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

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https://www.readbyqxmd.com/read/29991298/structure-evolution-and-phylogenetic-informativeness-of-eelpouts-cottoidei-zoarcales-mitochondrial-control-region-sequences
#1
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
#2
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
#3
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
#4
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
#5
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/29873574/constructing-the-genetic-population-demography-of-the-invasive-lionfish-pterois-miles-in-the-levant-basin-eastern-mediterranean
#6
Nir Stern, Carlos Jimenez, Mehmet Fatih Huseyinoglu, Vasilis Andreou, Louis Hadijioannou, Antonis Petrou, Bayram Öztürk, Daniel Golani, Shevy B S Rothman
The recent invasion of the lionfish Pterois miles to the Mediterranean draws major concerns to the fate of the indigenous ecosystem, based on previous knowledge of the species' detrimental capabilities as an introduced species in the Western Atlantic Ocean. In order to determine invasive patterns in the Eastern Mediterranean, we compared the genetic divergence of two mtDNA markers, the COI and D-loop, between and within the introduced Levantine and native range Red Sea populations of the lionfish. COI region presented a remarkably shallow genealogy, and both genes have failed to show a definite geographic population structure, with non-significant AMOVA and low pairwise FST values...
June 6, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29806523/alterations-in-mtdna-gastric-carcinogenesis-and-early-diagnosis
#7
S Rodrigues-Antunes, B N Borges
Gastric cancer remains one of the most prevalent cancers in the world. Due to this, efforts are being made to improve the diagnosis of this neoplasm and the search for molecular markers that may be involved in its genesis. Within this perspective, the mitochondrial DNA is considered as a potential candidate, since it has several well documented changes and is readily accessible. However, numerous alterations have been reported in mtDNA, not facilitating the visualization of which alterations and molecular markers are truly involved with gastric carcinogenesis...
May 26, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29790807/study-of-mitochondrial-dna-a1555g-and-c1494t-mutations-in-a-large-cohort-of-women-individuals
#8
Lin Wang, Xiaobin Wang, Xiaolong Cai, Rong Qiang
Mammalian mitochondrial A1555G and C1494T mutations are the most common causes of aminoglycoside-induced and non-syndromic hearing loss. However, these two mutations always are studied in the subject of pedigrees analysis. In the present study, we aimed to investigate the genetic characteristic of the A1555G and C1494T mutations on the population-level sampling, and to study the A1555G pattern of maternal transmission in three heteroplasmic families. Four thousand two hundred and ten unrelated women with normal hearing were enrolled as subjects...
May 23, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29774786/comparison-of-three-molecular-methods-for-species-identification-of-the-family-cichlidae-in-kwan-phayao-thailand
#9
Dutrudi Panprommin, Kanyanat Soontornprasit, Tanapat Pangeson
The species diversity of cichlids was investigated in Kwan Phayao from August 2016 to May 2017. Four cichlid species were found, including Oreochromis niloticus, Oreochromis mossambicus, Coptodon rendalli and Coptodon zillii. Due to similar characterizations, it is very difficult to identify each species. Three molecular methods were used to distinguish these four species. DNA barcodes or partial cytochrome c oxidase I (COI) gene sequences were amplified by PCR and sequenced. In Oreochromis sp. and Coptodon sp...
May 18, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29771167/transcript-free-energy-positively-correlates-with-codon-usage-bias-in-mitochondrial-genes-of-calypogeia-species-calypogeiaceae-marchantiophyta
#10
Sudipa Das, Arif Uddin, Debjyoti Bhattacharyya, Supriyo Chakraborty
The present study attempts to focus on the pattern of codon usage bias (CUB) in mitochondrial genes among four species of Calypogeia viz. C. arguta, C. integristipula, C. neogaea and C. suecica along with the factors influencing their CUB as no work was reported yet. The four taxa exhibit noticeable difference in their morphological features, habitat preference and growth forms. To understand the patterns of codon usage in Calypogeia mitochondrial genomes, we used bioinformatic tools to analyze the mitochondrial protein-coding sequences of four Calypogeia...
