Mitochondrial Dna Part a最新文献

{"title":"The heavy strand dilemma of vertebrate mitochondria on genome sequencing age: number of encoded genes or G + T content?","authors":"Nicholas Costa Barroso Lima, F. Prosdocimi","doi":"10.1080/24701394.2016.1275603","DOIUrl":"https://doi.org/10.1080/24701394.2016.1275603","url":null,"abstract":"Differential ultracentrifugation is a classic technique of cell biology and microbiology used to separate cell components, such as nuclei, mitochondria, chloroplasts, lysosomes, peroxisomes, vesicles, ribosomes, and cytoplasm (Garber & Yoder 1983). Regarding the study of the mitochondria, a cesium chloride (CsCl) solution has been used in a technique named Buoyant density ultracentrifugation to separate nuclear DNA from mitochondrial DNA (Welter et al. 1988; Zimmerman et al. 1988). Therefore, the two distinct bands obtained in the CsCl ultracentrifugation were used to define a heavy (H) and a light (L) DNA strand for a given mitochondrion. These studies have been classically conducted for many clades (Corneo et al. 1966; Sinclair et al. 1967; Brack et al. 1972; Beridze & Tabidze 1976; Garber & Yoder 1983) and they are still done in a smaller pace to isolate cell components for further analyses (Zhao et al. 2005). However, with the development of PCR and Sanger sequencing techniques, researchers did not need to separate the mitochondria from other cellular components to perform the sequencing of their DNA. Nowadays, more than 10 years after the development of next-generation sequencing (NGS) techniques, mitochondrial genomes can be obtained as a byproduct of whole genome sequencing. Although the amount of mitochondrial reads can differ because of the type of tissue, animal group and/or sample extraction protocols, we have found that one mitochondrial read can be found for each 200–1000 reads of the nuclear genome (Uliano-Silva et al. 2015; Perini Vda et al. 2016; Prosdocimi et al. 2016). In some cases the amount of reads from mitochondrial DNA is so high that assemblers masked them as repeats while performing whole genome assemblies. It was just after assembling and annotating many complete mitochondrial genomes of various organisms (Gomes de S a et al. 2015; Uliano-Silva et al. 2015; Perini Vda et al. 2016; Prosdocimi et al. 2016; Souto et al. 2016; Uliano-Silva et al. 2016) that we decided to take a closer look into the H and L strand assignments. We were astonish to realize that many vertebrate mitochondrial genomes published to date seem to be inaccurately annotated in terms of light and heavy strands (Arnason et al. 2006, 2007; Zhang et al. 2012; Yoon et al. 2013; Ren et al. 2014; Pan et al. 2015; Zhang et al. 2015; Zou et al. 2015; Meng et al. 2016; Sun et al. 2016). Classic works showed that mitochondrial L-strand could be defined as the one that has the lower content of guanines and thymines (Taanman 1999; Munn 1975). According to Vinograd et al. (1963), the titration of N–H protons of thymines and guanines would increase the buoyant density of denatured DNA, showing that Gþ T content is responsible for the buoyant density of mitochondrial strands. When sequencing and analyzing the mitogenome of the blue-fronted amazon parrot, Amazon aestiva (Lima et al. manuscript in preparation), we were confronted with observation that the majority of t","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"47 1","pages":"300 - 302"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87018949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA barcodes for dragonflies and damselflies (Odonata) of Mindanao, Philippines","authors":"P. A. Casas, K. Sing, Ping-Shin Lee, O. Nuñeza, R. Villanueva, John-James Wilson","doi":"10.1080/24701394.2016.1267157","DOIUrl":"https://doi.org/10.1080/24701394.2016.1267157","url":null,"abstract":"Abstract Reliable species identification provides a sounder basis for use of species in the order Odonata as biological indicators and for their conservation, an urgent concern as many species are threatened with imminent extinction. We generated 134 COI barcodes from 36 morphologically identified species of Odonata collected from Mindanao Island, representing 10 families and 19 genera. Intraspecific sequence divergences ranged from 0 to 6.7% with four species showing more than 2%, while interspecific sequence divergences ranged from 0.5 to 23.3% with seven species showing less than 2%. Consequently, no distinct gap was observed between intraspecific and interspecific DNA barcode divergences. The numerous islands of the Philippine archipelago may have facilitated rapid speciation in the Odonata and resulted in low interspecific sequence divergences among closely related groups of species. This study contributes DNA barcodes for 36 morphologically identified species of Odonata reported from Mindanao including 31 species with no previous DNA barcode records.