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

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https://www.readbyqxmd.com/read/30318963/genetic-diversity-and-patterns-of-demographic-expansion-in-natural-populations-of-milkfish-chanos-chanos-forssk%C3%A3-l-1775-in-the-philippines
#1
Brian S Santos, Zubaida U Basiao, Jonas P Quilang
The milkfish, Chanos chanos (Forsskål, 1775) is an important aquaculture species produced in the tropical Pacific region. Milkfish aquaculture is heavily reliant on seedstock; thus, there is a need to assess the genetic diversity of wild populations to identify areas that could be sources of high quality seedstock and broodstock. In this study, 631 milkfish specimens from 11 Philippine and, for comparison, two Indonesian wild populations were analysed for their genetic diversities using mitochondrial control region and cytochrome b...
October 13, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/30318961/establishment-of-mink-heart-identification-method-based-on-mitochondrial-cytochrome-b-gene-and-development-of-its-detection-kit
#2
Wang Yanshuang, Yuan Guangxin, Zhang Lihua, Li Mingcheng, Li Yingnuo
In this study, the mink heart mitochondrial DNA was used as the target gene to design the specific primers of mink heart mtDNA Cytb, the extraction and detection reagents of mink heart DNA were developed using DNA fingerprinting technique, and the specificity, reproducibility, and stability of the reagents were investigated. Molecular cloning and sequencing technique were used to clone the standard substance of mink heart DNA detection, then a DNA fingerprint detection method of mink heart and the quality standard for mink heart were established, and a DNA detection kit of mink heart was developed...
October 13, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/30289002/phylogeny-and-acoustic-signal-evolution-of-a-pure-tone-song-katydid-pseudophyllus-titan-orthoptera-tettigoniidae-based-on-the-complete-mitogenome
#3
Junjian Li, Qi Chen, Ming Wen, Jiatong Wang, Yinliang Wang, Bingzhong Ren
Ensifera is an extremely diverse group in the order Orthoptera, and it has been the subject of considerable research, especially in terms of phylogeny and bioacoustics. Katydids are known for using high-frequency broadband signals whereas most cricket songs are pure tones with a frequency range of 2-8 kHz. Pseudophyllus titan is a special katydid emits low-frequency pure tone songs similar to that of crickets. Acoustic communication of Ensifera were widely studied, but song evolution could deserve new examination taking into account the newly available phylogenies...
October 5, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/30231799/population-structure-genetic-diversity-and-phylogenetic-analysis-of-different-rural-and-commercial-chickens-of-pakistan-using-complete-sequence-of-mtdna-d-loop
#4
Ayesha Nisar, Abdul Waheed, Sawar Khan, Xingang Feng, Abbas Hussain Shah
Chicken is the most important poultry bird in Pakistan that not only provides nutrition but also contributes to country's economy. The Pakistani chicken and its germplasm resources are not genetically characterized and explored. Here, we focused at rural and commercial chickens of Pakistan and explored genetic diversity, population structure and phylogeny. We first collected feather samples from Rural and Broiler populations of Pakistani chickens, isolated DNA and sequenced complete D-loop of mtDNA. The length of complete D-loop ranged from 1231 to 1234 bp in Pakistani chickens...
September 19, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/30198386/a-mitochondrial-long-noncoding-rna-in-atlantic-cod-harbors-complex-heteroplasmic-tandem-repeat-motifs
#5
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
#6
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/29540087/phylogenetic-relationship-and-molecular-dating-of-indian-pangolin-manis-crassicaudata-with-other-extant-pangolin-species-based-on-complete-cytochrome-b-mitochondrial-gene
#7
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...
December 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29514573/the-missing-lynx-of-eurasia-at-its-southern-edge-a-connection-to-the-critically-endangered-balkan-lynx
#8
Numan Cömert, Oya Carlı, H Benan Dinçtürk
The populations of Eurasian lynx in Anatolia are as fragmented as the European populations. Although the origins of and the connections between the European lynx populations have been elucidated, there have been no genetic studies on the lynx populations in Turkey. The lack of genetic and evolutionary information about lynx in Anatolia, which is considered to be a biodiversity hotspot, makes it difficult to track the migration routes during the Quaternary. In this study, we present the genetic characteristics of two isolated lynx populations in Southwest Taurus Mountains and the Turkish Caucasus as well as two individuals from Erzincan area...
