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Mitochondrial DNA: Methods and Protocols 线粒体DNA:方法和方案
Mitochondrial Dna Pub Date : 2023-01-01 DOI: 10.1007/978-1-0716-2922-2
J. Stuart
{"title":"Mitochondrial DNA: Methods and Protocols","authors":"J. Stuart","doi":"10.1007/978-1-0716-2922-2","DOIUrl":"https://doi.org/10.1007/978-1-0716-2922-2","url":null,"abstract":"","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51714068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
Genetic variation in the Chinese soft-shell turtles (Pelodiscus spp.) revealed by sequences of mitochondrial Cytb gene 利用线粒体Cytb基因序列揭示中国软壳龟遗传变异
Mitochondrial Dna Pub Date : 2019-11-17 DOI: 10.1080/24701394.2019.1693551
G. Xiong, Xiao-qing Wang, Xianwen Zhou, Dan Zeng, Zhen-Nian Chen, Peizheng Wang, L. Kang
{"title":"Genetic variation in the Chinese soft-shell turtles (Pelodiscus spp.) revealed by sequences of mitochondrial Cytb gene","authors":"G. Xiong, Xiao-qing Wang, Xianwen Zhou, Dan Zeng, Zhen-Nian Chen, Peizheng Wang, L. Kang","doi":"10.1080/24701394.2019.1693551","DOIUrl":"https://doi.org/10.1080/24701394.2019.1693551","url":null,"abstract":"Abstract Genetic diversity is an important component of biodiversity and investigating and protecting the wild genetic diversity of species has always been an important research topic in conservation biology. Due to habitat destruction and over catching, wild Chinese soft-shell turtles (Pelodiscus spp.) have been severely damaged, resulting in the species being listed on the IUCN Red List of Threatened Species in 2000. However, only few studies with contradictory results on the genetic diversity of Pelodiscus turtles have been reported. To investigate the genetic diversity and population structure of Pelodiscus turtles, 123 specimens were collected from five localities in East Asia, and their genetic variation was analyzed on the basis of a 922-bp partial sequence of the mitochondrial cytb gene. Forty-nine polymorphic sites were detected, revealing 56 haplotypes. A pattern of high haplotype diversity (Hd = 0.994) and nucleotide diversity (π = 0.01655) was found in the examined range. A maximum likelihood phylogenetic tree and median-joining network analyses indicated that the Pelodiscus turtles divided in four populations throughout East Asia, and the Pelodiscus turtles probably originate from the Yangtze River and was introduced to Yellow River, Taiwan, and Japan through Xijiang River. These results served a helpful resource for conservation of Pelodiscus turtles.","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1693551","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60126488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Complete chloroplast genome sequence of Castanopsis concinna (Fagaceae), a threatened species from Hong Kong and South-Eastern China. 香港和中国东南部一种濒危物种甜槠(壳斗科)叶绿体全基因组序列。
Mitochondrial Dna Pub Date : 2017-01-01 DOI: 10.3109/19401736.2015.1110800
D. Hinsinger, J. S. Strijk
{"title":"Complete chloroplast genome sequence of Castanopsis concinna (Fagaceae), a threatened species from Hong Kong and South-Eastern China.","authors":"D. Hinsinger, J. S. Strijk","doi":"10.3109/19401736.2015.1110800","DOIUrl":"https://doi.org/10.3109/19401736.2015.1110800","url":null,"abstract":"AbstractThe complete chloroplast genome of Castanopsis concinna (Champion ex Bentham) A. de Candolle, an endemic species to Hong Kong and southeastern China, was determined in this study. Due to logging, historical habitat loss, and fragmentation, conservation efforts for C. concinna are becoming increasingly urgent as the species is now known from only a handful of locations. To aid efforts to preserve and propagate the species ex situ, knowledge on the distribution of genetic diversity in the remaining populations is crucial. Here we report the complete chloroplast genome sequence of one individual collected in Hong Kong in 2014. The total genome size was 160 606 bp in length, containing a pair of inverted repeats (IRs) of 25 677 bp, which were separated by a large single copy (LSC) and small single copy (SSC) of 90 368 and 18 884 bp, respectively. The overall GC content of the plastid genome was 36.8%. 136 genes were annotated, including 82 protein-coding genes, 46 tRNA genes and 8 rRNA genes. In these...","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2015.1110800","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69458502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Mitochondrial genome of the ringstraked guitarfish Rhinobatos hynnicephalus (Elasmobranchii: Rajiformes). 环纹吉他鱼(Rhinobatos hynnicephalus)线粒体基因组研究。
Mitochondrial Dna Pub Date : 2015-08-01 Epub Date: 2013-10-03 DOI: 10.3109/19401736.2013.836520
Xiao Chen, Weiming Ai, Xiaofang Shi, Tingwei Gao