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"23 1","pages":"206 - 211"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73369495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic identification for prey birds of the Endangered peregrine falcon (Falco peregrinus)","authors":"Sang-Hyun Han, Hong-Shik Oh","doi":"10.1080/24701394.2016.1261853","DOIUrl":"https://doi.org/10.1080/24701394.2016.1261853","url":null,"abstract":"Abstract To reveal the dietary ecology of the peregrine falcon (Falco peregrinus), we conducted a molecular analysis for mitochondrial genes (COI and CYTB) to identify the prey species collected from a feeding place found on Sasu Island, South Korea. The results from noninvasive genetic analysis showed that the sequences obtained came from nine species of birds (Cuculus canorus, Eurystomus orientalis, Limosa limosa, Microscelis amaurotis, Oriolus chinensis, Phasianus colchicus, Sterna hirundo, Streptopelia orientalis, and Turdus pallidus). Five of the species (C. canorus, M. amaurotis, S. hirundo, S. orientalis, and T. pallidus) had previously been observed on this island, but the other four species (E. orientalis, L. limosa, O. chinensis, and P. colchicus) were newly identified as present. No mtDNA sequences of land animals such as amphibians, reptiles, and mammals were found in the dietary remains, suggesting that the peregrine falcon preys mostly on other birds rather than on other animals inhabiting Sasu Island. This island has rich avian diversity and abundant animal populations and therefore supplies sufficient dietary resources for the peregrine falcon. Our findings suggested that a DNA-based molecular method may be useful to identify the prey species of these birds and may be valuable in future studies of the Endangered peregrine falcon.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"95 1","pages":"175 - 180"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84322267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Population structure and genetic diversity of Indian Major Carp, Labeo rohita (Hamilton, 1822) from three phylo-geographically isolated riverine ecosystems of India as revealed by mtDNA cytochrome b region sequences","authors":"B. Behera, V. Baisvar, S. Kunal, D. Meena, D. Panda, S. Pakrashi, P. Paria, P. Das, D. Bhakta, D. Debnath, Suvra Roy, V. Suresh, J. Jena","doi":"10.1080/24701394.2016.1267156","DOIUrl":"https://doi.org/10.1080/24701394.2016.1267156","url":null,"abstract":"Abstract The population structure and genetic diversity of Rohu (Labeo rohita Hamilton, 1822) was studied by analysis of the partial sequences of mitochondrial DNA cytochrome b region. We examined 133 samples collected from six locations in three geographically isolated rivers of India. Analysis of 11 haplotypes showed low haplotype diversity (0.00150), nucleotide diversity (π) (0.02884) and low heterogeneity value (0.00374). Analysis of molecular variance (AMOVA) revealed the genetic diversity of L. rohita within population is very high than between the populations. The Fst scores (−0.07479 to 0.07022) were the indication of low genetic structure of L. rohita populations of three rivers of India. Conspicuously, Farakka-Bharuch population pair Fst score of 0.0000, although the sampling sites are from different rivers. The phylogenetic reconstruction of unique haplotypes revealed sharing of a single central haplotype (Hap_1) by all the six populations with a point mutations ranging from 1–25 nucleotides.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"11 1","pages":"199 - 205"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84599986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitochondria COI-based genetic diversity of the cotton leafhopper Amrasca biguttula biguttula (Ishida) populations from India","authors":"S. Kranthi, A. Ghodke, Raghavendra K Puttuswamy, M. Mandle, R. Nandanwar, U. Satija, R. Pareek, H. Desai, S. Udikeri, Dhara Jothi Balakrishna, Bheemanna M Hugar, D. Monga, K. Kranthi","doi":"10.1080/24701394.2016.1275595","DOIUrl":"https://doi.org/10.1080/24701394.2016.1275595","url":null,"abstract":"Abstract Amrasca biguttula biguttula (Ishida), the cotton leafhopper, is a polyphagous insect pest of Asia and Southeast Asian countries. We sequenced a mitochondrial COI gene fragment from 67 individuals of cotton leafhopper collected from 7 major cotton growing states of North, Central, and South India. Genetic divergence analysis of leaf hopper population across India confirmed the presence of single species. Thirty haplotypes, in total, were determined across different regions of India. While population from North India was dominated by single haplotype, the south and central Indian populations show dispersion of different haplotypes across the region. The neutrality test rejection for the north Indian population also suggests population expansion. The genetic differentiation and gene flow analysis together confirmed the phylogeographic structure of the A. biguttula biguttula Ishida as isolated by distance.