December 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29514536/neither-barriers-nor-refugia-explain-genetic-structure-in-a-major-biogeographic-break-phylogeography-of-praying-mantises-in-the-brazilian-atlantic-forest
#9
Bernardo F Santos, Marcus V Scherrer, Ana Carolina Loss
The Atlantic Forest is one of the world's top biodiversity hotspots, but the diversification processes of its biota are still poorly known, with competing models attributing dominant roles to either Quaternary climatic changes or geographic barriers. Many studies identify the Doce river as a major phylogeographic break, but the reasons for this phenomenon are highly debated. Here we test the predictions of the refugial and barrier models for a common species of praying mantis, Miobantia fuscata, focusing in the areas immediately south and north of the Doce river...
December 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29488434/phylogeographic-pattern-of-liza-affinis-populations-in-chinese-coastal-waters-estimation-of-larval-dispersal-potential
#10
Lu Liu, Liqin Liu, Tianxiang Gao, Na Song
To examine phylogeographic pattern of Liza affinis populations in Chinese coastal waters, eight geographic populations were collected and analyzed using sequence analysis based on the first hypervariable region of mitochondrial control region. A total of 117 haplotypes from eight populations were obtained from 223 individuals and 22 of them were shared among different populations. High values of haplotype diversity and nucleotide diversity were observed for eight populations. The topology of the NJ tree was shallow, and there were no significant genealogical branches or clusters corresponding to sampling localities...
December 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29488422/species-composition-of-the-genus-scombrops-teleostei-scombropidae-in-the-waters-around-the-japanese-archipelago-detection-of-a-cryptic-species
#11
Shiro Itoi, Yukako Mochizuki, Minori Tanaka, Hikaru Oyama, Tadasuke Tsunashima, Riko Yamada, Hirotoshi Shishido, Yasuji Masuda, Shizuko Nakai, Noriyuki Takai, Hideto Fukushima, Koko Abe, Takahito Kojima, Haruo Sugita
Current literature states that family Scombropidae consists of a single genus Scombrops comprising three species worldwide, with two of them, Scombrops boops and Scombrops gilberti, distributed in the waters around the Japanese Archipelago. Although these two scombropids are commercially important species, little is known about the ecology of these fishes. It is difficult to discriminate between these two species based on external characteristics because of their morphological similarity. Here, we report two different morphotypes characterized by the relative growth between the otolith size and the standard length (SL) of the scombropid specimens caught in southern waters off Kyushu Island, Japan, and show the genetic relationship between the morphotypes by means of phylogenetic analyses using complete DNA sequences of the cytochrome b gene...
December 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29482423/genetic-diversity-and-population-structure-of-penis-fish-urechis-unicinctus-based-on-mitochondrial-and-nuclear-gene-markers
#12
Jie Gong, Ruoping Zhao, Jiaheng Deng, Yancui Zhao, Jincheng Zuo, Ling Huang, Meidong Jing
Urechis unicinctus is distributed only in Bohai Gulf of China and Korean and Japanese coast. The wild populations of this species have sharply declined in China and Japan. We collected 105 samples from six localities of Bohai Gulf and Korea coast, and investigated genetic diversity and population structure with mitochondrial COI, 16S-rRNA and nuclear 28S-rRNA gene fragments. Genetic diversity of U. unicinctus based on COI sequences was still high (Hd: 0.9595, π: 0.0101), however, 28S-rRNA gene sequences showed low level of genetic diversity (Hd: 0...
December 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29457530/a-new-insight-into-the-classification-of-dusky-thrush-complex-bearings-on-the-phylogenetic-relationships-within-the-turdidae
#13
Yuanqiu Dong, Bo Li, Lizhi Zhou
Dusky thrush complex comprises of two sister species breeding in SC Siberia, which is the member of thrush Turdus from Turdidae. The phylogenetic resolution of Dusky thrush complex remains controversial, and a detailed research is still necessary. In this research, we determined the complete mtDNAs of both species, and estimated phylogenetic trees based on the mtDNA alignment of these and 21 other Turdidae species, to clarify the taxa status of the Dusky thrush complex. The squenced lengths of these three mitochondrial genomes were 16,737, 16,788 and 16,750 bp...
December 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29429383/additional-evidence-of-the-link-between-mtdna-copy-number-and-the-body-mass-index
#14
D A Skuratovskaia, J K Sofronova, P A Zatolokin, K Y Popadin, M A Vasilenko, L S Litvinova, I O Mazunin
No abstract text is available yet for this article.
December 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29421947/population-genetic-structure-and-molecular-diversity-of-leucinodes-orbonalis-based-on-mitochondrial-coi-gene-sequences
#15
Murali Palraju, Ramaraj Paulchamy, Janarthanan Sundaram
Leucinodes orbonalis is a destructive pest found throughout eggplant cultivating fields of Tamil Nadu, India. The genetic diversity and its population structure were investigated in this pest using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences from 20 populations of L. orbonalis collected from various agro-climatic conditions. The study indicated almost no genetic diversity among various populations. The COI nucleotide sequence based haplotype analysis also revealed no significant genetic variation among various populations...