{"title":"Mitochondrial genome of the ringstraked guitarfish Rhinobatos hynnicephalus (Elasmobranchii: Rajiformes).","authors":"Xiao Chen,&nbsp;Weiming Ai,&nbsp;Xiaofang Shi,&nbsp;Tingwei Gao","doi":"10.3109/19401736.2013.836520","DOIUrl":"https://doi.org/10.3109/19401736.2013.836520","url":null,"abstract":"<p><p>The complete mitochondrial genome of the ringstraked guitarfish Rhinobatos hynnicephalus is firstly presented in this study, which is also the first representative in the family Rhinobatidae. It is 16,776 bp in length and contains 37 genes and one control region as the typical gene arrangement and transcriptional direction in vertebrates. The overall base composition is 31.7% A, 26.8% C, 13.5% G and 28.1% T. The 22 tRNA genes ranged from 67 bp (tRNA-Ser2) to 75 bp (tRNA-Leu1). The origin of L-strand replication (OL) sequence was identified between tRNA-Asn and tRNA-Cys genes. The termination associated sequence (TAS) and the conserved sequence blocks (CSB 1--3) were recognized in the control region.</p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2013.836520","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31777557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
Multiple introductions of the eastern fox squirrel (Sciurus niger) in California. 加利福尼亚东部狐松鼠(Sciurus niger)的多次引进。
Mitochondrial Dna Pub Date : 2015-08-01 Epub Date: 2014-01-17 DOI: 10.3109/19401736.2013.878903
Sieara C Claytor, Alan E Muchlinski, Elizabeth Torres
{"title":"Multiple introductions of the eastern fox squirrel (Sciurus niger) in California.","authors":"Sieara C Claytor,&nbsp;Alan E Muchlinski,&nbsp;Elizabeth Torres","doi":"10.3109/19401736.2013.878903","DOIUrl":"https://doi.org/10.3109/19401736.2013.878903","url":null,"abstract":"<p><p>Eastern fox squirrels (Sciurus niger) have been introduced into California within the past 130 years. Recently, their range has been expanding at an alarming rate. Genetic diversity was assessed in 101 control region sequences of eastern fox squirrels from three geographic regions within California (Los Angeles County, Alameda and Contra Costa counties and Sacramento County) to determine if a single or multiple introductions occurred within California, as indicated by the detection of multiple haplotypes. A total of 11 haplotypes were discovered, with haplotypes rarely shared among geographic regions and no clustering by region in a haplotype network. This suggests that the introduction to different regions within California came from different source populations within the native range of the species. Haplotype diversity was highest in Los Angeles County. Due to a lack of phylogeographic structure in fox squirrels in their native range, it is difficult to identify the sources of all introductions. </p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2013.878903","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32041747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
Haplotypes and variable position detection in the mitochondrial DNA coding region encompassing nucleotide positions 10,716-11,184. 线粒体DNA编码区核苷酸位置10,716-11,184的单倍型和可变位置检测。
Mitochondrial Dna Pub Date : 2015-08-01 Epub Date: 2014-01-07 DOI: 10.3109/19401736.2013.869675
Imad Hadi Hameed, Ameer Ibrahim Abdulzahra, Mohammed Abdullah Jebor, Cheah Yoke Kqueen, Aamera Jaber Ommer
{"title":"Haplotypes and variable position detection in the mitochondrial DNA coding region encompassing nucleotide positions 10,716-11,184.","authors":"Imad Hadi Hameed,&nbsp;Ameer Ibrahim Abdulzahra,&nbsp;Mohammed Abdullah Jebor,&nbsp;Cheah Yoke Kqueen,&nbsp;Aamera Jaber Ommer","doi":"10.3109/19401736.2013.869675","DOIUrl":"https://doi.org/10.3109/19401736.2013.869675","url":null,"abstract":"<p><p>This study evaluates the mitochondrial noncoding regions by using the Sanger sequencing method for application in Forensic Science. FTA® Technology (FTA™ paper DNA extraction) was utilized to extract DNA. Portion of coding region encompassing positions from (10,716 to 11,184) amplified in accordance with the Anderson reference sequence. PCR products purified by EZ-10 spin column were then sequenced and detected using the ABI 3730 × L DNA Analyzer. A new polymorphic positions 10,750 and 10,790 that are described may be suitable sources in future for identification purpose. The data obtained can be used to identify variable nucleotide positions characterized by frequent occurrence, most promising for identification variants.</p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2013.869675","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32006055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 31
The complete mitochondrial genome of the Trachinotus ovatus (Teleostei, Carangidae). 卵形粗尾鱼(Teleostei, Carangidae)线粒体全基因组。
Mitochondrial Dna Pub Date : 2015-08-01 Epub Date: 2013-10-03 DOI: 10.3109/19401736.2013.836516
Zhenzhen Xie, Shuisheng Li, Mi Yao, Danqi Lu, Zhihao Li, Zining Meng, Yong Zhang, Haoran Lin
