231 resultados para MtDNA
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摘要 II 5. 在不同注量离子束辐照后筛选出来的呼吸缺陷型酵母菌株中扩增获得位 于第 12 染色体上的 SOF1 基因,而在同样的扩增体系中没有得到野生型 菌株的该基因。 6. 选取离子束辐照后筛选出来的呼吸缺陷型酵母菌株再次进行辐照,发现 其在低剂量范围(<0.93Gy)辐照下非常敏感,而在高剂量范围(> 0.93Gy)又表现出一定程度的辐射抗性。 结论: 1. 离子束辐照酵母细胞,直接或间接作用于酵母线粒体DNA,导致线粒体 DNA损伤,形成呼吸缺陷的酵母菌株。 2. I 类内含子和 II 类内含子对于离子束辐照的敏感性不同: II 类内含子比较 稳定,II 类内含子可能利用自身编码的反转录酶通过目的DNA引导的反 转录机制对受到辐照损伤的II 类内含子进行修复。 3. 离子束辐照后 SOF1 基因可能发生了突变,影响酵母细胞的生长。 4. 呼吸缺陷型酵母菌株因其线粒体 DNA发生变化及线粒体功能的改变, 使 呼吸缺陷型酵母菌株在不同剂量区的离子束辐照下表现不同辐射敏感 性。目的: 研究啤酒酵母的线粒体 DNA 在重离子辐照作用下的突变效应及其突变机 理。 材料与方法: 利用兰州重离子研究装置(HIRFL)加速的氖、碳离子辐照酵母细胞,用 TTC 显色培养基筛选呼吸缺陷型酵母菌株,并用 mtDNA 限制性酶切手段分析其突变 规律。采用 PCR扩增并对目的产物测序的方法对辐照后线粒体DNA上的 I 类内 含子和 II类内含子进行研究。 结果: 1. TTC 显色实验表明:离子束辐照导致酵母线粒体上的电子传递链发生改 变,产生的还原氢减少,造成呼吸缺陷。 2. 利用限制性酶切实验对线粒体 DNA进行研究,结果表明:离子束辐照诱 变筛选出来的呼吸缺陷型酵母菌株其线粒体DNA变化明显: 主要表现为 酶切条带缺失严重。即使在同一注量下筛选出来的呼吸缺陷型酵母菌株, 其酶切图谱也不相同。 3. 通过 PCR 手段对辐照后酵母线粒体 DNA 碱基序列进一步进行分析,发 现经不同注量离子束辐照后筛选出来的呼吸缺陷型酵母菌株,其I 类内含 子(ai4 and ai5)经设计不同引物进行扩增,没有获得目的条带,说明此 序列发生了突变,可能对离子束辐照比较敏感。 4. 经不同注量离子束辐照后筛选出来的呼吸缺陷型酵母菌株,其 II 类内含 子(ai2)的碱基序列与野生型相比没有变化,表现出在离子束辐照作用 下比较稳定的特性。
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根据ISO11268-1:1993方法,完成了土壤中苯并[a]芘对赤子爱胜蚓(Eisenia fetida)的人工污染模拟实验.并采用Clontech PCR-SelectTMcDNASubtration Kit构建了污染组和对照组蚯蚓之间的抑制消减文库.经测序和比对分析,在苯并[a]芘诱导上调文库中发现5个线粒体DNA(mtDNA)编码的基因,且在上调文库中具有较高的频率.它们分别为:细胞色素c氧化酶亚基Ⅰ、Ⅱ、Ⅲ,NADH氢脱氢酶亚基1,ATP合成酶亚基.研究表明,土壤中苯并[a]芘污染改变了蚯蚓线粒体基因组的表达水平,线粒体基因组表达异常是多环芳烃污染胁迫的重要分子生物标记物.
