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The heavy strand dilemma of vertebrate mitochondria on genome sequencing age: number of encoded genes or G + T content? 脊椎动物线粒体重链困境对基因组测序的影响:编码基因数还是G + T含量?
4区 生物学 Q4 GENETICS & HEREDITY Pub Date : 2018-02-17 DOI: 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)。
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引用次数: 17
DNA barcodes for dragonflies and damselflies (Odonata) of Mindanao, Philippines 菲律宾棉兰老岛蜻蜓和豆娘的DNA条形码
4区 生物学 Q4 GENETICS & HEREDITY Pub Date : 2018-02-17 DOI: 10.1080/24701394.2016.1267157
P. A. Casas, K. Sing, Ping-Shin Lee, O. Nuñeza, R. Villanueva, John-James Wilson
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.
可靠的物种鉴定为利用蛇目动物作为生物指标和保护提供了坚实的基础。蛇目动物是一个迫切需要关注的问题,因为许多物种濒临灭绝。从棉兰老岛收集的36种经形态学鉴定的齿鼠属(Odonata)中获得134个COI条形码,隶属于10科19属。种内序列差异在0 ~ 6.7%之间,有4种差异大于2%;种间序列差异在0.5 ~ 23.3%之间,有7种差异小于2%。因此,在种内和种间DNA条形码差异之间没有明显的差距。菲律宾群岛的众多岛屿可能促进了蛇目动物的快速物种形成,并导致密切相关的物种群之间的种间序列差异很小。本文对棉兰老岛已报道的36种蜥目动物进行了形态鉴定,其中31种没有DNA条形码记录。
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引用次数: 8
Genetic identification for prey birds of the Endangered peregrine falcon (Falco peregrinus) 濒危游隼捕食鸟类的遗传鉴定
4区 生物学 Q4 GENETICS & HEREDITY Pub Date : 2018-02-17 DOI: 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.
摘要为了揭示游隼(Falco peregrinus)的饮食生态,我们对在韩国Sasu岛一个觅食地采集的猎物进行了线粒体基因(COI和CYTB)的分子分析。无创遗传分析结果表明,获得的序列来自9种鸟类(Cuculus canorus、Eurystomus orientalis、Limosa Limosa、Microscelis amaurotis、Oriolus chinensis、Phasianus colchicus、Sterna hirundo、Streptopelia orientalis和Turdus pallidus)。其中5种(C. canorus、M. amaurrotis、S. hirundo、S. orientalis和T. pallidus)曾在岛上发现,其余4种(E. orientalis、L. limosa、O. chinensis和P. colchicus)是新发现的。在饮食遗骸中没有发现两栖动物、爬行动物和哺乳动物等陆地动物的mtDNA序列,这表明游隼主要捕食其他鸟类,而不是栖息在萨苏岛的其他动物。岛上鸟类种类丰富,动物种群丰富,为游隼提供了充足的饮食资源。我们的研究结果表明,基于dna的分子方法可能有助于识别这些鸟类的猎物种类,并可能在未来对濒危游隼的研究中有价值。
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引用次数: 7
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 mtDNA细胞色素b区序列揭示了印度主要鲤鱼(Labeo rohita, Hamilton, 1822)的种群结构和遗传多样性
4区 生物学 Q4 GENETICS & HEREDITY Pub Date : 2018-02-17 DOI: 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.
摘要通过线粒体DNA细胞色素b区部分序列分析,研究了罗虎(Labeo rohita Hamilton, 1822)的种群结构和遗传多样性。我们检查了从印度三条地理上孤立的河流的六个地点收集的133个样本。11个单倍型分析显示,单倍型多样性低(0.00150),核苷酸多样性(π)低(0.02884),异质性低(0.00374)。分子变异分析(AMOVA)表明,群体内的遗传多样性高于群体间的遗传多样性。Fst分数(- 0.07479 ~ 0.07022)表明印度三河地区罗氏菌居群遗传结构较低。值得注意的是,尽管采样点来自不同的河流,但Farakka-Bharuch种群对Fst得分为0.0000。单倍型的系统发育重建结果显示,6个群体的单倍型(Hap_1)具有相同的中心单倍型,点突变范围在1-25个核苷酸之间。
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引用次数: 11
Mitochondria COI-based genetic diversity of the cotton leafhopper Amrasca biguttula biguttula (Ishida) populations from India 印度棉叶蝉Amrasca biguttula biguttula (Ishida)居群线粒体coi遗传多样性分析
4区 生物学 Q4 GENETICS & HEREDITY Pub Date : 2018-02-17 DOI: 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.
摘要棉叶蝉(Amrasca biguttula biguttula, Ishida)是亚洲和东南亚国家的一种多食性害虫。我们对来自印度北部、中部和南部7个主要棉花种植区的67只棉叶蝉的线粒体COI基因片段进行了测序。对全印度叶跳种群的遗传分化分析证实了单种的存在。总共有30个单倍型在印度的不同地区被确定。印度北部的人口以单一的单倍型为主,而印度南部和中部的人口则表现出不同的单倍型在该地区的分散。对北印度人口中性测试的拒绝也表明人口扩张。遗传分化和基因流分析共同证实了石田A. biguttula biguttula石田A. biguttula石田的系统地理结构是距离隔离的。
{"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}
引用次数: 12
Characterization of mitochondrial DNA polymorphisms in the Han population in Liaoning Province, Northeast China 辽宁省汉族人群线粒体DNA多态性特征分析
4区 生物学 Q4 GENETICS & HEREDITY Pub Date : 2018-02-17 DOI: 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.
