Pub Date : 2018-02-17DOI: 10.1080/24701394.2016.1267158
U. Gaur, M. Tantia, B. Mishra, S. B. Bharani Kumar, R. K. Vijh, A. Chaudhury
Abstract The indigenous domestic duck (Anas platyrhynchos domestica) which is domesticated from Mallard (Anas platyrhynchos) contributes significantly to poor farming community in coastal and North Eastern regions of India. For conservation and maintenance of indigenous duck populations it is very important to know the existing genetic diversity and population structure. To unravel the population structure and genetic diversity among the five indigenous duck populations of India, the mitochondrial D-loop sequences of 120 ducks were analyzed. The sequence analysis by comparison of mtDNA D-loop region (470 bp) of five Indian duck populations revealed 25 mitochondrial haplotypes. Pairwise FST value among populations was 0.4243 (p < .01) and the range of nucleotide substitution per site (Dxy) between the five Indian duck populations was 0.00034–0.00555, and the net divergence (Da) was 0–0.00355. The phylogenetic analysis in the present study unveiled three clades. The analysis revealed genetic continuity among ducks of coastal region of the country which formed a separate group from the ducks of the inland area. Both coastal as well as the land birds revealed introgression of the out group breed Khaki Campbell, which is used for breed improvement programs in India. The observations revealed very less selection and a single matrilineal lineage of indigenous domestic ducks.
{"title":"Mitochondrial D-loop analysis for uncovering the population structure and genetic diversity among the indigenous duck (Anas platyrhynchos) populations of India","authors":"U. Gaur, M. Tantia, B. Mishra, S. B. Bharani Kumar, R. K. Vijh, A. Chaudhury","doi":"10.1080/24701394.2016.1267158","DOIUrl":"https://doi.org/10.1080/24701394.2016.1267158","url":null,"abstract":"Abstract The indigenous domestic duck (Anas platyrhynchos domestica) which is domesticated from Mallard (Anas platyrhynchos) contributes significantly to poor farming community in coastal and North Eastern regions of India. For conservation and maintenance of indigenous duck populations it is very important to know the existing genetic diversity and population structure. To unravel the population structure and genetic diversity among the five indigenous duck populations of India, the mitochondrial D-loop sequences of 120 ducks were analyzed. The sequence analysis by comparison of mtDNA D-loop region (470 bp) of five Indian duck populations revealed 25 mitochondrial haplotypes. Pairwise FST value among populations was 0.4243 (p < .01) and the range of nucleotide substitution per site (Dxy) between the five Indian duck populations was 0.00034–0.00555, and the net divergence (Da) was 0–0.00355. The phylogenetic analysis in the present study unveiled three clades. The analysis revealed genetic continuity among ducks of coastal region of the country which formed a separate group from the ducks of the inland area. Both coastal as well as the land birds revealed introgression of the out group breed Khaki Campbell, which is used for breed improvement programs in India. The observations revealed very less selection and a single matrilineal lineage of indigenous domestic ducks.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88267756","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}
Pub Date : 2018-02-17DOI: 10.1080/24701394.2016.1275603
Nicholas Costa Barroso Lima, F. Prosdocimi
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
差异超离心是细胞生物学和微生物学的经典技术，用于分离细胞成分，如细胞核、线粒体、叶绿体、溶酶体、过氧化物酶体、囊泡、核糖体和细胞质(Garber & Yoder 1983)。关于线粒体的研究，在一种名为浮力密度超离心的技术中，氯化铯(CsCl)溶液被用于分离核DNA和线粒体DNA (Welter et al. 1988;Zimmerman et al. 1988)。因此，在CsCl超离心中获得的两个不同的条带用于定义给定线粒体的重(H)和轻(L) DNA链。这些研究通常是针对许多进化支进行的(Corneo et al. 1966;Sinclair et al. 1967;Brack et al. 1972;Beridze & Tabidze 1976;Garber & Yoder 1983)，他们仍然以较小的速度分离细胞成分以进行进一步分析(Zhao et al. 2005)。然而，随着PCR和Sanger测序技术的发展，研究人员不需要将线粒体从其他细胞成分中分离出来进行DNA测序。在新一代测序技术发展10多年后的今天，线粒体基因组作为全基因组测序的副产品已经可以获得。尽管线粒体读取量可能因组织类型、动物组和/或样品提取方案而有所不同，但我们发现，每200-1000个核基因组读取可以找到一个线粒体读取(Uliano-Silva et al. 2015;Perini Vda et al. 2016;prodocimi et al. 2016)。在某些情况下，线粒体DNA的读取量如此之高，以至于组装者在进行全基因组组装时将其掩盖为重复序列。