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Inferring how the Pleistocene climate oscillations have repopulated the extant population structure of Chondrus crispus Stackh. in the North Atlantic Ocean is important both for our understanding of the glacial episode promoting diversification and for the conservation and development of marine organisms. C. crispus is an ecologically and commercially important red seaweed with broad distributions in the North Atlantic. Here, we employed both partial mtDNA Cox1 and nrDNA internal transcribed spacer region 2 (ITS2) sequences to explore the genetic structure of 17 C. crispus populations from this area. Twenty-eight and 30 haplotypes were inferred from these two markers, respectively. Analysis of molecular variance (AMOVA) and of the population statistic Theta(ST) not only revealed significant genetic structure within C. crispus populations but also detected significant levels of genetic subdivision among and within populations in the North Atlantic. On the basis of high haplotype diversity and the presence of endemic haplotypes, we postulate that C. crispus had survived in Pleistocene glacial refugia in the northeast Atlantic, such as the English Channel and the northwestern Iberian Peninsula. We also hypothesize that C. crispus from the English Channel refugium repopulated most of northeastern Europe and recolonized northeastern North America in the Late Pleistocene. The observed phylogeographic pattern of C. crispus populations is in agreement with a scenario in which severe Quaternary glaciations influenced the genetic structure of North Atlantic marine organisms with contiguous population expansion and locally restricted gene flow coupled with a transatlantic dispersal in the Late Pleistocene.
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The population genetic structure of the crimson snapper Lutjanus erythropterus in East Asia was examined with a 427-bp hypervariable portion of the mtDNA control region. A total of 262 samples were collected and 75 haplotypes were obtained. Neutrality tests (Tajima's and Fu's) suggested that Lutjanus erythropterus in East Asia had experienced a bottleneck followed by population expansion since the late Pleistocene. Despite the low phylogeographic structures in mtDNA haplotypes, a hierarchical examination of populations in 11 localities from four geographical regions using analysis of molecular variance (AMOVA) indicated significant genetic differentiation among regions (Phi(CT) = 0.08564, p < 0.01). Limited gene flow between the eastern region (including a locality in the western Pacific Ocean and two localities in the East Sea) and three geographic regions of the South China Sea largely contributed to the genetic subdivision. However, comparisons among three geographic regions of the South China Sea showed little to no genetic difference. Populations of Lutjanus erythropterus in East Asia are inferred to be divided into two major groups: an eastern group, including populations of the western Pacific Ocean and the East Sea, and a South China Sea group, consisting of populations from northern Malaysia to South China. The results suggest that fishery management should reflect the genetic differentiation and diversity in East Asia. (c) 2006 International Council for the Exploration of the Sea. Published by Elsevier Ltd. All rights reserved.
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To understand the systematic status of Larimichthys crocea in the Percoidei, we determined the complete mitochondrial (mt) genome sequence using 454 sequencing-by-synthesis technology. The complete mt genome is 16,466 bp in length including the typical structure of 22 tRNAs, 2 rRNAs, 13 protein-coding genes and the noncoding control region (CR). Further sequencing for the complete CR was performed using the primers Cyt b-F and 12S-R on six L crocea individuals and two L polyactis individuals. Interestingly, all seven CR sequences from L crocea were identical while the three sequences from L polyactis were distinct (including one from GenBank). Although the conserved blocks such as TAS and CSB-1, -2, and -3 are readily identifiable in the control regions of the two species, the typical central conserved blocks CSB-D, -E, and -F could not be detected, while they are found in Cynoscion acoupa of Sciaenidae and other Percoidei species. Phylogenetic analysis shows that L crocea is a relatively recently emerged species in Sciaenidae and this family is closely related to family Pomacanthidae within the Percoidei. L crocea, as the first species of Sciaenidae with complete mitochondrial genome available, will provide important information on the molecular evolution of the group. Moreover, the genus-specific pair of primers designed in this study for amplifying the complete mt control region will be very useful in studies on the population genetics and conservation biology of Larimichthys. (c) 2008 Elsevier B.V. All rights reserved.
