闽浙地区香鱼线粒体Cyt b基因和D-loop区序列多态性分析

对浙江瑞安、福建宁德、福建东张水库3个地理群体共31例香鱼(Plecoglossus altivelis)的线粒体细胞色素b(Cyt b)基因和线粒体D-loop区序列进行了PCR扩增、序列测定、核苷酸组成和多态性分析。Cyt b基因中, A、T、C和G 4种核苷酸的比例分别为19.72%、29.71%、32.25%和18.32%, A + T含量为49.43%, G + C含量为50.57%。D-loop区序列中, A、T、C和G 4种核苷酸的比例分别为29.99%、29.29%、23.80%和16.92%, A + T含量为59.28%, G + C含量为40.72%。在长度为1 141 bp的Cyt b基因序列中, 仅存在1个变异位点, 核苷酸多样性指数(π值)为0.00028, 31个样本中仅出现两种单倍型; 857 bp长的D-loop区序列中, 仅存在5个变异位点, 核苷酸多样性指数(π值)为0.00199, 仅出现5种单倍型。这表明闽浙地区香鱼的遗传多样性水平很低, 应当加大对香鱼的保护力度。     

雀形目15种鸟类Co Ⅰ与Cyt b基因序列的比较

对雀形目Passeriformes 6科15种鸟类线粒体DNA的Cyt b基因全序列(1 143 bp)和CoⅠ基因部分序列(1 176 bp)进行了比较,结果显示Cyt b和CoⅠ基因序列的变异位点分别为454个和366个,简约信息位点为337个和303个,而且CoⅠ基因比Cyt b基因略微保守,进化速率也较低.采用邻接法、最大简约法、最大似然法和贝叶斯法分别构建了CoⅠ和Cyt b基因两组数据集的分子系统发生树及其合一树,并对建树结果进行了比较分析.基于以上两点,本文认为CoⅠ基因比Cyt b基因更适合于确定雀形目科级阶元之间的系统发生关系,而且它也能够作为雀形目物种鉴定的分子标记,但在物种鉴定方面不如Cyt b基因稳定和准确.     

太湖新银鱼m tDNA COII和Cytb基因的克隆与序列分析

设计了5对特异性引物,扩增、拼接并测定出太湖新银鱼线粒体tRNAAsp-COII-tRNALys和tRNAGlu-Cytb-tRNAThr两段基因序列片段。基因定位和序列分析发现,太湖新银鱼线粒体COII基因全序列长度为691 bp,序列AT含量为52.80%,编码230个氨基酸;线粒体Cytb基因序列全长为1141 bp,AT含量为48.90%,它编码380个氨基酸。分别位于线粒体COII和Cytb基因两翼的4个tRNA基因(tRNAAsp、tRNALys、tRNAGlu和tRNAThr)同时被测定出来。将太湖新银鱼与有明银鱼、小齿日本银鱼的同源序列进行比对分析,并基于线粒体COII Cytb基因合并数据的核苷酸和氨基酸两种序列形式,以黑斑蛙为外群,对10种鱼类进行分子系统树的构建,结果一致表明:小齿日本银鱼与有明银鱼的亲缘关系近于太湖新银鱼;鲱科与鲑科的亲缘关系近于银鱼科鱼类;此外在本研究硬骨鱼类的4个科中,白鲟科作为原始而古老的类群,是在系统进化的过程中首先分化出来的一支。     

基于线粒体D-loop区和Cyt b基因分析广西禾花鲤三个群体遗传结构

研究基于线粒体D-loop区和Cyt b基因部分序列, 分析了广西全州、融水、环江三地禾花鲤(Cyprinus carpio)的遗传结构。在3个群体中共鉴定到19种D-loop与Cyt b序列的组合单倍型, 总的单倍型多样性(H_d)和核苷酸多样性(π)分别为0.916±0.010和0.008±0.004, 禾花鲤线粒体DNA具有单倍型多样性高和核苷酸多样性低的特点。环江群体单倍型多样性最低, 但是核苷酸多样性却最高, 反映了环江群体存在最明显的谱系混杂。分子方差分析(AMOVA)显示遗传变异主要来源于群体内部(71.54%), 禾花鲤三个群体间有显著的遗传分化(F_st=0.285; P<0.01)。系统发育分析表明, 多数样本的线粒体单倍型属于华南鲤(C. carpio rubrefusus)类型, 同时三地禾花鲤中均检测到一定频率的西鲤(C. carpio carpio)或远东鲤(C. carpio haematopterus)类型的线粒体单倍型, 提示禾花鲤可能受到鲤养殖品种的杂交渐渗。研究初步揭示了广西禾花鲤的种质资源现状, 为禾花鲤这一地方特色“稻鱼共作”品种的选育和苗种管理提供了必要的依据。     

