安徽麝线粒体DNA细胞色素b基因全长序列分析

自80年代安徽麝[Moschus (moschiferus/berezovskii)anhuiensis]被发现以来,其分类地位一直众说纷纭。在本研究中,我们对安徽麝模式皮张标本进行了线粒体DNA细胞色素b基因全长序列分析。研究结果表明,安徽麝同麝属中其他种的遗传分化已经相当明显.分子系统学的分析表明,安徽麝是一个单系群,它同麝属其他种的DNA序列差异已达到种间分化的程度。因此,线粒体DNA序列的证据支持将安徽麝列为麝属中一有效种（Moschus anhuiensis),而不是前人认为的原麝或林麝的亚种。     

基于线粒体DNA细胞色素b基因和控制区序列分析西藏雅鲁藏布江黄斑褶鮡种群遗传多样性

采用线粒体DNA（mtDNA）Cyt b基因和D-loop控制区为分子标记,对分布于西藏雅鲁藏布江大峡谷以上里龙段和以下墨脱段2个群体的黄斑褶 （Pseudecheneis sulcata）共60个样本进行遗传多样性研究。获得联合基因有效序列长度为1 893 bp,包括Cyt b基因1 060 bp和D-loop控制区833 bp。结果显示,里龙和墨脱2个群体的单倍型多样性值（Hd）均较高（0.701和0.761）,核苷酸多样性值（π）均较低（0.001 00和0.001 09）;高频率的单倍型Hap1和Hap2为2个群体所共享,推测为祖先单倍型;同时,里龙和墨脱群体分别存在5个和6个特有单倍型,且在2个群体中不共享;分子方差分析（AMOVA）显示遗传变异主要来源于种群内部,群体间呈中度遗传分化水平（Fst = 0.090 44,P < 0.05）;中性检验（Tajima''s D、Fu''s Fs）和核苷酸不配对（SSD、Hir）分析结果揭示,黄斑褶 种群曾经历过种群扩张现象。本研究推测,黄斑褶 2个群体间的基因流动存在障碍,雅鲁藏布大峡谷的海拔落差及水文情势等生态屏障可能是阻碍黄斑褶 迁徙和交流的主要原因。     

犬科的线粒体细胞色素b DNA序列及其分子系统学研究

通过对犬科的赤狐、蓝狐、貉和狼４种的线粒体细胞色素ｂ约３７２ｂｐＤＮＡ片段序列分析,结合ＧｅｎＢａｎｋ中狗、西门豺和非洲野犬３种的该区段ＤＮＡ序列的比较,共发现１１３个核苷酸位点存在变异（约３０％）。ＮＪ法构建的分子系统树显示,非洲野犬最先从犬科动物中分化出来;犬属的我狼、狗和西门豺等３种为系统树上独立的一支,且其分歧的时间较赤狐、蓝狐和貉早;赤狐和蓝狐具有较近的亲缘关系。上述结果与形态的观点基本     

黑线姬鼠两亚种(中国东北地区及俄罗斯远东地区的东北亚种和朝鲜半岛的朝鲜亚种) 的线粒体DNA 序列缺少趋异性

为了检测黑线姬鼠两亚种(来自中国东北地区、俄罗斯远东地区的东北亚种和朝鲜半岛的朝鲜亚种)线
粒体DNA 的变异水平并确定朝鲜亚种的分类地位,我们测序分析了两亚种的线粒体DNA 细胞色素b 的部分序列
(1 054 bp)和控制区的部分序列(860 bp),并与基因库中黑线姬鼠相应的单倍型序列进行了比较。可以看出东
北亚种的序列显示出某些分异,可以被分为2 或3 个亚群,所以我们提出需要更多标本的DNA 分析来确定东北
亚种的分类地位。另外,来自韩国的朝鲜亚种的序列,与来自中国东北地区龙江和哈尔滨的东北亚种的两个亚
群相似(1 个亚群是细胞色素b 的两个单倍型,另1 个是控制区的两个单倍型),表明基于线粒体DNA 序列的遗
传多样性与现今基于形态特征对这些姬鼠的分类所得结果是不一致的。因此我们认为来自韩国的朝鲜亚种是一
个只在形态特异上不同于东北亚种的地方亚种,我们建议通过其他DNA 标记来进一步验证其亚种地位。我们还
认为朝鲜半岛不是最近的冰川期黑线姬鼠残遗种的保护区。     