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Barcodes based on mitochondrial cytochrome oxidase (mtDNA CO1) sequences are being used for broad taxonomic groups of animals with demonstrated success in species identification and cryptic species discovery, but it has become clear that complementation by a nuclear marker system is necessary, in particular for the barcoding of plants. Here, we propose the nuclear internal transcribed spacer (ITS) as a potentially usable and complementary marker for species identification of red macroalgae, as well as present a primary workflow for species barcoding. Data show that for most red macroalgal genera (except members of the family Delesseriaceae), the size of ITS region ranges from 600 to 1200 bp, and contains enough variation to generate unique identifiers at either the species or genus levels. Consistent with previous studies, we found that the ITS sequence can resolve closely related species with the same fidelity as mtDNA CO1. Significantly, we confirmed that length polymorphism in the ITS region (including 5.8S rRNA gene) can be utilized as a character to discriminate red macroalgal species. As a complementary marker, the verifiable nuclear ITS region can speed routine identification and the detection of species, advance ecological and taxonomic inquiry, and permit rapid and accurate analysis of red macroalgae.
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Perciformes, the largest order of vertebrates with 20 suborders, is the most diverse fish order that dominates vertebrate ocean life. The complete mitochondrial control region (CR) of Trichiurus japonicus (Trichiuridae, Scombroidei) and Pampus sp. (Stromateidae, Stromateoidei) were amplified and sequenced. Together with data from GenBank, the tandem repeats in the mitochondrial CR from 48 species, which covered nine suborders of Perciformes, are reported in this study. The tandem repeats tend to be long in the suborder Percoidei and Stromateoidei. The identical repeats in 21 species of Cichlidae suggest a common origin and have existed before species divergence. Larimichthys crocea shows tandem repeats instead of the