普氏野马线粒体DNA D-loop区序列多态性研究

目的:了解中国新疆吉木萨尔野马繁殖中心的普氏野马(Equus przewalskii)遗传多样性及其遗传背景.方法:采用PCR产物直接测序法,对15匹普氏野马线粒体DNA D-loop高变区进行测序分析.结果:测定15个个体的线粒体DNA D-loop高变区15464～15866片段序列402bp.检测到12种单倍型,包括37个多态位点,占全部序列的9.2%,其中转换位点24个、颠换位点20个、转换位点和颠换并存位点8个、缺失位点3个.A%+T%含量(56.1%)高于G%+C%含量(43.9%),平均A含量为28.4%,T含量为27.7%,C含量为29%,G含为14.9%.单倍型间平均遗传距离为0.030,单倍型多态性(h)为1±0.00116,核苷酸多态性(π)为2.90%.15匹普氏野马线粒体DNA D-loop高变区之间平均核苷酸变异率为2.48%.结论:研究表明我国新疆吉木萨尔野马繁殖中心的普氏野马线粒体DNA D-loop区序列存在丰富的多态性.     

太湖新银鱼mtDNA COⅡ和Cytb基因的克隆与序列分析

设计了5对特异性引物,扩增、拼接并测定出太湖新银鱼线粒体tRNA^Asp-COⅡ—tRNAL^ys和tRNA^Glu-cytb—tRNA^Thr两段基因序列片段。基因定位和序列分析发现,太湖新银鱼线粒体COⅡ基因全序列长度为691bp。序列AT含量为52．80％,编码230个氨基酸;线粒体Cytb基因序列全长为1141bp,AT含量为48．90％,它编码380个氨基酸。分别位于线粒体COⅡ和Cytb基因两翼的4个tRNA基因（tRNA^Asp、tRNA^Lys、tRNA^Gls和tRNA^Thr）同时被测定出来。将太湖新银鱼与有明银鱼、小齿日本银鱼的同源序列进行比对分析,并基于线粒体COⅡ＋Cytb基因合并数据的核苷酸和氨基酸两种序列形式,以黑斑蛙为外群,对10种鱼类进行分子系统树的构建,结果一致表明：小齿日本银鱼与有明银鱼的亲缘关系近于太湖新银鱼;鲱科与鲑科的亲缘关系近于银鱼科鱼类;此外在本研究硬骨鱼类的4个科中,自鲟科作为原始而古老的类群,是在系统进化的过程中首先分化出来的一支。     

中国狼不同地理种群遗传多样性及系统进化分析

为了解中国狼不同地理种群遗传多样性及系统发育情况,从中国境内狼的主要分布区青海、新疆、内蒙古和吉林4个地区采集样品,用分子生物学技术手段成功地获得44个个体线粒体DNA控制区第一高变区(HVRⅠ)序列和40个线粒体Cyt b部分序列。线粒体控制区HVRⅠ共检测到51个变异位点,位点变异率为8.76%;线粒体Cyt b部分序列发现31个变异位点,位点变异率为5.33%,未见插入及缺失现象,变异类型全部为碱基置换。共定义了16个线粒体HVRⅠ单倍型,其中吉林与内蒙种群存在共享单倍型,估计这两地间种群亲缘关系较近。4个地理种群中新疆种群拥有较高的遗传多样性(0.94)。中国狼种群总体平均核苷酸多态性为2.27%,与世界其他国家地区相比,中国狼种群拥有相对较高的遗传多样性。通过线粒体HVRⅠ单倍型构建的系统进化树可以看出,中国狼在进化上分为2大支,其中位于青藏高原的青海种群独立为一支,推测其可能长期作为独立种群进化。基于青海种群与新疆,内蒙种群的线粒体Cyt b遗传距离,推测中国狼2个世系可能在更新世冰川时期青藏高原受地质作用急速隆起后出现分歧,分歧时间大约在1.1 MY前。     

云南中缅树鼩线粒体细胞色素b和D-loop区遗传多样性研究

对3个地方种群的49只样本的线粒体Cyt b基因全序列（1140 bp）及33只样本的控制区D-loop基因区段（745 bp）进行了序列测定。结果表明：Cyt b基因多态性位点有47个,其中单变异位点位点23个,简约信息位点24个。共定义了24个单倍型,其中种群间的共享单倍型有2个（8.33%）,其余均为某个种群所特有,单倍型多样度范围为0.80952（剑川种群）~0.91532（禄劝种群）,核苷酸多样度指数介于0.00326（禄劝种群）~0.00635（剑川种群）之间;D-loop基因多态性位点有18个,其中单变异位点8个,简约信息位点10个。共定义了16个单倍型,无种群间的共享单倍型,单倍型多样度范围为0.76615（禄劝种群）~0.93333（丽江种群）,核苷酸多样度指数介于0.00269（禄劝种群）~0.00583（丽江种群）之间。从各单倍型的TCS网络进化图显示横断山种群位于分支的末端,表现出中缅树鼩由南向北的扩散模式,支持＂岛屿起源＂假说。     