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"41 1","pages":"228 - 235"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82214370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of mitochondrial DNA polymorphisms in the Han population in Liaoning Province, Northeast China","authors":"Feng-ling Xu, Jun Yao, M. Ding, Zhang-sen Shi, Xue Wu, Jing-jing Zhang, Bao-jie Wang","doi":"10.1080/24701394.2016.1275597","DOIUrl":"https://doi.org/10.1080/24701394.2016.1275597","url":null,"abstract":"Abstract This study characterized the genetic variations of mitochondrial DNA (mtDNA) to elucidate the maternal genetic structure of Liaoning Han Chinese. A total of 317 blood samples of unrelated individuals were collected for analysis in Liaoning Province. The mtDNA samples were analyzed using two distinct methods: sequencing of the hypervariable sequences I and II (HVSI and HVSII), and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the coding region. The results indicated a high gene diversity value (0.9997 ± 0.0003), a high polymorphism information content (0.99668) and a random match probability (0.00332). These samples were classified into 305 haplotypes, with 9 shared haplotypes. The most common haplogroup was D4 (12.93%). The principal component analysis map, the phylogenetic tree map, and the genetic distance matrix all indicated that the genetic distance of the Liaoning Han population from the Tibetan group was distant, whereas that from the Miao group was relatively close.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"25 1","pages":"250 - 255"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89126254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic variations and population structure in three populations of beardless barb, Cyclocheilichthys apogon (Valenciennes, 1842) inferred from mitochondrial cytochrome b sequences","authors":"Anan Kenthao, P. Wangsomnuk, P. Jearranaiprepame","doi":"10.1080/24701394.2016.1242581","DOIUrl":"https://doi.org/10.1080/24701394.2016.1242581","url":null,"abstract":"Abstract This study aimed to investigate the relation of dispersal barrier and genetic diversity, population structure, and demographic history of 46 samples of beardless barb, Cyclocheilichthys apogon (Valenciennes, 1842) collected from three different locations in North-eastern Thailand. The analysis of molecular variance (AMOVA) was employed in order to determine the genetic variability within and among populations of this fish. The neutrality tests and mismatch distribution analysis were additionally applied to assess the neutrality and demographic expansion of the populations, respectively. Contiguous sequences within range from 1100 to1140 bp were obtained with varying 16 different haplotypes with high-haplotype diversity (0.8773 ± 0.0327) and low-nucleotide diversity (0.00215 ± 0.00020). The variations within and among populations accounted for 98.98 and 1.02% of the total variation, respectively. The low level of pairwise Fst estimations indicated a possible gene flow among populations and a suggestion of genetic homogeneity at this geographical range. A supportive idea of having a single-maternal lineage and past demographic expansion or selection experiencing has distinctly appeared among these populations. The current data suggests that all three populations distinctly exist as a single stock unit and that is an important factor in identifying genetic variation of C. apogon in this geographical area to be used in establishing effective plans and strategies for a conservation and management.