基于线粒体细胞色素b基因对大耳姬鼠和龙姬鼠分类关系的探讨

大耳姬鼠Apodemus latronum的分类地位,尤其它和龙姬鼠A.draco的关系,还存在着争议.用PCR扩增了采集自5个不同地点的大耳姬鼠的线粒体细胞色素b(cyt b)基因,并和GenBank已有的3条大耳姬鼠cyt b序列一起分析其碱基组成和变异情况.采用邻接法(Neighbor-joining,NJ)、最大简约法(Maximum parsimony,MP)、最大似然法(Maximum likelihood,ML)和贝叶斯法(Bayesian inference,BI)构建了大耳姬鼠和龙姬鼠的系统发育树.4种方法构建的系统发育树拓扑结构一致,大耳姬鼠和龙姬鼠均各自形成单系,龙姬鼠先与台湾森鼠A.semotus聚在一起,再与大耳姬鼠形成姐妹群.此外,大耳姬鼠和龙姬鼠两者间的K2P平均遗传距离达到0.14.因此,认为大耳姬鼠是一个独立的种,而不是龙姬鼠的一个亚种.     

云南4个地区高山姬鼠线粒体细胞色素b遗传分化的研究

基于云南昆明、中甸、丽江和剑川4个种群(n=43)的线粒体细胞色素b(Cyt b)基因全序列的遗传变异分析,探讨了该地区高山姬鼠种群的遗传分化。在1 140 bp Cyt b基因序列中,有50个变异位点(占全变异的4.38%),定义了22个单倍型。在4个种群中,昆明种群单倍型多样性和核苷酸多样性最高。分子变异分析表明,种群间的遗传变异占30.2%,种群内的遗传变异占69.8%。FST分析表明,除中甸种群和丽江种群之间差异不显著(P>0.05),其它种群间的差异均极显著(P<0.01)。22个单倍型在系统发生树中明显聚为两支(A和B),进化网络关系显示昆明种群处于进化分支最末端,推测种群进化方向可能从横断山地区到昆明地区,支持了姬鼠属从北向南扩散的理论。     

剑尾鱼线粒体细胞色素b基因的序列分析

目的　克隆和测定剑尾鱼 (Xiphophorushelleri)线粒体细胞色素b基因 (cytb)的全序列。方法　提取剑尾鱼肝脏的总DNA。设计合成特异引物进行PCR扩增。扩增产物经琼脂糖电泳检测、纯化后克隆到pGEM Teasyvectorsystem中的T载体上 ,筛选转化子 ,提取质粒 ,酶切鉴定。挑取重组质粒pGEM T xhcytb 11进行序列测定。结果　获得了剑尾鱼线粒体cytb基因的全序列 ,共 114 0bp。结论　用BLAST与GenBank中的线粒体DNA序列进行比较 ,显示剑尾鱼与其他鱼类的cytb基因具有较高的同源性 ;根据剑尾鱼与其他 13种鱼的cytb基因序列同源性所建立的进化树 ,与传统的分类地位基本吻合     