正是在组装和注释了各种生物体的许多完整线粒体基因组之后(Gomes de S a et al. 2015;Uliano-Silva et al. 2015;Perini Vda et al. 2016;prodocimi et al. 2016;Souto et al. 2016;Uliano-Silva et al. 2016)，我们决定更仔细地研究H和L链的分配。我们惊讶地发现，迄今为止发表的许多脊椎动物线粒体基因组似乎在轻链和重链方面的注释不准确(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;bbb10等人2016;Sun et al. 2016)。经典研究表明，线粒体l -链可以定义为鸟嘌呤和胸腺嘧啶含量较低的那条链(Taanman 1999;穆恩1975)。根据Vinograd等人(1963)的研究，滴定胸腺嘧啶和鸟嘌呤的N-H质子会增加变性DNA的浮力密度，表明Gþ T含量是线粒体链浮力密度的原因。在对蓝额亚马逊鹦鹉(amazon aestiva)的有丝分裂基因组进行测序和分析时(Lima等人的手稿正在准备中)，我们发现该分子中的大多数基因都是由l链编码的，即Gþ T含量较低的那条链(在本例中为38.06%)。第一个描述亚马逊属物种完整线粒体基因组的工作表明，大多数基因存在于h链中(Urantowka et al. 2013)。我们还惊讶地发现，鸡的最重要的鸟类线粒体基因组(Desjardins & Morais 1990)提供了关于重链和轻链分配的相互矛盾的信息。Desjardins和Morais(1990)在他们的结果的第一段中说重链呈现了大部分基因，但他们也表明，这条链的Gþ T含量较低(37.3%)，并且他们的大部分基因都编码在这条链上，如图2所示。另一方面，在1981年最经典和被引用的线粒体基因组研究中，安德森和合作者首次描述了整个人类线粒体基因组。他们指出，人类线粒体的大多数基因都编码于光链(Anderson et al. 1981)。然而，与Anderson的研究相反(Anderson et al. 1981)， Taanman(1999)认为人类线粒体h链是编码基因数量较多的一段。为了阐明这个问题，我们从RefSeq(2016年11月)下载了所有可用的脊椎动物线粒体，并计算了它们的Gþ T含量，并将这些信息与每条链上描述的基因数量相关联。我们发现几乎所有的脊椎动物有丝分裂基因组(4205个中有4200个)都有包含最多基因和最低Gþ T的轻链(补充表1)。唯一的例外是来自不同分支的5种鱼类，其中2种来自同一属的Johnius。这些例外存在于重链编码的大部分基因(登录号:NC_005800, NC_013879, NC_021130, NC_022464和NC_008222)。
{"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":null,"pages":null},"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}
Pub Date : 2018-02-17DOI: 10.1080/24701394.2016.1275595
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
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.
{"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":null,"pages":null},"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}
Pub Date : 2018-02-17DOI: 10.1080/24701394.2016.1275597
Feng-ling Xu, Jun Yao, M. Ding, Zhang-sen Shi, Xue Wu, Jing-jing Zhang, Bao-jie Wang
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.
{"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":null,"pages":null},"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}
Pub Date : 2018-02-17DOI: 10.1080/24701394.2016.1261853
Sang-Hyun Han, Hong-Shik Oh
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.
{"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":null,"pages":null},"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}
Pub Date : 2018-02-17DOI: 10.1080/24701394.2016.1267156
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
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.
{"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":null,"pages":null},"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}
Pub Date : 2018-01-02DOI: 10.1080/24701394.2016.1242581
Anan Kenthao, P. Wangsomnuk, P. Jearranaiprepame
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.
{"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":null,"pages":null},"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}
Pub Date : 2018-01-02DOI: 10.1080/24701394.2016.1258405
Geremías Sánchez-Pinedo, N. Díaz-Viloria, J. L. Ortíz-Galindo, Nelson Ferreira-Fontoura, R. Pérez-Enríquez, L. Sánchez‐Velasco, J. De La Cruz‐Agüero
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.
摘要:在Sciaenidae科中，Micropogonias属由墨西哥太平洋沿岸的三个已知物种组成:Micropogonias altipinnis, M. ectenes和M. megalops。这些物种表现出重叠的诊断特征，这使得物种鉴定变得困难。本研究将太平洋Micropogonias物种之间的形态差异(分生、身体形态和耳石)与DNA序列(mtDNA的CO1和16S部分以及nDNA的28S部分)联系起来。分生分析表明，三种鱼在鳐数、鳃耙数和背鳍最长棘长度上存在纬度差异，形态计量特征(体和耳石)判别分析显示三种形态实体(p < 2%)。遗传结果表明，这三个物种是一个物种，分型和形态的差异可能是表型可塑性或早期物种形成的结果。在这个意义上，M. ectenes和M. megalops被认为是M. altipinnis的初级近义词。
{"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":null,"pages":null},"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}
Pub Date : 2018-01-02DOI: 10.1080/24701394.2016.1233532
C. Arstad, Paulo Refinetti, David J. Warren, K. Giercksky, P. Ekstrøm
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.
{"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":null,"pages":null},"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}
Pub Date : 2018-01-02DOI: 10.1080/24701394.2016.1242582
G. E, Yongju Zhao, Yongfu Huang
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.
{"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":null,"pages":null},"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}
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