May 17, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29764251/future-of-human-mitochondrial-dna-editing-technologies
#11
N Verechshagina, N Nikitchina, Y Yamada, Н Harashima, M Tanaka, K Orishchenko, I Mazunin
ATP and other metabolites, which are necessary for the development, maintenance, and functioning of bodily cells are all synthesized in the mitochondria. Multiple copies of the genome, present within the mitochondria, together with its maternal inheritance, determine the clinical manifestation and spreading of mutations in mitochondrial DNA (mtDNA). The main obstacle in the way of thorough understanding of mitochondrial biology and the development of gene therapy methods for mitochondrial diseases is the absence of systems that allow to directly change mtDNA sequence...
May 15, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29716429/population-genetic-structure-and-phylogeography-of-sterlet-acipenser-ruthenus-acipenseridae-in-the-ob-and-yenisei-river-basins
#12
Maria A Pobedintseva, Alexey I Makunin, Iliya G Kichigin, Anastasia I Kulemzina, Nataliya A Serdyukova, Svetlana A Romanenko, Nadezhda V Vorobieva, Elena A Interesova, Marina A Korentovich, Vladimir F Zaytsev, Andrey V Mischenko, Vladimir A Zadelenov, Andrey A Yurchenko, Dmitry Yu Sherbakov, Alexander S Graphodatsky, Vladimir A Trifonov
The sterlet (Acipenser ruthenus Linnaeus, 1758) is a relatively small sturgeon widely distributed in Eurasian rivers from the Danube to the Yenisei. During the twentieth century, all wild sterlet populations have declined due to anthropogenic factors including: overfishing, poaching, construction of dams, and pollution. Despite the necessity of characterization both wild and captive stocks, few studies of population genetics have been performed thus far. Here we studied the genetic diversity and geographic structure of sterlet populations across the eastern range - Ob-Irtysh and Yenisei basins - by sequencing a 628-bp fragment of mitochondrial DNA control region...
May 2, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29701079/utility-of-mitochondrial-co1-sequences-for-species-discrimination-of-spirotrichea-ciliates-protozoa-ciliophora
#13
Mi-Hyun Park, Jae-Ho Jung, Euna Jo, Kyung-Min Park, Ye-Seul Baek, Se-Joo Kim, Gi-Sik Min
Ciliates are a diverse species group of the Protozoa, and nuclear and mitochondrial genes have been utilized to discover new species and discriminate closely related species. The mitochondrial cytochrome c oxidase subunit 1 (CO1) gene has been used to discriminate metazoan species and has also been applied for some groups in the phylum Ciliophora. However, it is difficult to produce a universal primer as a standard barcode, because unlike metazoans, mitochondrial DNA sequences of ciliates are long and highly variable...
April 27, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29697299/dna-barcoding-revealed-a-new-species-of-neolissochilus-rainboth-1985-from-the-kaladan-river-of-mizoram-north-east-india
#14
Lalramliana, Samuel Lalronunga, Sumit Kumar, Mahender Singh
Neolissochilus kaladanensis sp. nov., a new cyprinid species, is described from the Kaladan River drainage of Mizoram. It differs from all other valid Neolissochilus species in having higher number of gill rakers on the lower arm of the first gill arch (13-14 vs. 12 or below in all the species). The analysis of mitochondrial gene cytochrome c oxidase subunit I (COI) sequences separated N. kaladanensis sp. nov. from all other Neolissochilus and Tor species with an average genetic distance of 6.0%. It is further separated from the morphologically most similar species N...
April 26, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29697024/historical-explanation-of-genetic-variation-in-the-mediterranean-horseshoe-bat-rhinolophus-euryale-chiroptera-rhinolophidae-inferred-from-mitochondrial-cytochrome-b-and-d-loop-genes-in-iran
#15
Nargess Najafi, Vahid Akmali, Mozafar Sharifi
Molecular phylogeography and species distribution modelling (SDM) suggest that late Quaternary glacial cycles have portrayed a significant role in structuring current population genetic structure and diversity. Based on phylogenetic relationships using Bayesian inference and maximum likelihood of 535 bp mtDNA (D-loop) and 745 bp mtDNA (Cytb) in 62 individuals of the Mediterranean Horseshoe Bat, Rhinolophus euryale, from 13 different localities in Iran we identified two subspecific populations with differing population genetic structure distributed in southern Zagros Mts...
