白鱼线粒体DNA控制区结构和种群遗传多样性分析

用特异性引物对白鱼（Anabarilius grahami）DNA进行PCR扩增,获得了白鱼线粒体DNA控制区基因全序列（930 bp）。控制区T、C、A和G碱基组成为29.8%、22.5%、33.0%和14.7%。对照其他已报道的鱼类控制区结构,对白鱼控制区结构进行了分析,识别了其终止序列区、中央保守区和保守序列区,找到了终止相关的序列TAS以及保守序列（CSB-F、CSB-D、CSB-1、CSB-2、CSB-3）。同时运用DNA分析软件对白鱼一个驯养种群（中国科学院昆明动物研究所珍稀鱼类繁育中心）及两个自然地理种群（江川县明星鱼洞、江川县牛摩村）进行了遗传多样性分析。结果显示：两个自然种群存在较强基因交流,未出现遗传分化;人工驯养种群遗传多样性最高,种群复壮程度较好。     

鱇[鱼良]白鱼线粒体DNA控制区结构和种群遗传多样性分析

用特异性引物对鱇(鱼良)白鱼(Anabarilius grahami)DNA进行PCR扩增,获得了鱇(鱼良)白鱼线粒体DNA控制区基冈全序列(930bp).控制区T、C、A和G碱基组成为29.8%、22.5%、33.0和14.7%.对照其他已报道的鱼类控制区结构,对鱇(鱼良)白鱼控制区结构进行了分析,识别了其终止序列区、中央保守区和保守序列区,找到了终止相关的序列TAS以及保守序列(CSB-F、CSB-D、CSB-1、CSB-2、CSB-3).同时运用DNA分析软件对鱇(鱼良)白鱼一个驯养种群(中国科学院昆明动物研究所珍稀鱼类繁育中心)及两个自然地理种群(江川县明星鱼洞、江川县牛摩村)进行了遗传多样性分析.结果显示:两个自然种群存在较强基因交流,未出现遗传分化;人工驯养种群遗传多样性最高,种群复壮程度较好.     

都柳江鲤、鲫和草鱼种群mtDNA控制区及遗传多样性分析

采用PCR和DNA测序技术对贵州都柳江鲤(Cyprinus carpio)、鲫(Carassius auratus)和草鱼(Ctenopharyngodon idellus)种群的mtDNA控制区序列及遗传多样性进行了研究。获得了都柳江鲤、鲫和草鱼mtDNA控制区长度分别为899~901 bp、787 bp和901~905 bp的序列。该3种鱼类控制区碱基A、T含量较高,G含量最低。识别了该3种鱼类mtDNA控制区终止序列区、中央保守区和保守序列区等保守序列。其中,除CSB-2和CSB-3碱基组成相同外,其余核心序列碱基组成存在着差异。都柳江鲤、鲫和草鱼种群mtDNA控制区分别有24、24和11个多态位点,分属12、17和8个单倍型。都柳江鲤、鲫种群遗传多样性较高,草鱼种群遗传多样性较低。因此,有必要开展都柳江草鱼种群遗传多样性的保护。     

鲹科鱼类线粒体DNA控制区结构及系统发育关系

采用PCR技术获得了9种鲹科鱼类的线粒体DNA控制区全序列,并结合从GenBank中下载的3种鲹科鱼类的相应序列采用ClustalW排序后,对控制区结构进行分析,识别了其终止序列区、中央保守区和保守序列区3个区域,指出了终止相关序列的主体是TACAT与其反向互补序列ATGTA以及一系列保守序列(CSB-F、CSB-E、CSB-D和CSB-1、CSB-2、CSB-3),并给出了它们的一般形式,同时在康氏似鲹控制区的5′和3′两端发现重复序列。以尖吻鲈作为外类群,应用邻接法构建的分子系统树表明:鲹科鱼类分为鲹亚科、鰤亚科、鲳鲹亚科和鰆鲹亚科4个亚科,各自形成单系群;鲹亚科与鰤亚科形成姐妹群,鲳鲹亚科再与他们聚在一起,鰆鲹亚科处于鲹科鱼类的基部,与前面3个亚科聚在一起。     

