journal
MENU ▼
Read by QxMD icon Read
search

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

journal
https://www.readbyqxmd.com/read/29774786/comparison-of-three-molecular-methods-for-species-identification-of-the-family-cichlidae-in-kwan-phayao-thailand
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/29661047/evolutionary-history-of-genus-macrobrachium-inferred-from-mitochondrial-markers-a-molecular-clock-approach
#13
Deepak Jose, Mahadevan Harikrishnan
Caridea, an infraorder of shrimps coming under Pleocyemata was first reported from the oceans before 417 million years followed by their radiation recorded during the Permian period. Hitherto, about 3877 extant caridean species were accounted within which one quarter constitute freshwater species. Freshwater prawns of genus Macrobrachium (Infraorder Caridea; Family Palaemonidae), with more than 240 species are inhabitants of diverse aquatic habitats like coastal lagoons, lakes, tropical streams, ponds and rivers...
April 17, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29658380/genetic-diversity-and-population-genetic-structure-of-the-only-population-of-aoluguya-reindeer-rangifer-tarandus-in-china
#14
Yan Ju, Huamiao Liu, Min Rong, Ranran Zhang, Yimeng Dong, Yongna Zhou, Xiumei Xing
Aoluguya Reindeer is the only reindeer species in China and currently approximately 1000 Aoluguya Reindeer remain semi-domesticated. A relative low diversity estimate was found by investigating genetic variability and demographic history of its population. Mismatch distribution curve of its nucleotide sequences and neutral test indicate its population has not experienced expansion. Genetic diversity and population structure were also analysed by using its mtDNA and microsatellites technology. Statistical results of these analyses showed there were varying degrees of population inbreeding and suggested that gene flow existed among its populations at one time...
April 16, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29595343/on-the-persistence-and-detectability-of-ancient-beothuk-mitochondrial-dna-genomes-in-living-first-nations-peoples
#15
Ashley Collier, Steven M Carr
Claims have long been made as to the survival to the present day of descendants of the Newfoundland Beothuk, a group generally accepted to have become extinct with the death of the last known member, Shanawdithit, in 1829. Interest has recently been revived by the availability of commercial genetic testing, which some claim can assign living individuals to specific Native American groups. We compare complete mitogenome sequences (16569 bp) from aDNA of eight distinct Beothuk lineages, including Shanawdithit's uncle Nonosabasut and his wife Demasduit, with three Newfoundland Mi'kmaq lineages and 21 other living Native Americans drawn from GenBank...
March 29, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29591722/high-throughput-terrestrial-biodiversity-assessments-mitochondrial-metabarcoding-metagenomics-or-metatranscriptomics
#16
John-James Wilson, Guo-Jie Brandon-Mong, Han-Ming Gan, Kong-Wah Sing
Consensus on the optimal high-throughput sequencing (HTS) approach to examine biodiversity in mixed terrestrial arthropod samples has not been reached. Metatranscriptomics could increase the proportion of taxonomically informative mitochondrial reads in HTS outputs but has not been investigated for terrestrial arthropod samples. We compared the efficiency of 16S rRNA metabarcoding, metagenomics and metatranscriptomics for detecting species in a mixed terrestrial arthropod sample (pooled DNA/RNA from 38 taxa)...
March 29, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29580117/evidence-for-panmixia-despite-barriers-to-gene-flow-in-the-hooked-mussel-ischadium-recurvum-mytilidae-brachidontinae-along-the-north-american-coastline
#17
Frank M Fontanella, Yvette Garner, Jasmine Starnes, Megan Whitaker
The discovery of phylogeographic patterns within broadly distributed marine species can be particularly challenging because absolute physical barriers to dispersal can be inconspicuous. Genetic boundaries often lie where ocean currents meet, forming sharp physical and ecological gradients, which may act as barriers to successful migrants. In eastern North America, coastal species often show phylogeographic differentiation associated with two recognized genetic barriers: the Gulf/Atlantic and the Virginia/Carolina discontinuities...
March 26, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29557238/genetic-variations-of-dna-barcoding-region-of-bumble-bees-hymenoptera-apidae-from-south-korea
#18
Taeman Han, Seung-Hyun Kim, Hyung Joo Yoon, In Gyun Park, Haechul Park
We reassessed species diversity and genetic structure in Korean bumble bees using DNA barcode analyses of 484 cytochrome c oxidase subunit I (COI) sequences from 24 morphospecies. Based on COI, all of the Korean species formed distinct clades in the phylogenetic trees, except for Bombus (Megabombus) koreanus in the maximum likelihood tree. Five species exhibited low interspecific genetic distances (range: 1.2-2.7%), indicating that they are recently diverged species. COI data could not be used to identify bumble bees at the subspecies level...
March 20, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29540087/phylogenetic-relationship-and-molecular-dating-of-indian-pangolin-manis-crassicaudata-with-other-extant-pangolin-species-based-on-complete-cytochrome-b-mitochondrial-gene
#19
Ved Prakash Kumar, Ankita Rajpoot, Anupam Srivastav, Parag Nigam, Vinay Kumar, Madhanraj A, Surendra Prakash Goyal
Pangolins are a group of eight endangered mammalian species included in the family Manidae (Order Pholidota) and divided into four each African (Arboreal species; Phataginus tetradactyla, Phataginus tricuspis, Ground dwelling species; Smutsia gigantea and Smutsia temminckii) and Asian (Ground dwelling; Manis crassicaudata, Manis pentadactyla, Manis javanica and Manis culionensis) species. The taxonomy of all the eight extant pangolin species based on molecular genetics studies, remains unresolved and poorly examined...
March 15, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29527965/comparative-analysis-of-the-mitochondrial-genomes-of-six-newly-sequenced-diatoms-reveals-group-ii-introns-in-the-barcoding-region-of-cox1
#20
Cloe S Pogoda, Kyle G Keepers, Sarah E Hamsher, Joshua G Stepanek, Nolan C Kane, J Patrick Kociolek
Diatoms are the most diverse lineage of algae and at the base of most aquatic food webs, but only 11 of their mitochondrial genomes have been described. Herein, we present the mitochondrial genomes of six diatom species, including: Melosira undulata, Nitzschia alba, Surirella sp., Entomoneis sp., Halamphora coffeaeformis, and Halamphora calidilacuna. Comparison of these six genomes to the 11 currently published diatom mitochondrial genomes revealed a novel ubiquitous feature block consisting of tatC-orf157-rps11...
March 11, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
journal
journal
53040
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"