翘嘴鳜线粒体DNA细胞色素b基因序列分析

测定了翘嘴鳜（Siniperca chuatsi）的线粒体细胞色素b基因编码区全序列1140个核苷酸序列,并且由此推导出对应的氨基酸序列,A/T所占比例为53.4％,G C约占46.6％。该基因中密码子第1位核苷酸中4种碱基组成较为均衡,第2位核苷酸中T的使用率较高,G的使用率较低;而密码子第3位C/A的使用率高,而G的使用率仅为3.7％;在氨基酸序列中Leu所占比例16.36％,远高于其它氨基酸;而Cys使用比例仅为0.79％。本研究为鳜类的系统发育,资源保护和利用提供了核苷酸序列方面的资料,至于翘嘴鳜线粒体细胞色素b基本序列中密码子不同位置碱基使用比率以及氨基酸组成是翘嘴鳜特有还是鳜类共有特征,尚有待进一步研究。     

基于线粒体细胞色素b基因分析海南岛褐家鼠种群遗传多样性

褐家鼠(Rattus norvegicus)是海南岛的主要害鼠之一,海南岛是我国南方海上的重要交通口岸,但关于海南岛褐家鼠的种群遗传多样性以及和邻近地区褐家鼠种群间的基因交流情况还缺乏了解。本研究测序分析了来自海南岛、广东、越南等地91只褐家鼠的细胞色素b基因,分析了不同种群中的Cyt b单倍型,种群间的遗传分化程度(F_(st)),构建了全世界60个褐家鼠的Cyt b单倍型之间的系统进化关系。结果发现,海南岛琼中/澄迈和崖城的褐家鼠种群没有共享的Cyt b单倍型,种群间出现了明显的遗传分化(F_(st)=0.453),但这两个群体分别与广东和菲律宾/越南的褐家鼠分享共同的单倍型,表明海南岛褐家鼠与广东和菲律宾/越南褐家鼠近代存在着基因交流。系统进化分析结果表明,多数海南岛和广东褐家鼠的Cyt b单倍型来自共同的单倍型组CⅢ和CⅦ,说明海南岛和广东省的褐家鼠可能由一个或多个共同的祖先种群扩散而来。由于褐家鼠喜欢与人伴生,褐家鼠很可能随着黎族人在新石器时代中期(大约3 000年前)或更早以前,从广西、广东沿海地区迁移至海南。     

基于线粒体细胞色素b基因序列探讨红喉姬鹟两亚种的分类地位

以线粒体DNA细胞色素b基因的全序列作为遗传标记 ,探讨红喉姬普通亚种 (Ficedulaparvaal bicilla)和指名亚种 (F .p .parva)的分类地位。应用Kimura 2 parameter法计算出红喉姬普通亚种个体间的遗传距离为 0 1%～ 0 2 % ,而与指名亚种之间的遗传距离为 6 4 % ,两亚种之间的遗传距离远远大于种间的遗传距离。结合形态学的特征我们认为 :红喉姬指名亚种和普通亚种应为两个独立种 ,分别为红喉姬 (F .albicilla)和红胸姬 (F .parva) ,两者的分化时间为 3 15～ 3 2 5百万年     

The complete mitochondrial genome of the Korean field mouse Apodemus peninsulae (Rodentia, Murinae) from Korea

We have determined the complete mitochondrial genome of a subspecies of the Korean field mouse, Apodemus peninsulae peninsulae, from South Korea. The total length of the A. p. peninsulae genome is 16,268 bp with a base composition of 34.5% A, 30.7% T, 22.6% C, and 12.2% G.     

Sequence evolution in and around the mitochondrial control region in birds

By cloning and sequencing 3.4 kilobases of snow goose mtDNA we found that the ND5 gene is followed by the genes for cytochrome b, tRNA^Thr, tRNA^Pro, ND6, tRNA^Glu, the control region, tRNA^Phe, and srRNA. This order is identical to that of chicken, quail, and duck mtDNA but differs from that of mammals and a frog (Xenopus). The mean extent of difference due to base substitution between goose and chicken is generally closer to the same comparison between rat and mouse but less than that between human and cow. For one of the nine regions compared (tRNA^Glu), the bird differences appear to be anomalous, possibly implicating altered functional constraints. Within the control region, several short sequences common to mammals are also conserved in the birds. Comparison of the goose control region with that of quail and chicken suggests that a sequence element with similarity to CSB-1 duplicated once prior to the divergence of goose and chicken and again on the lineage leading to chicken. Between goose (or duck) and chicken there are four times more transversions at the third positions of fourfold-degenerate codons in mitochondrial than in nuclear genes.Abbreviations CSB conserved sequence block - cytb cytochrome b - ND NADH dehydrogenase - srRNA small-subunit ribosomal RNA Deceased July 21, 1991 Correspondence to: T.W. Quinn at the University of Denver     