鲹科鱼类线粒体DNA控制区结构及系统发育关系

采用PCR技术获得了9种鲹科鱼类的线粒体DNA控制区全序列,并结合从GenBank中下载的3种鲹科鱼类的相应序列采用Clustal W排序后,对控制区结构进行分析,识别了其终止序列区、中央保守区和保守序列区3个区域,指出了终止相关序列的主体是TACAT与其反向互补序列ATGTA以及一系列保守序列（CSB-F、CSB-E、CSB-D和CSB-1、CSB-2、CSB-3）,并给出了它们的一般形式,同时在康氏似鲹控制区的5′和3′两端发现重复序列。以尖吻鲈作为外类群,应用邻接法构建的分子系统树表明：鲹科鱼类分为鲹亚科、鰤亚科、鲳鲹亚科和鰆鲹亚科4个亚科,各自形成单系群;鲹亚科与鰤亚科形成姐妹群,鲳鲹亚科再与他们聚在一起,鰆鲹亚科处于鲹科鱼类的基部,与前面3个亚科聚在一起。     

南蝠线粒体DNA控制区结构及贵州7个种群遗传多样性的分析研究

采用PCR技术获得了贵州7个南蝠(Ia io)自然种群42个个体的线粒体DNA控制区全序列,长度为1256～1340 bp.对控制区结构进行分析,识别了其延伸的终止结合序列区(包括ETAS1和ETAS2元件)、中央保守区(包括F、E、D、C、B元件)和保守序列区(包括CSB1、CSB2和CSB3元件);同时,在延伸的终止结合序列区还发现了若干能形成发夹结构的主体序列TACAT—ATGTA.在7个自然种群42个个体中共定义了16个单倍型.遗传多样性分析表明:贵州南蝠种群具有较高的单倍型多样性(h=0.945)和中等的核苷酸多样性(π=0.012).基因流、AMOVA和系统进化树分析表明贵州这7个南蝠自然群体间没有发生遗传分化.     

红腹锦鸡线粒体DNA控制区结构和遗传变异研究

红腹锦鸡(Chrysolophus pictus)是中国特有珍稀鸟类,仅见于中国中部和西部的山地,为国家二级重点保护动物.采用聚合酶链式反应和直接测序的方法测定了采自湖南新宁县和龙山县的28只红腹锦鸡线粒体DNA控制区序列.在获得的1 123 bp的碱基序列中,碱基含量为T 32.79%、C 26.07%、A 26.62%和G14.52%,共检测出20个多态性核苷酸变异位点,其中简约信息位点11个.对比其它已报导的雉类控制区结构,对红腹锦鸡控制区结构进行了分析,识别了其高变Ⅰ区、中间保守Ⅱ区和保守Ⅲ区,找到了与终止相关的序列TAS以及保守序列(F、E、D、C).28个样本共发现11种单倍型,其中单倍型hap1和hap2的比例很高.新宁种群的遗传多样性比龙山种群的高,两个种群存在基因流较频繁,未出现明显遗传分化.     

麦穗鱼线粒体基因组序列测定及分析

利用麦穗鱼Pseudorasbora parva和相关鱼类的部分线粒体基因序列,设计出2对长批引物和30对短批引物,采用基于长PCR的2次PCR扩增法测定并注释麦穗鱼线粒体基因组全序列。结果表明,麦穗鱼线粒体基因组长16600bp,A+T含量为58.9%,37个基因位置及组成与其它硬骨鱼一致,均由13个蛋白编码基因、22个tRNA、2个rRNA基因和1个控制区(D-loop)组成。其中L链仅含8个tRNA(Pro、T yr、Ser、Ala、Asn、Cys、Glu、Gln)及ND6基因,其余基因皆由H链编码。基因排列紧密,间隔序列共计13处64bp,长度从1～32bp不等;基因重叠区7处23bp,重叠碱基数在1～7bp之间。13个蛋白编码基因中,除COI起始密码子为GTG外,其余均以ATG为起始密码子;有8个基因(ND1、ND2、COI、ATP6、ATP8、ND4L、ND5、ND6)3’端有完全的TAA或TAG终止密码子,其它5个基因终止密码子为不完整的TA(ND3和ND4)或T(COⅡ,COⅢ,Cyt b)。除tRNASer(AGY)外,其余21个tRNA基因的二级结构均为典型的三叶草结构。预测的lrRNA二级结构共有6个结构域,53个茎环结构,srRNA二级结构包含43个茎环结构。控制区(D-loop)存在3个结构区:终止序列区(TAS)、中央保守区(CSB-F、CSB-D)和保守序列区(CSB-1、CSB-2、CSB-3),其中TAS与DNA复制终止相关,出现茎环结构。     