April 26, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29671673/cancer-specific-snps-originate-from-low-level-heteroplasmic-variants-in-human-mitochondrial-genomes-of-a-matched-cell-line-pair
#16
Annica Hedberg, Erik Knutsen, Anne Silje Løvhaugen, Tor Erik Jørgensen, Maria Perander, Steinar D Johansen
Low-level mitochondrial heteroplasmy is a common phenomenon in both normal and cancer cells. Here, we investigate the link between low-level heteroplasmy and mitogenome mutations in a human breast cancer matched cell line by high-throughput sequencing. We identified 23 heteroplasmic sites, of which 15 were common between normal cells (Hs578Bst) and cancer cells (Hs578T). Most sites were clustered within the highly conserved Complex IV and ribosomal RNA genes. Two heteroplasmic variants in normal cells were found as fixed mutations in cancer cells...
April 19, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29671658/diversity-of-marine-planktonic-ostracods-in-south-china-sea-a-dna-taxonomy-approach
#17
Lei Xu, Lianggen Wang, Jiajia Ning, Hong Li, Yingying Ji, Feiyan Du
Ostracods (Crustacea, Ostracoda) are small bivalved crustaceans, contributing over 200 described species to the marine zooplankton community. They are widely distributed and are relatively abundant components of the mesozooplankton, playing an important role in the transport of organic matter to deep layers. However, identification of ostracods based on micro-morphological characters is extremely difficult and time-consuming. Previous fragmentary taxonomic studies of ostracods in the South China Sea (SCA), were based solely on morphology...
April 19, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29671657/molecular-species-delimitation-in-the-genus-rhamma-johnson-1992-lepidoptera-lycaenidae-theclinae
#18
Carlos Prieto, Rayner Nuñez, Axel Hausmann
In this work, we used mtDNA data as a tool to delimit species and we compared the resulting molecular operational taxonomic units (barcode index number, BIN) with morphology-based identifications in the Colombian species of Rhamma Johnson, 1992 exploring the usefulness of DNA barcodes for taxonomy, species identification and delimitation. We obtained cytochrome oxidase I (COI) sequences for 134 morphologically identified specimens, representing 12 species of Rhamma from Colombia. Ten of these species have not been previously barcoded...
April 19, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29671653/genetic-diversity-analysis-of-the-oriental-river-prawn-macrobrachium-nipponense-in-huaihe-river
#19
Feng Cui, Yanyan Yu, Fangyin Bao, Song Wang, Ming Song Xiao
The oriental river prawn (Macrobrachium nipponense) is an economically and nutritionally important species of decapod crustaceans in China. Genetic structure and demographic history of Macrobrachium nipponense were examined using sequence data from portions of the mitochondrial DNA cytochrome oxidase subunit I (COI) gene. Samples of 191 individuals were collected from 10 localities in the upper to middle reaches of the Huaihe River. Variability was detected at a total of 42 nucleotide sites along 684 bp length of homologous sequence (6...
April 19, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29669453/dna-barcoding-of-fishes-from-river-diphlu-within-kaziranga-national-park-in-northeast-india
#20
Boni Amin Laskar, Vikas Kumar, Shantanu Kundu, Achom Darshan, Kaomud Tyagi, Kailash Chandra
DNA barcoding technique has been gaining importance in biodiversity research for its easy and rapid ability of delineating organisms' partial DNA sequences into molecular operational taxonomic units (MOTUs), and identification based on referral sequences from expert identified species. We generated mtCOI barcode sequences from morphologically identified fishes from River Diphlu in northeast India. A portion of this river falls within an important rhinoceros and tiger conservation site, the Kaziranga National Park...
April 18, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
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