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"35 1","pages":"82 - 90"},"PeriodicalIF":0.0,"publicationDate":"2018-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78841149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proposed synonymy for Micropogonias altipinnis (Günther 1864), Micropogonias ectenes (Jordan & Gilbert 1882), and Micropogonias megalops (Gilbert 1890)","authors":"Geremías Sánchez-Pinedo, N. Díaz-Viloria, J. L. Ortíz-Galindo, Nelson Ferreira-Fontoura, R. Pérez-Enríquez, L. Sánchez‐Velasco, J. De La Cruz‐Agüero","doi":"10.1080/24701394.2016.1258405","DOIUrl":"https://doi.org/10.1080/24701394.2016.1258405","url":null,"abstract":"Abstract Within the Sciaenidae family, the genus Micropogonias is composed of three recognized species along the Pacific coast of Mexico: Micropogonias altipinnis, M. ectenes, and M. megalops. These species exhibit overlapping diagnostic characters, which make species identification difficult. This study ties morphological differences (meristic, morphometry of body, and otolith) with DNA sequences (CO1 and 16S fractions of mtDNA and 28S of nDNA) among Micropogonias species in the Pacific. Meristic analysis showed a latitudinal variation among the three species in the number of rays, the number of gill rakers, and length of the longest spine of the dorsal fin. Discriminant analysis of morphometric characters (body and otolith) showed three morphological entities (p < 0.001). However, the mean genetic divergences among the three species with partial sequences of mtDNA (CO1 and 16S), and nuclear (28S) were lower than those reported at the interspecific level (>2%). Genetic results suggest that the three species are one species and that the differences in meristics and morphometry could be the result of phenotypic plasticity or incipient speciation. In this sense, M. ectenes and M. megalops are proposed as junior synonyms of M. altipinnis.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"66 1","pages":"136 - 146"},"PeriodicalIF":0.0,"publicationDate":"2018-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75967399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sheep mitochondrial heteroplasmy arises from tandem motifs and unspecific PCR amplification","authors":"G. E, Yongju Zhao, Yongfu Huang","doi":"10.1080/24701394.2016.1242582","DOIUrl":"https://doi.org/10.1080/24701394.2016.1242582","url":null,"abstract":"Abstract The mitochondrial DNA control region (D-loop) is a widely used molecular marker in evolutionary and phylogeographic research. However, the occurrence of heteroplasmy of the D-loop region within individuals has rarely been investigated. In this study, a total of 85 Chinese sheep were used to amplify a partial D-loop region, and 15 heteroplasmic animals (17.64%) were identified. A comparative analysis of the PCR amplification and cloning of the D-loop sequences from the heteroplasmic samples revealed most of the sequencing profile from the heteroplasmic regions started at the beginning of a 75-bp random repeat motif. In addition, a total of 22 nonsyngeneic sequences with a D-loop were found in 61 of the clones obtained from the 4 random heteroplasmic and 3 homozygote animals, and their genomic locations were compared for homology. In summary, the D-Loop sequencing profiles appear to be heteroplasmic and could arise from tandem repeat motifs and unspecific replication during PCR amplification; however, they are not likely due to the presence of multiple mitochondrial genomes within an individual.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"11 1","pages":"91 - 95"},"PeriodicalIF":0.0,"publicationDate":"2018-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86332259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Scanning the mitochondrial genome for mutations by cycling temperature capillary electrophoresis","authors":"C. Arstad, Paulo Refinetti, David J. Warren, K. Giercksky, P. Ekstrøm","doi":"10.1080/24701394.2016.1233532","DOIUrl":"https://doi.org/10.1080/24701394.2016.1233532","url":null,"abstract":"Abstract To bypass possible nuclear contamination and to exclusively amplify DNA from the mitochondrion, a set of 23 primers was selected. On the mitochondrial DNA selection fragments, a second set of fragments was used to amplify and identify mutant fractions with a detection limit of 1% . This mutation scanning method analyzed 76% of the mitochondrial genome and was used to examine 94 tumours from different tissues of origin. In all, 87 tumours had one or more mutations, leaving seven samples without observed mutations. Sanger sequencing verified samples carrying mutations with a mutant fraction exceeding 30%. The generated data validate that several regions of the mitochondrial DNA have more mutations than others.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"18 1","pages":"19 - 30"},"PeriodicalIF":0.0,"publicationDate":"2018-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82028985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}