摘要本研究通过对辽宁汉族线粒体DNA (mtDNA)遗传变异的分析,阐明辽宁汉族母系遗传结构。在辽宁省共收集了317份无血缘关系个体的血液样本进行分析。采用两种不同的方法对mtDNA样本进行分析:对高变序列I和II (HVSI和HVSII)进行测序,对编码区进行聚合酶链反应-限制性片段长度多态性(PCR-RFLP)分析。基因多样性值(0.9997±0.0003)较高,多态性信息含量(0.99668)较高,随机匹配概率(0.00332)较高。这些样本被分类为305个单倍型,其中9个共有单倍型。最常见的单倍群为D4(12.93%)。主成分分析图谱、系统发育树图谱和遗传距离矩阵均表明辽宁汉族群体与藏族群体的遗传距离较远,而与苗族群体的遗传距离较近。
{"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}
引用次数: 5
Genetic variations and population structure in three populations of beardless barb, Cyclocheilichthys apogon (Valenciennes, 1842) inferred from mitochondrial cytochrome b sequences 根据线粒体细胞色素b序列推断的三个无须barb, Cyclocheilichthys apogon (valencienne, 1842)群体的遗传变异和群体结构
4区 生物学 Q4 GENETICS & HEREDITY Pub Date : 2018-01-02 DOI: 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.
摘要本研究旨在探讨在泰国东北部3个不同地点采集的46份无须刺,Cyclocheilichthys apogon (Valenciennes, 1842)的传播屏障与遗传多样性、种群结构和人口统计学历史的关系。采用分子变异分析(AMOVA)来确定该鱼种群内和种群间的遗传变异。此外,中性检验和错配分布分析分别用于评估人口的中性和人口扩张。在1100 ~ 1140 bp范围内获得了16种不同单倍型的连续序列,高单倍型多样性为0.8773±0.0327,低单倍型多样性为0.00215±0.00020。种群内变异和种群间变异分别占总变异的98.98%和1.02%。低水平的成对Fst估计表明种群之间可能存在基因流动,表明该地理范围内存在遗传同质性。在这些人群中明显出现了一种支持性的观点,即具有单母血统和过去的人口扩张或选择经历。目前的资料表明,这3个种群明显是作为一个种群单位存在的,这是确定该地理区域阿格龙遗传变异的重要因素,可用于制定有效的保护和管理计划和策略。
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引用次数: 4
Proposed synonymy for Micropogonias altipinnis (Günther 1864), Micropogonias ectenes (Jordan & Gilbert 1882), and Micropogonias megalops (Gilbert 1890)
4区 生物学 Q4 GENETICS & HEREDITY Pub Date : 2018-01-02 DOI: 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":"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}
引用次数: 0
Sheep mitochondrial heteroplasmy arises from tandem motifs and unspecific PCR amplification 绵羊线粒体异质性是由串联基序和非特异性PCR扩增引起的
4区 生物学 Q4 GENETICS & HEREDITY Pub Date : 2018-01-02 DOI: 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.
线粒体DNA控制区(D-loop)是一种广泛应用于进化和系统地理学研究的分子标记。然而,个体内D-loop区域异质性的发生鲜有研究。本研究利用85只中国绵羊扩增部分D-loop区,鉴定出15只异质动物(占17.64%)。通过对异质区D-loop序列的PCR扩增和克隆比较分析,发现大部分异质区序列图谱都是从一个75-bp的随机重复基序开始的。此外,从4只随机异质动物和3只纯合子动物中获得的61只克隆中,共发现22条带有d环的非同源序列,并对其基因组位置进行了同源性比较。总之,D-Loop测序谱似乎是异质性的,可能是由串联重复基序和PCR扩增过程中的非特异性复制引起的;然而,它们不太可能是由于个体内存在多个线粒体基因组。
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引用次数: 5
Scanning the mitochondrial genome for mutations by cycling temperature capillary electrophoresis 通过循环温度毛细管电泳扫描线粒体基因组的突变
4区 生物学 Q4 GENETICS & HEREDITY Pub Date : 2018-01-02 DOI: 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.
为了避免可能的核污染,并专门扩增线粒体DNA,选择了一组23引物。在线粒体DNA选择片段上,第二组片段用于扩增和鉴定突变部分,检测限为1%。这种突变扫描方法分析了76%的线粒体基因组,并用于检查来自不同起源组织的94个肿瘤。总共有87个肿瘤有一个或多个突变,剩下7个样本没有观察到突变。Sanger测序证实携带突变的样本突变率超过30%。生成的数据证实了线粒体DNA的一些区域比其他区域有更多的突变。
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引用次数: 6
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Mitochondrial Dna Part a
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