西藏小型猪线粒体D-loop区及微卫星多态性的遗传学分析

目的通过分析西藏小型猪线粒体控制区(D-loop区)及微卫星位点的遗传多态性,检测西藏小型猪的遗传背景,从而为其作为实验动物提供分子生物学方面的可靠依据。方法利用特异性引物对西藏小型猪的线粒体D-loop区及10个具有多态性的微卫星位点进行扩增,割胶纯化并对线粒体D-loop区进行测序,另外采用聚丙烯酰胺凝胶电泳的方法分离微卫星位点的等位基因。结果西藏小型猪线粒体D-loop区全序列没有多态性,微卫星位点则具有高度的遗传多态性和杂合度,分别为0.584和0.573。结论西藏小型猪线粒体基因组无多态性,证明其在母系进化和遗传上与其他猪种较为一致,本实验所用的西藏小型猪生长于一个封闭的环境,导致其微卫星位点遗传多态性的中低度水平。     

2种珍稀裂腹鱼类线粒体DNA部分序列片段的比较分析

对扁吻鱼(Aspiorhynchus laticeps)及塔里木裂腹鱼(Schizothorax biddulphi)线粒体CO I(624 bp)、Cyt b(712 bp)和D-loop(457 bp)基因片段进行了PCR扩增和序列测定.通过分析比较发现,3个片段A+T含量与其他鱼类相比均较高,G含量偏低这一现象在...     

中国柽柳沙鼠线粒体DNA 的地理变异及其亚种分化

柽柳沙鼠广泛分布于中亚荒漠地区,在我国分布于蒙新干旱区西部。本研究采用线粒体Cyt b 基因和D-loop控制区两个片段共1 569 bp作为分子标记,对我国蒙新区西部45 个柽柳沙鼠的核苷酸多样性、单倍型多样性及系统发生进行分析,并探讨其亚种分化。45 个柽柳沙鼠线粒体DNA 共定义33 个单倍型,包含142 个核苷酸变异位点(占全序列的9.05% ),其中单态位点34 个,简约信息位点108 个,未发现碱基插入或缺失的现象。基于单倍型的系统发生树和网络关系图显示,柽柳沙鼠的谱系分为两大支:伊犁盆地的种群聚为独立的一支,准噶尔盆地和额济纳地区的种群聚为一支,两大支的分歧时间为0.24 Ma年前,大约在庐山冰期。通过Beast 模拟,柽柳沙鼠在近15 000年有一次快速的种群衰退,表明柽柳沙鼠种群受到了末次盛冰期的影响。基于Cyt b 基和D-loop 序列的证据,我们认为分布于新疆伊犁盆地的柽柳沙鼠为哈萨克亚种(M. t. jaxartensis),分布于我国新疆准噶尔盆地以及甘肃、内蒙地区的为敦煌亚种(M. t. satchouensis)。     

鲤鱼野生群体线粒体部分基因片段序列比较

通过对线粒体16S rRNA基因、D-loop区和Cyt b基因部分片段测定,探讨我国鲤鱼C.carpio野生群体和云南大头鲤C.pellegrini的遗传变异和亲缘关系.数据和并后用于分析的序列共1 492 bp,变异位点221个,含简约信息位点217个,其中新疆群体用于分析的序列长度为1 478 bp.以云南大头鲤为外群,推测鲤鱼群体问的系统发育关系和分化时间,MP法和NJ法得到相似的系统树,新疆群体与其他群体的差异较大,遗传距离较远,单独聚为一支,其他群体间相似性较高聚在一起,新疆群体与其他群体间的分化时间约为2.42×106～2.45×106年前.     

Evolution of the cetacean mitochondrial D-loop region.

We sequenced the mitochondrial DNA D-loop regions from two cetacean species and compared these with the published D-loop sequences of several other mammalian species, including one other cetacean. Nucleotide substitution rates, DNA sequence simplicity, possible open reading frames (ORFs), and potential RNA secondary structure were investigated. The substitution rate is an order of magnitude lower than would be expected on the basis of reports on human sequence variation in this region but are consistent with interspecific primate and rodent D-loop sequence variation and with estimates of substitution rates from whole mitochondrial genomes. Deletions/insertions are less common in the cetacean D-loop than in other vertebrate species. Areas of high sequence simplicity (clusters of short repetitive motifs) across the region correspond to areas of high sequence divergence. Three regions predicted to form secondary structures are homologous to such putative structures in other species; however, the presumptive structures most conserved in cetaceans are different from those reported for other taxa. While all three species have possible long ORFs, only a short sequence of seven amino acids is shared with other mammalian species, and those changes that had occurred within it are all nonsynonymous. We conclude that DNA slippage, in addition to point mutation, contributes to the evolution of the D-loop and that regions of conserved secondary structure in cetaceans and an ORF are unlikely to contribute significantly to the conservation of the central region.     