typical structure of the central conserved sequence blocks, which was first reported in Perciformes and vertebrates. This might have resulted from interruption of the polymerase activity during the H-strand synthesis. The four broader patterns presented here for the tandem repeats, including those in both the 5' and 3' ends, only in the either 5' or 3' end, and in the central conserved domain of the control region, will be useful for understanding the evolution of species.
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本文以山东近海野生和养殖牙鲆Paralichthys olivaceus(T.& S.)为研究对象,采用同工酶电泳和随机扩增多态性DNA(RAPD)两种方法,进行了群体遗传学研究;另外,用PCR扩增了牙鲆、桂皮斑鲆Pseudorhombus cinnamomeus(T.& S.)、石鲽Kareius bicoloratus,Basilewsky和大菱鲆Psetta maxima 4种鲽形目鱼类mtDNA 16s rRNA基因区的部分片段,采用生物信息、学方法构建了鲽形目分子系统树。主要结果如下:1.首先建立了适于牙鲆同工酶分析的水平淀粉凝胶和垂直聚丙烯酰胺凝胶电泳系统;对获得的牙鲆15种同工酶基本酶谱进行了生化遗传分析,进而对自然和养殖群体的生化遗传结构进行了分析,共记录了29个基因座位,发现了9个多态座位。2.野生群体的生化遗传参数多态基因座位比例(31.O%)、等位基因平均数(1.38)和群体平均杂合度(0.0802)都明显高于养殖群体(24.1%,1.28,O.0788);在野生群体中有9个多态基因座位,而养殖群体仅7个多态基因座位;其中,除了Cat和Idhp-1(仅养殖群体)(P < 0.05)有显著差异、Ldh-C(P < O.01)完全偏离Hardy-Weinberg定律外,其余多态座位基因频率均符合Hardy-Weinberg遗传平衡定律。野生和养殖群体的遗传相似性系数(I)为0.9877,它们的遗传距离(D)是0.0124;两群体间的遗传分化系数G_(st)为0.0681,D_m为0.01,表明总变异中的6.8%的遗传变异产生于群体间的基因差异。3.采用11个随机引物对20个野生个体和24个养殖个体进行了RAPD群体遗传多样性分析,分别扩增出88条和86条DNA带,片段大小在200-2500bp之间,平均每个引物扩增的带数是7.8-8.0。两个群体的多态座位比例分别是43.2%和34.9%,平均杂合度是0.2739和0.2255,而Shannon遗传多样性指数表明两群体的遗传变异中有88.12%的遗传变异来自种群内,只有11.88%的变异来自群体间。遗传分化指数G_(st)的结果也验证了Shannon遗传多样性指数的结果:总群体的遗传变异中约有12%是由两群体间的基因差异产生的。4.本文对牙鲆两个群体的同一批样品分别采用经典的同工酶方法和RAPD方法进行了较系统的比较分析。发现,RAPD所显示的多态性要比同工酶的高得多,因为大部分RAPD的变异是源于非编码区和重复DNA,可以遍布整个基因组,而同工酶仅是功能基因的产物,只表现编码区的变异。因此,自然选择在同工酶编码区的作用要多于RAPD标记。在遗传相似性系数(I)和遗传距离(D)上,RAPD的分析结果与同工酶的分析结果也是有差异的,用同工酶分析两个群体遗传距离只有0.0124,而用RAPD研究可达0.0508。遗传分化指数的差异也很大,同工酶为0.0681,RAPD为0.1237。5.RAPD和同工酶的分析结果是类似的,即自然群体的多态座位比例和平均杂合度要比养殖群体高,降低幅度在同工酶中界于1.7~22.3%之间,在RAPD中则界于15.9~19.2%之间。这充分证明了养殖群体的遗传多样性水平已有明显的丧失,值得我们注意。6.构建了鲽形目鱼类mtDNA 16S rRNA基因的分子系统树。通过分子克隆法将牙鲆、桂皮斑鲆、大菱鲆和石鲽mtDNA 16S rRNA目的基因片段连接到质粒载体上,经MegaBACE测序仪测序,分别获得了590、595、582和590bp序列,通过生物信息学方法对其进行了序列分析和核酸变异比较,结合NCBI上6种鲽形目鱼类的同源序列探讨了这4种鱼类在鲽形目中的遗传分化和分子系统进化,构建了系统树,其中,桂皮斑鲆的16S rRNA基因在系统树中的位置与物种形态资料的系统演化不相符,而其它三种很好地呈现了它们在鲽形目中的系统位置。同时,可以看出mtDNA 16S rRNA基因片段可以构建一个相对准确的树,特别是NJ树和ML树比较接近,更为客观一些。由比对序列获得的物种之间的遗传距离也基本可以反映种、属、科间的不同变异水平。