{"title":"The complete mitochondrial genome of the Trachinotus ovatus (Teleostei, Carangidae).","authors":"Zhenzhen Xie,&nbsp;Shuisheng Li,&nbsp;Mi Yao,&nbsp;Danqi Lu,&nbsp;Zhihao Li,&nbsp;Zining Meng,&nbsp;Yong Zhang,&nbsp;Haoran Lin","doi":"10.3109/19401736.2013.836516","DOIUrl":"https://doi.org/10.3109/19401736.2013.836516","url":null,"abstract":"<p><p>We present the complete mitochondrial genome of the Trachinotus ovatus in this study. The mitochondrial genome is 16,563 bp long and consists of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region. The gene order and composition of T. ovatus mitochondrial genome was similar to that of most other vertebrates. The nucleotide compositions of the light strand are 29.03% of A, 28.86% of C, 26.23% of T and 15.88% of G. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. Two copies of tandem repeat sequence (56 bp) was observed in the 5' end of the control region.</p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2013.836516","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31777554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 33
The complete mitochondrial genome of the Ningxiang pig. 宁乡猪的完整线粒体基因组。
Mitochondrial Dna Pub Date : 2015-08-01 Epub Date: 2013-09-19 DOI: 10.3109/19401736.2013.834433
Dong Xu, Qing-Hui Li, Chang-Qing He, Yu-Lan Chai, Hai-Ming Ma
{"title":"The complete mitochondrial genome of the Ningxiang pig.","authors":"Dong Xu,&nbsp;Qing-Hui Li,&nbsp;Chang-Qing He,&nbsp;Yu-Lan Chai,&nbsp;Hai-Ming Ma","doi":"10.3109/19401736.2013.834433","DOIUrl":"https://doi.org/10.3109/19401736.2013.834433","url":null,"abstract":"<p><p>In this work, we reported the complete mitochondrial genome sequence of the Ningxiang pig (Human Province), which was determined through PCR-based method. The total length of the mitogenome is 16,690 bp. The overall composition of the mitogenome was estimated to be 34.70% for A, 25.81% for T, 26.18% for C, 13.30% for G, respectively, indicating that an A + T(60.52%)-rich feature occurs in the Ningxiang pig. It contains the typical structure, including 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The arrangement of these genes was the same as that found in the Landrace pig. All the protein initiation codons are ATG, except for ND2. ND3 and ND5 are ATA, ND4L is GTG. The complete mitochondrial genome sequence of the Ningxiang pig in Human Province provides an important data for further study about genetic mechanism.</p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2013.834433","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31742599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
Complete mitochondrial genome of the Antarctic soft-shelled clam, Laternula elliptica (Bivalvia; Laternulidae). 南极软壳蛤，Laternula elliptica (Bivalvia)的线粒体全基因组;Laternulidae)。
Mitochondrial Dna Pub Date : 2015-08-01 Epub Date: 2013-10-01 DOI: 10.3109/19401736.2013.836515
Hyun Park, Do Hwan Ahn
{"title":"Complete mitochondrial genome of the Antarctic soft-shelled clam, Laternula elliptica (Bivalvia; Laternulidae).","authors":"Hyun Park,&nbsp;Do Hwan Ahn","doi":"10.3109/19401736.2013.836515","DOIUrl":"https://doi.org/10.3109/19401736.2013.836515","url":null,"abstract":"<p><p>The complete mitogenome of the Antarctic soft-shelled clam, Laternula elliptica was determined to be 14,622 bp in length, and to contain 13 protein coding genes (PCGs), 22 tRNA genes, and large (rrnL) and small (rrnS) rRNA genes. Its total A + T content is 55.09%. The L. elliptica mitogenome is the smallest one among those of bivalvia, due to the existence of relatively small intergenic non-coding sequences. All genes are transcribed from the light-strand as a template like bivalve taxa except Unionoidea.</p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2013.836515","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31773561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 9
Evolution of mitochondrial DNA and its relation to basal metabolic rate. 线粒体DNA的进化及其与基础代谢率的关系。
Mitochondrial Dna Pub Date : 2015-08-01 Epub Date: 2014-01-17 DOI: 10.3109/19401736.2013.873895
Ping Feng, Huabin Zhao, Xin Lu
{"title":"Evolution of mitochondrial DNA and its relation to basal metabolic rate.","authors":"Ping Feng,&nbsp;Huabin Zhao,&nbsp;Xin Lu","doi":"10.3109/19401736.2013.873895","DOIUrl":"https://doi.org/10.3109/19401736.2013.873895","url":null,"abstract":"<p><p>Energy metabolism is essential for the survival of animals, which can be characterized by maximum metabolic rate (MMR) and basal metabolic rate (BMR). Because of the crucial roles of mitochondria in energy metabolism, mitochondrial DNA (mtDNA) has been subjected to stronger purifying selection in strongly locomotive than weakly locomotive birds and mammals. Although maximum locomotive speed (an indicator of MMR) showed a negative correlation with the evolutionary rate of mtDNA, it is unclear whether BMR has driven the evolution of mtDNA. Here, we take advantage of the large amount of mtDNA and BMR data in 106 mammals to test whether BMR has influenced the mtDNA evolution. Our results showed that, in addition to the locomotive speed, mammals with higher BMR have subjected to stronger purifying selection on mtDNA than did those with lower BMR. The evolution of mammalian mtDNA has been modified by two levels of energy metabolism, including MMR and BMR. Our study provides a more comprehensive view of mtDNA evolution in relation to energy metabolism. </p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2013.873895","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32042035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
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