December 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29390935/revisiting-dna-barcoding-of-true-bugs-of-the-infraorder-pentatomomorpha-hemiptera-heteroptera-from-india
#16
Gaurang G Gowande, Sanket Tembe, Hemant V Ghate
Cytochrome c oxidase subunit I gene (COI) sequences of roughly 509 bp length for various species of the Infraorder Pentatomomorpha were generated. K2P divergences within and between species and genera were calculated and compared using newly generated sequences and the ones available on online portals. Mean interspecific (within-genus) genetic divergence (14.23%) was ∼ eight times greater than mean intraspecific (within-species) divergence (1.79%). Distance-based as well as character-based approaches were used towards constructing (COI) trees...
December 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29385929/extensive-mitochondrial-heteroplasmy-in-the-neotropical-ants-of-the-ectatomma-ruidum-complex-formicidae-ectatomminae
#17
Rubi N Meza-Lázaro, Chantal Poteaux, Natalia J Bayona-Vásquez, Michael G Branstetter, Alejandro Zaldívar-Riverón
We assembled mitogenomes from 21 ant workers assigned to four morphospecies (E. ruidum spp. 1-4) and putative hybrids of the Ectatomma ruidum complex (E. ruidum spp. 2x3), and to E. tuberculatum using NGS data. Mitogenomes from specimens of E. ruidum spp. 3, 4 and 2 × 3 had a high proportion of polymorphic sites. We investigated whether polymorphisms in mitogenomes are due to nuclear mt paralogues (numts) or due to the presence of more than one mitogenome within an individual (heteroplasmy). We did not find loss of function signals in polymorphic protein-coding genes, and observed strong evidence for purifying selection in two haplotype-phased genes, which indicate the presence of two functional mitochondrial genomes coexisting within individuals instead of numts...
December 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29385875/complete-mitogenomes-from-kurdistani-sheep-abundant-centromeric-nuclear-copies-representing-diverse-ancestors
#18
Sarbast Ihsan Mustafa, Trude Schwarzacher, J S Heslop-Harrison
The geographical centre of domestication and species diversity for sheep (Ovis aries) lies around the Kurdistan region of Northern Iraq, within the 'Fertile Crescent'. From whole genome sequence reads, we assembled the mitochondrial genomes (mtDNA or mitogenome) of five animals of the two main Kurdistani sheep breeds Hamdani and Karadi and found they fitted into known sheep haplogroups (or matrilineages), with some SNPs. Haplotyping 31 animals showed presence of the main Asian (hpgA) and European (hpgB) haplogroups, as well as the rarer Anatolian haplogroup hpgC...
December 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29385872/mitochondrial-diversity-and-phylogeography-of-acrossocheilus-paradoxus-teleostei-cyprinidae
#19
Yu-Min Ju, Kui-Ching Hsu, Jin-Quan Yang, Jui-Hsien Wu, Shan Li, Wei-Kuang Wang, Fang Ding, Jun Li, Hung-Du Lin
Mitochondrial DNA cytochrome b sequences (1141 bp) in 229 specimens of Acrossocheilus paradoxus from 26 populations were identified as four lineages. The pairwise genetic distances among these four lineages ranged from 1.57 to 2.37% (mean= 2.00%). Statistical dispersal-vicariance analysis suggests that the ancestral populations were distributed over mainland China and Northern and Western Taiwan. Approximate Bayesian computation approaches show that the three lineages in Taiwan originated from the lineage in mainland China through three colonization routes during two glaciations...
December 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29385868/the-non-monotypic-status-of-the-neotropical-fish-genus-hemiodontichthys-siluriformes-loricariidae-evidenced-by-genetic-approaches
#20
Margarida Lima Carvalho, Guilherme José da Costa Silva, Silvana Melo, Fernando Yuldi Ashikaga, Cristiane Kioko Shimabukuro-Dias, Priscilla Cardim Scacchetti, Renato Devidé, Fausto Foresti, Claudio Oliveira
The combination of cytogenetic and molecular data with those traditionally obtained in areas like systematics and taxonomy created interesting perspectives for the analysis of natural populations under different aspects. In this context, this study aimed to evaluate the genetic differentiation among populations of the genus Hemiodontichthys Bleeker, 1862, through combined genetic techniques and included the analysis of populations sampled in the Araguaia River, Guamá River, Madeira River and two populations from the Purus River...
December 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
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