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斑海豹,西北太平洋广泛分布的冷水性海洋哺乳动物,为我国的二类保护野生动物,属于濒危物种,也是唯一能在我国海域自然繁殖的鳍脚类动物。辽东湾结冰区是斑海豹在世界上8个繁殖区中最南端的一个。为了能够更好地保护斑海豹资源,对渤海海域斑海豹的栖息地、种群动态及分布时间、重金属体内积累、以及斑海豹的分子遗传特性进行了研究。结果如下: 斑海豹在渤海海域的栖息地有辽宁双台子河口水域、大连虎平岛和山东庙岛群岛海域三处,其中的上岸点分别为河口泥沙滩、海里的浅石滩和海岛周围的小岛礁三种类型。斑海豹出现在三个栖息地的时间为每年的3~5月,2002~2008年间各栖息地的斑海豹的数量变化不明显。 对斑海豹肌肉、肝和肾脏组织重金属元素含量的分析结果显示,汞(Hg)、镉(Cd)、铅(Pb)和砷(As)等有毒元素在斑海豹体内的积累远未达到致死浓度。 对斑海豹的部分mtDNA 序列分析发现,辽东湾斑海豹群体的遗传距离、控制区DNA的单元型多样度和核苷酸多样度均远小于日本群体,辽东湾群体的遗传多样性水平较低。 微卫星引物标记对辽东湾斑海豹群体的遗传多样性研究显示,平均有效等位基因数(2~4个)和期望杂合度(0.24~0.72)等指标均较低,表明辽东湾斑海豹群体遗传多样性水平下降,可能曾出现过一定程度的瓶颈效应。 对斑海豹的41个MHC-I基因的序列分析,得到40个等位基因。斑海豹MHC-I基因多态性水平高,说明辽东湾斑海豹种群MHC-I基因的丰富性。 以上研究结果对于我国辽东湾斑海豹种群的保护和管理具有一定意义。
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为了进一步研究青蟹属系统进化的科学问题,并揭示我国东南沿海青蟹群体遗传结构和群体进化细节信息,本论文主要开展了以下两个方面的研究:(1)基于线粒体12S rRNA、16S rRNA和COI三种基因序列探讨中国东南沿海青蟹的种类归属与青蟹属的系统进化;(2)利用线粒体COI基因标记分析中国东南沿海拟穴青蟹的群体遗传结构。序列特征、遗传距离和系统进化分析结果都表明本文研究的青蟹均为S. paramamosain。NJ、BAYES和ML系统进化树显示S. paramamosain与S. tranquebarica互为姐妹种,S. olivecea应该是4种青蟹中最早分化出来的种类。10个地理群体130只拟穴青蟹的线粒体DNA(mitochondrial DNA,mtDNA)细胞色素氧化酶亚基I(COI)基因序列Mantel检验结果显示群体间的遗传分化程度与地理距离没有显著的相关性。分子进化中性检验结果表明自然选择在分子进化过程中起了重要作用,并暗示该物种在最近经历了一个快速的群体爆发及扩张事件。
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概括了线粒体DNA(mtDNA)的特点与其作为遗传标记的优越性,着重回顾了该分子标记在分子生态学多个研究领域的应用,并阐述了其在青藏高原生物多样性、分子系地理学研究中的应用前景.
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受高原抬升所致的水系变迁及人类活动的影响,分布于南门峡河流的裂腹鱼亚科鱼类与黄河干支流种群间的基因交流受到长期限制.作为孤立小群体,探讨其分类学地位及其在小生境中的进化机制对了解青藏高原鱼类多样性和物种的形成、进化具有重要意义.本文采用聚合酶链式反应(PCR)和直接测序方法获得了南门峡裂腹鱼亚科鱼类(n=29)及其近缘种(n=19)共48个个体的线粒体DNA(mtDNA)细胞色素b(cyt b)基因的全序列(1 140 bp),并以厚唇裸重鱼和尖裸鲤为外群构建了MP和Bayesian系统进化树.南门峡裂腹鱼亚科鱼类29个个体的序列经排序后,发现有100个(8.77%)多态性位点,共定义了16个单倍型,在系统进化树上分布于截然不同的两个族群中.其中5个单倍型(NMX3、6、7、13、15)与其近缘种花斑裸鲤和青海湖裸鲤形成单系群(MP 99%,Bayesian 98%),而其余11个单倍型(NMX1、2、4、5、8、9、10、11、12、14、16)与黄河干支流的黄河裸裂尻鱼形成另一个单系群(MP 99%,Bayesian 99%).序列差异分析显示,分布于不同族群的南门峡裂腹鱼亚科鱼类之间存在较大的碱基差异(平均为7.42%),显示出种间差异水平,表明分布于南门峡河流的裂腹鱼亚科鱼类可能是花斑裸鲤和黄河裸裂尻鱼形态相似种的复合体.结合青藏高原隆升所致的气候环境变化和高原北部水系变迁的事件,推断形态趋同进化可能导致了南门峡河流裂腹鱼亚科鱼类形态相似种的共存,而小生境自然选择压力是引发适应性形态趋同进化的主要原因.