SEQUENCE AND ANALYSIS OF COMPLETE MITOCHONDRIAL GENOME OF PSEUDORASBORA PARVA

利用麦穗鱼Pseudorasbora parva和相关鱼类的部分线粒体基因序列,设计出2对长批引物和30对短批引物,采用基于长PCR的2次PCR扩增法测定并注释麦穗鱼线粒体基因组全序列.结果表明,麦穗鱼线粒体基因组长16600 bp,A+T含量为58.9％,37个基因位置及组成与其它硬骨鱼一致,均由13个蛋白编码基因、22个tRNA、2个rRNA基因和1个控制区(D-loop)组成.其中L链仅含8个tRNA(Pro、Tyr、Ser、Ala、Asn、Cys、Glu、Gln)及ND6基因,其余基因皆由H链编码.基因排列紧密,间隔序列共计13处64 bp,长度从1～32 bp不等;基因重叠区7处23 bp,重叠碱基数在1～7bp之间.13个蛋白编码基因中,除COI起始密码子为GTG外,其余均以ATG为起始密码子;有8个基因(ND1、ND2、COI、ATP6、ATP8、ND4L、ND5、ND6)3端有完全的TAA或TAG终止密码子,其它5个基因终止密码子为不完整的TA (ND3和ND4)或T(COⅡ,COⅢ,Cyt b).除tRNAser(AGY)外,其余21个tRNA基因的二级结构均为典型的三叶草结构.预测的lrRNA二级结构共有6个结构域,53个茎环结构,srRNA二级结构包含43个茎环结构.控制区(D-loop)存在3个结构区:终止序列区(TAS)、中央保守区( CSB-F、CSB-D)和保守序列区(CSB-1、CSB-2、CSB-3),其中TAS与DNA复制终止相关,出现茎环结构.     

鳜类鱼类的线粒体DNA控制区结构及其系统发育分析

鳜类为低等鲈形目鱼类,是东亚特有类群。然而,关于其系统位置、分类以及一些物种的有效性等尚有争议。采用PCR扩增直接测序的方法,获得了鳜、大眼鳜、斑鳜、暗鳜、波纹鳜、长体鳜、中国少鳞鳜线粒体DNA控制区基因的序列。对比其他已报道鱼类控制区的结构识别序列,对鳜类鱼类控制区的结构进行了分析,识别了终止序列区、中央保守区和保守序列区,并找到了DNA复制终止相关的序列ETAS和中央保守区的保守序列CSB-F、CSB-E、CSB-D以及保守序列区的保守序列CSB1、CSB2、CSB3。几种鳜鱼间共有191个变异位点,其中,终止序列区的变异最高,占总变异的61．3％,中央保守区和保守序列区占总变异的38．7％。这一结果可为全面了解鱼类线粒体DNA控制区的结构特征提供资料。同时,利用高度变异的控制区序列,以鲈科和错科作为外群,使用邻接法和最大简约法构建了这几种鳜鱼的系统发育树。结果表明：鳜类为一单系类群,鳜、大眼鳜、斑鳜、暗鳜、波纹鳜、长体鳜构成一支鳜鱼群,其中,鳜与大眼鳜为姐妹种;中国少鳞鳜为另一支少鳞鳜群;长体鳜未单独成一支,而是聚入鳜鱼群内,应更名为Siniperca roulei。研究结果支持将现生鳜类分为两个类群的观点。     

Mitochondrial DNA structure and organization of the control region of South American camelids

This work presents the mitochondrial DNA molecular organization of the control region (CR) of South American camelids. Sequencing of five individuals each of guanaco, llama, alpaca and vicuna species showed that this region spans 1060 bp including three conserved sequence blocks (CSB I–III) adjacent to the tRNAPhe gene, a conserved central domain and one extended termination‐associated sequence in the 3′ domain of the CR close to the tRNAPro gene. A repeated array formed by three units of 26 bp was detected between CSB I and II. Alignment of the CR sequences from the four species shows a 337‐bp segment that includes most of the nucleotide variability with 10 polymorphic sites. We suggest the use of this segment as a molecular marker to infer data on camelid genetic relationships and population diversity studies.     

齐口裂腹鱼线粒体DNA控制区结构分析

利用直接测序法对齐口裂腹鱼(Schizothorax prenanti)线粒体DNA控制区进行了测序,并对其序列结构进行了分析.结果表明,齐口裂腹鱼线粒体控制区碱基组成中碱基A和T的含A明显高于G和C的含量,所有类型碱基组成中碱基G的含量最低,这与其他硬骨鱼类控制区碱基组成一致.通过与哺乳类和鲤形目鱼类控制区序列进行对...     