The main regulatory region of mammalian mitochondrial DNA: Structure-function model and evolutionary pattern

Summary The evolution of the main regulatory region (D-loop) of the mammalian mitochondrial genome was analyzed by comparing the sequences of eight mammalian species: human, common chimpanzee, pygmy chimpanzee, dolphin, cow, rat, mouse, and rabbit. The best alignment of the sequences was obtained by optimization of the sequence similarities common to all these species.The two peripheral left and right D-loop domains, which contain the main regulatory elements so far discovered, evolved rapidly in a species-specific manner generating heterogeneity in both length and base composition. They are prone to the insertion and deletion of elements and to the generation of short repeats by replication slippage. However, the preservation of some sequence blocks and similar cloverleaf-like structures in these regions, indicates a basic similarity in the regulatory mechanisms of the mitochondrial genome in all mammalian species.We found, particularly in the right domain, significant similarities to the telomeric sequences of the mitochondrial (mt) and nuclear DNA ofTetrahymena thermophila. These sequences may be interpreted as relics of telomeres present in ancestral linear forms of mtDNA or may simply represent efficient templates of RNA primase-like enzymes.Due to their peculiar evolution, the two peripheral domains cannot be used to estimate in a quantitative way the genetic distances between mammalian species. On the other hand the central domain, highly conserved during evolution, behaves as a good molecular clock.Reliable estimates of the times of divergence between closely and distantly related species were obtained from the central domain using a Markov model and assuming nonhomogeneous evolution of nucleotide sites.     

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.     

Sequence variations of mitochondrial DNA D-loop region are highly frequent events in familial breast cancer

Mitochondrial DNA (mtDNA) is known for its high frequencies of polymorphisms and mutations. The non-coding displacement (D)-loop, especially a mononucleotide repeat (poly-C) between 303 and 315 nucleotides (D310), has been recently identified as a frequent hotspot of mutations in human neoplasia, including breast cancer. To further explore the sequence variations of mitochondrial D-loop region in familial breast cancer and their possible associations with breast cancer risk, PCR-SSCP and direct DNA sequencing methods were used to detect the variants of the mtDNA D-Loop in 23 familial breast cancer patients as well as three high-risk cancer families. Compared to that in sporadic breast tumors (53.3%, 16/30) and healthy blood donors (6.7%, 2/30), we identified a total of 126 sequence alterations in 23/23 (100%) of familial breast cancer patients, including eight novel nucleotide variants. Among these changes, A to G at nt.263, T to C at nt.489, T to C at nt.310, TC insertion at nt.311, CA deletion at nt.522, and C to G at nt.527 were highly frequent ones. In addition, among three high-risk cancer families, we found that individuals affected with breast cancer harbored more mtDNA sequence variants in mtDNA D310 area than other affected family members. Together, our data indicate that sequence variants within the mtDNA D-Loop region are frequent events in Chinese familial breast cancer patients. Some of these nucleotide abnormalities, particularly those in D310 segment, might be involved in the breast carcinogenesis and could be included in a panel of molecular biomarkers for cancer susceptibility early-detection strategy.     

动物mtDNA控制区及保守与异质

本文通过文献综述,对动物线粒体DNA控制区进行了阐述.从线粒体控制区（control region）基因组的研究出发,重点介绍了动物线粒体控制区基因组结构特点.主要结论：由于碱基替换、插入和缺失以及重复序列数目的变异致使D-loop成为mtDNA中变异最多的区域,但突变和结构重排并不是发生在整个D-loop区域,而是在高变区;大多研究集中在mtDNA D-loop保守区和异质方面：对D-loop序列分析,能较好地阐明动物的起源,在动物亲缘关系鉴定、系统进化和物种形成方式的研究等领域具有广阔的研究和应用前景.     

贵州黄牛mtDNA D-loop 遗传多样性研究

对贵州4个地方黄牛品种共计82个个体的线粒体DNA D-loop区全序列910 bp进行分析,检测到31种单倍型,其核苷酸多态位点65个,约占所测核苷酸总长的7.14%,其中有62个转换,2个颠换,1个转换/颠换共存。贵州4个黄牛品种mtDNA D-loop区核苷酸多样度（π值）为2.16%～2.61%,单倍型多样度（H）为0.695～0.909,表明贵州黄牛mtDNA遗传多样性比较丰富。根据单倍型构建了贵州4个黄牛品种的NJ分子系统树。聚类表明,贵州黄牛有普通牛和瘤牛2大母系起源,其影响较为均一。并探讨了用核苷酸多样度π值的大小来衡量黄牛群体遗传分化程度的可行性。