从细胞色素b基因序列探讨笛鲷属的分子系统发生关系

测定了9种中国南海的笛鲷属鱼类的细胞色素b基因的部分序列,结合来自GenBank中1种分布于菲律宾和9种分布于美国大西洋的笛鲷属鱼类的相应同源序列,用邻接法和最大简约法构建分子系统树。结果显示:红鳍笛鲷(Lutjanuserythropterus)与红笛鲷(L.sanguineus)之间的同源序列碱基差异百分率只有0.32%,支持二者是同种异名的观点;中国南海的笛鲷属鱼类间的平均碱基差异要高于美国大西洋笛鲷属鱼类。在MP和NJ树中,美国大西洋笛鲷表现为亲缘关系较近,来源于中国南海的笛鲷鱼类相对集中在树的基部,分歧较大。这与所研究的笛鲷地理分布和地理隔离基本相一致,同时也说明中国南海笛鲷分化较早并且分歧较大。     

Population diversity of Cistopus indicus inferred from mitochondrial DNA (Cytochrome b) variation from China and Vietnam

ABSTRACT

The octopus Cistopus indicus is an important target of cephalopod fisheries in China. It is widely distributed in the South Pacific and tropical Indian Ocean, from the South China Sea, the Philippines, Malaysia, to Indian and Pakistan seas. We collected specimens from five sites in China and Vietnam (Zhoushan, Wenzhou, Shacheng, Zhanjiang and Mangjie). A fragment of 675bp of cytochrome b (Cytb) was amplified from 95 individuals. A total of 27 haplotypes and 78 variable nucleotide sites was observed. High haplotype diversity and low nucleotide diversity were observed in all populations. The phylogenetic analysis separated these populations into two clades; one was composed of three populations (Zhoushan, Wenzhou and Shacheng), the other of two (Zhanjiang, Mangjie). AMOVA analysis detected that 4.67% of the genetic variation occurred within populations and 95.33% occurred among populations. FST values ranged from 0.014 to 0.993, highlighting the high genetic variation among the populations. Assuming a molecular clock with a rate of 2.15–2.6%/Ma for the Cytb gene, the two clades may have diverged 2.88–3.49 million years ago (Pliocene). Neutral evolution tests and mismatch distribution analysis suggested recent population expansion. The present results revealed valuable information for genetic assessment, management and conservation of this species.     

PCR-RFLP analysis of the cytochrome b gene in horse mitochondrial DNA

The mitochondrial DNA sequence of cytochrome b gene in a Thoroughbred horse was determined. By comparing DNA sequences between the Thoroughbred and published sequence data (two horses and one Grevyi zebra), polymerase chain reaction (PCR) primers were designed for amplification of a 590 bp DNA fragment in the cytochrome b gene, and PCR-restriction fragment length polymorphism (RFLP) analysis was studied in 140 horses of six breeds using three restriction enzymes ( AciI, BamHI, RsaI ). Two morphs were found using each of the three enzymes. By combining three enzymes morphs, the 140 horses examined were classified into four types. Type 2 was most frequent in all breeds.     