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构建了甘肃鼠兔、黄河鼠兔、藏鼠兔、高原鼠兔和红耳鼠兔的mtDNA限制性内切酶图谱,并以PAUP程序建立其分子系统树。结果表明,鼠兔亚属的4个物种与耗兔亚属的红耳鼠兔存在明显的长度变异(1kb),从而为两亚属的划分提供了新的遗传标记。同时,甘肃鼠兔和黄河鼠兔的遗传分化已达明显的物种级别,因而进一步证实它们均为独立种。在系统树中,黄河鼠兔与高原鼠兔亲缘关系最近,然后是藏鼠兔,最后是甘肃鼠兔与前3种构成一对姊妹群。依据遗传距离计算了分歧年代。两亚属的分歧时间约距今8.8×104ha,相当于中国哺乳动物时代的保德期中期;鼠兔亚属内4种的分歧发生于约距今(2.5~4.2)×104ha的上新世晚期,相当于榆社期晚期。
Resumo:
How coniferous trees in northern China changed their distribution ranges in response to Quaternary climatic oscillations remains largely unknown. Here we report a study of the phylogeography of Pinus tabulaeformis, an endemic and dominant species of coniferous forest in northern China. We examined sequence variation of maternally inherited, seed-dispersed mitochondrial DNA (mtDNA) (nad5 intron 1 and nad4/3-4) and paternally inherited, pollen- and seed-dispersed chloroplast DNA (cpDNA) (rpl16 and trnS-trnG) within and among 30 natural populations across the entire range of the species. Six mitotypes and five chlorotypes were recovered among 291 trees surveyed. Population divergence was high for mtDNA variation (G(ST) = 0.738, N-ST = 0.771) indicating low levels of seed-based gene flow and significant phylogeographical structure (N-ST > G(ST), P < 0.05). The spatial distribution of mitotypes suggests that five distinct population groups exist in the species: one in the west comprising seven populations, a second with a north-central distribution comprising 15 populations, a third with a southern and easterly distribution comprising five populations, a fourth comprising one central and one western population, and a fifth comprising a single population located in the north-central part of the species' range. Each group apart from the fourth group is characterized by a distinct mitotype, with other mitotypes, if present, occurring at low frequency. It is suggested, therefore, that most members of each group apart from Group 4 are derived from ancestors that occupied different isolated refugia in a previous period of range fragmentation of the species, possibly at the time of the Last Glacial Maximum. Possible locations for these refugia are suggested. A comparison of mitotype diversity between northern and southern subgroups within the north-central group of populations (Group 2) showed much greater uniformity in the northern part of the range both within and between populations. This could indicate a northward migration of the species from a southern refugium in this region during the postglacial period, although alternative explanations cannot be ruled out. Two chlorotypes were distributed across the geographical range of the species, resulting in lower levels of among-population chlorotype variation. The geographical pattern of variation for all five chlorotypes provided some indication of the species surviving past glaciations in more than one refugium, although differentiation was much less marked, presumably due to the greater dispersal of cpDNA via pollen.
Resumo:
The disjunct distribution of forests in the Qinghai-Tibetan Plateau (QTP) and adjacent Helan Shan and Daqing Shan highlands provides an excellent model to examine vegetation shifts, glacial refugia and gene flow of key species in this complex landscape region in response to past climatic oscillations and human disturbance. In this study, we examined maternally inherited mitochondrial DNA (nad1 intron b/c and nad5 intron 1) and paternally inherited chloroplast DNA (trnC-trnD) sequence variation within a dominant forest species, Picea crassifolia Kom. We recovered nine mitotypes and two chlorotypes in a survey of 442 individuals from 32 populations sampled throughout the species' range. Significant mitochondrial DNA population subdivision was detected (G(ST) = 0.512; N-ST = 0.679), suggesting low levels of recurrent gene flow through seeds among populations and significant phylogeographical structure (N-ST > GST, P < 0.05). Plateau haplotypes differed in sequence from those in the adjacent highlands, suggesting a long period of allopatric fragmentation between the species in the two regions and the presence of independent refugia in each region during Quaternary glaciations. On the QTP platform, all but one of the disjunct populations surveyed were fixed for the same mitotype, while most populations at the plateau edge contained more than one haplotype with the mitotype that was fixed in plateau platform populations always present at high frequency. This distribution pattern suggests that present-day disjunct populations on the QTP platform experienced a common recolonization history. The same phylogeographical pattern, however, was not detected for paternally inherited chloroplast DNA haplotypes. Two chlorotypes were distributed throughout the range of the species with little geographical population differentiation (G(ST) = N-ST = 0.093). This provides evidence for highly efficient pollen-mediated gene flow among isolated forest patches, both within and between the QTP and adjacent highland populations. A lack of isolation to pollen-mediated gene flow between forests on the QTP and adjacent highlands is surprising given that the Tengger Desert has been a geographical barrier between these two regions for approximately the last 1.8 million years.