Lineage Specificity of the Evolutionary Dynamics of the mtDNA D-Loop Region in Rodents

This paper reports an intraorder study on the D-loop-containing region of the mitochondrial DNA in rodents. A complete multialignment of this region is not feasible with the exception of some conserved regions. The comparative analysis of 25 complete rodent sequences from 23 species plus one lagomorph has revealed that only the central domain (CD), a conserved region of about 80 bp in the extended termination-associated sequences (ETAS) domain, adjacent to the CD, the ETAS1, and conserved sequence block (CSB) 1 blocks are present in all rodent species, whereas the presence of CSB2 and CSB3 is erratic within the order. We have also found a conserved region of 90 bp located between tRNAPro and ETAS1 present in fat dormouse, squirrel, guinea pig, and rabbit. Repeated sequences are present in both the ETAS and the CSB domain, but the repeats differ in length, copy number, and base composition in different species. The potential use of the D-loop for evolutionary studies has been investigated; the presence/absence of conserved blocks and/or repeated sequences cannot be used as a reliable phylogenetic marker, since in some cases they may be shared by distantly related organisms but not by close ones, while in other ones a relationship between tree topology and presence/absence of such motifs is observed. Better results can be obtained by the use of the CD, which, however, due to its reduced size, when used for tracing a phylogenetic tree, shows some nodes with low statistical support. Received: 26 February 2001 / Accepted: 6 June 2001     

Structure of the Mitochondrial DNA Control Region of the Sinipercine Fishes and Their Phylogenetic Relationship

The mitochondrial DNA control region of Siniperca chuatsi, S. kneri, S. scherzeri, S. obscura, S. undulata, Coreosiniperca roulei and Coreoperca whiteheadi were amplified by PCR amplification and directly sequenced. The mtDNA control region of the sinipercine fishes could be separated into three domains, namely, the terminal associated sequence domain, the central conserved sequence domain and the conserved sequence block domain. The extended terminal associated sequence (ETAS), three conserved sequence blocks (CSB-F, CSB-E, CSB-D) in the central conserved sequence domain and three conserved sequence blocks (CSB1, CSB2, CSB3) in the conserved sequence block domain were also identified. The phylogenetic relationships among these sinipercine fishes were constructed through neighbor-joining and maximum parsimony methods using Percidae and Serranidae as outgroups. Results showed that sinipercine fishes were a monophyletic group, with Siniperca forming one group, and Coreoperca forming another group. Coreosiniperca roulei did not form an independent group but was merged into the genus Siniperca. Thus it should be renamed as Siniperca roulei.     

三倍体湘云鲫线粒体DNA序列变异性分析

对26尾三倍体湘云鲫的线粒体tRNA-Thr基因、tRNA-Pro基因和部分控制区的核苷酸序列进行了测定,获得26条长度为837—839 bp的同源基因序列,共发现65个多态性核苷酸变异位点,多态位点比例为0.077,定义了8种单元型。在湘云鲫8种单元型中确认了DNA复制终止相关的序列TAS、中央保守区序列(CSB-F、CSB-E和CSB-D)和保守序列CSB1,8种单元型含有3—5个TAS序列。在65个变异位点中,大部分序列变异为转换,8种单元型之间的序列差异在0.1%—6.3%之间。该研究为三倍体湘云鲫的繁殖和遗传改良提供了一些有价值的信息。     

Sequence length and variation in the mitochondrial control region of two freshwater gobiid fishes belonging to Rhinogobius (Teleostei: Gobioidei)

The control region (D-loop) of mitochondrial DNA (mtDNA) was amplified and sequenced for eight samples of the rhinogobies Rhinogobius maculafasciatus and R. giurinus from Taiwan and southern China. The control regions of both species are of 841–842 bp; the length of these sequences being the most compact among all known sequences in teleost fishes. Three conserved sequence blocks (CSB) were observed. The full D-loop and tRNA Phe gene sequences were determined and compared with other fishes. The interspecific sequence divergence between the two species is 11.3–11.7%; and the intraspecific variation in R. guirinus 0.8–1.8%. Results suggest that the control region of Rhinogobius is informative for phylogenetic reconstruction at both intraspecific and interspecific levels in this gobiid genus.