Genetic diversity of Asian water buffalo (Bubalus bubalis): mitochondrial DNA D-loop and cytochrome b sequence variation

Swamp and river buffalo mitochondrial DNA (mtDNA) was sequenced for 303 bp of the cytochrome b gene for 54 animals from 14 populations, and for 158 bp of the D-loop region for 80 animals from 11 populations. Only one cytochrome b haplotype was found in river buffalo. Of the four haplotypes identified in swamp buffalo, one found in all populations is apparently ancestral both to the other swamp haplotypes and to the river haplotype. The phylogenetic relationships among the 33 D-loop haplotypes, with a cluster of 11 found in swamp buffalo only, also support the evolution of domesticated swamp and river buffalo from an ancestral swamp-like animal, most likely represented today by the wild Asian buffalo ( Bubalus arnee ). The time of divergence of the swamp and river types, estimated from the D-loop data, is 28 000 to 87 000 years ago. We hypothesise that the species originated in mainland south-east Asia, and that it spread north to China and west to the Indian subcontinent, where the rive type evolved and was domesticated. Following domestication in China, the domesticated swamp buffalo spread through two separate routes, through Taiwan and the Philippines to the eastern islands of Borneo and Sulawesi, and south through mainland southeast Asia and then to the western islands of Indonesia.     

Genetic diversity of mitochondrial cytochrome b gene in Chinese native buffalo

The origins of the domestic water buffalo remain contentious. To better understand the origins of Chinese water buffalo, we sequenced the complete mitochondrial cytochrome b (MT-CYB) gene from 270 individuals representing 13 Chinese domestic swamp buffalo populations. We found genetic evidence of introgression of river buffalo into Chinese swamp buffalo herds. Swamp buffalo haplotypes can be divided into two highly divergent lineages (A and B), suggesting that Chinese native swamp buffalo have two maternal origins. We found that the A→G transition in the buffalo MT-CYB gene stop codon resulted in buffalo haplotypes being terminated by one of two stop codons: AGA or AGG. AGA is common to river buffalo and lineage A of swamp buffalo, while AGG is specific to lineage B of swamp buffalo. Lineage A appears to have been domesticated in China. Further genetic evidence is required to clarify the origins of lineage B.     

A phylogenetic study of the genus Apodemus by sequencing the mitochondrial DNA control region

The sequences of the mitochondrial DNA control region (D-loop) and flanking tRNA genes (about 1000 bp) of 20 samples of wood mice (genus Apodemus ) were analyzed in order to clarify the relationships between different species belonging to the genus. The phylogenetic trees obtained using different methods showed similar topologies with distinct Karstomys ( Apodemus epimelas and Apodemus mystacinus ) and Sylvaemus ( Apodemus alpicola , Apodemus flavicollis , Apodemus hermonensis , Apodemus sylvaticus and Apodemus uralensis ) subtrees. Within Sylvaemus all species appeared to be closely related to each other, probably as result of a bush-like radiation event. Nevertheless, A. hermonensis seemed to be the first diverging branch followed by A. sylvaticus ; A. alpicola and A. flavicollis appeared to be very closely related. Three individuals of uncertain taxonomical status were included in the analysis: hypotheses as to their status are discussed. Further phylogenetic analysis was carried out combining the D-loop sequences of part of the samples of certain taxonomical status with 12S rRNA and cytochrome b sequences obtained by other researchers. Furthermore, I present a structure analysis of the D-loop in Apodemus as compared other rodent species.     

Characterization of cytochrome b diversity in Chinese domestic horses

Previous mitochondrial DNA (mtDNA) D‐loop and microsatellite studies have shown that Chinese horses have multiple maternal origins and high genetic diversity. To better characterize maternal genetic origins and diversity of Chinese domestic horses, we conducted a comprehensive analysis of 407 complete 1140 bp sequences of the horse mitochondrially encoded cytochrome b (CYTB) gene, including 323 horses from 13 Chinese indigenous breeds and 84 reference sequences from GenBank. A total of 114 haplotypes were identified, of which 73 appeared among the 13 Chinese horse breeds. The high mitochondrially encoded cytochrome b haplotypic diversity suggests multiple maternal origins in Chinese horses.