Colombia, Ecuador, Peru, Bolivia, northwestern and northeastern Argentina and southern Brazil. Additionally, the analysis included some GenBank sequences from southern, central and northeastern Brazil. The first mt set (mt ATP8+mt 16S rRNA with 41 tigrina) revealed the existence of seven different tigrina-like haplogroups. They could represent, at least, 4-6 different tigrina species following the Phylogenetic Species Concept (PSC)...
October 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
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