Variability of Nucleotide Sequences of Mitochondrial DNA Cytochrome b Gene in Chars of the Genus Salvelinus

Nucleotide sequences of two (405- and 1050-bp) regions of mitochondrial DNA (mtDNA) cytochrome c gene were established in chars of the genus Salvelinus from Russian Far East and Siberia. Based on the divergence and phylogenetic analysis of nucleotide sequences of the mtDNA cytochrome b gene, S. laecomaenis was shown to carry the most ancient mitochondrial lineage, which is close to the ancestral one. The archaic mtDNA of S. levanidovi occupied an isolated position on the phylogenetic trees. The mtDNA lineage of the southern S. malma was close to the S. alpinus–S. malma malmacomplex group. Within the S. alpinus–S. m. malma complex, three groups of mtDNA types having particular geographic distributions were distinguished. The Kolyma–Chukotka group includes lake S. taranetzi, S. boganidae, andS. elgyticus from Chukotka, lake chars from Kolyma. The Okhotsk group is represented by northernS. malma, lake chars from northern Sea of Okhotsk, and anadromous S. taranetzi. The Siberian group is close to the Okhotsk one and consists of Taimyr and Baikal region chars as well as Arctic char from Finland. The divergence of char mitochondrial lineages was dated to the Pliocene–Pleistocene.     

Variation of Human Mitochondrial DNA: Distribution of Hot Spots in Hypervariable Segment I of the Major Noncoding Region

Mitochondrial DNA (mtDNA) samples belonging to fifteen phylogenetically related mtDNA types specific to the populations of Europe (H, V, J, T, U, K, I, W, and X) and Northern Asia (A, C, D, G, Y, and Z) were typed for sequence variation in hypervariable segment I (HVSI). The approach used allowed to distinguish several hypervariable sites at nucleotide positions 16093, 16129, 16189, 16311, and 16362. Identical mutations at these sites were found in 10–11 out of 15 mtDNA groups examined. Positions 16126, 16172, 16192, 16256, 16261, 16291, 16293, and 16298 appeared to be less variable, since parallel mutations at these sites were found in 6–8 European and Asian mtDNA groups. The examples of the effects of mutations in hypervariable positions at the major noncoding mtDNA region on the frequency of reverse mutations in other mtDNA regions are presented. It was shown that such effects of nucleotide context on the mutation rate could be observed in phylogenetic mtDNA networks such as cyclic structures like rhombs and cubes. Analogous structures in the networks could be seen also in the case of the appearance of recombinant mtDNA types resulted from homologous recombination between mtDNA molecules in heteroplasmic mixture. The problem of the effect of polynucleotide context on the intensity of mtDNA mutagenesis is discussed. Recombination processes along with site-directed mutagenesis caused by action of genetic factors (of nuclear genome) and/or of the environment are considered as possible mechanisms of mitochondrial genome evolution.     

Characterization of Variability in Some Pathogenic Species of Alternaria Based on the Nucleotide Sequence of Ribosomal DNA

The internal transcribed spacer (ITS) sequences within the ribosomal DNA (rDNA) region were targeted to delineate genetic variability among eight Alternaria species that cause economically important diseases in crops. The rDNA regions of Alternaria species comprising of rRNA genes and the ITS regions were cloned and sequenced. Phylogenetic relationship based on the rDNA sequences and PCR-RFLP of amplified rDNA sequences clustered eight species of Alternaria into three major groups. A. macrospora and A. helianthi accumulated wide genetic variations and are distantly related to rest of the six species which formed two major groups. Group I comprised of three species viz., A. dianthicola, A. brassicae and A. citri, while group II had A. longipes, A. porri and A. alternata. Incorporation of unique stretches of nucleotides and single nucleotide substitutions within relatively conserved ITS1 and ITS2 regions led to clustering of the members of Alternaria species in each group. The divergent sequences within the ITS regions can be employed to design species-specific PCR primer for use in molecular diagnostics.     

广义青篱竹属(Arundinaria)核糖体DNA ITS序列及亲缘关系研究

利用PCR扩增产物直接测序的方法分析广义青篱竹属(Arundinaria)中有关争议类群的代表种或模式种(毛竹为外类群)等18种竹种的核糖体DNA内转录间隔区(Internal Transcribed Spacers,ITS)序列。通过最简约性分析产生的ITS系统发育树表明,供试竹种形成一个自然的单系类群,这说明广义青篱竹属中这些不同的类群归属青篱竹属是合理的。17种竹种可聚为2大分支：其中斑苦竹(A,oleosa)、仙居苦竹(A．hsienchuensis)、茶秆竹(A．amabilis)、长叶苦竹(A．chino)、苦竹(A．amara)、宜兴苦竹(A．yixingensis)、菲白竹(A．fortunei)、翠竹(A．pygmaea)为一个分支;而大明竹(A．graminea)、巴山木竹(A．fargesii)、冷箭竹(A．faberi)、凤竹(A．hupehense)、鼓节矢竹(Pseudosasa japonica cv．Tsutsumiana)、矢竹(Pseudosasa japonica)、短穗竹(Brachystachyum densiflorum)、肿节竹(A．oedogonata)、少穗竹(A．sulcata)组合在另一分支。ITS系统发育树还表明,大明竹与巴山木竹、鼓节矢竹与矢竹、少穗竹与短穗竹和肿节竹关系极为密切,均得到较高的Bootstrap(分别为99％、100％和87％)的支持;茶秆竹与仙居苦竹关系非常密切,茶秆竹可归隶到青篱竹属中;翠竹和菲白竹关系密切,且与苦竹类竹种分为两个分支。     

Comparative Restriction Enzyme Analysis of Mitochondrial DNA in Several Populations of Lake Resident Chars of the Genus Salvelinus

Restriction enzyme analysis was employed in studying the mitochondrial DNA (mtDNA) ATPase6/ND4L region in several Northeast Asian populations of resident lake char of the genus Salvelinus. On evidence of mitotypes, genetic similarity was assumed for populations of neiva (Ueginskoe Lake), lake resident char from the northern coast of the Sea of Okhotsk (Mak-Mak Lake and Elekchanskie lakes), and dolly varden. Mitotype AAAA proved to be common for these populations. Lake char populations of the Juliet and Maxi lakes (the basin of the Kolyma River) had mitotype DBAA, which is similar to mitotype DBAB observed earlier in Taranetz char from Chukotka. The divergence between mitotypes AAAA and DBAA was estimated at 0.3%. Different origins were assumed for the lake resident char populations from the basins of the Sea of Okhotsk and of the Kolyma River, the former originating in the Pacific and the latter, in the Arctic basins.     

黄瓜线粒体DNA类质粒pC1的性质和核酸序列研究

津研四号黄瓜线粒体中除主环ＤＮＡ外,还有４种ＤＮＡ类质粒：ｐＣ１、ｐＣ２、ｐＣ３、ｐＣ４。将环形类质粒ｐＣ１ｌｐｋ ｇｃ ｐＵＣ１９的ＥｃｏＲⅠ位点上,克隆至Ｅ．ｃｏｌｉ ＪＭ１０９中。以克隆的ｐＣ１为探针,进行同源性检测,ｐＣ１与津研四号黄瓜的核基因组、叶绿体基因组、线粒体基因组和线粒体中其他类质粒不同源。对ｐＣ１进行序列测定和分析,ｐＣ１长度２ ８８９ｂｐ,含有多个正向和反向重复序列,有３个８     

国产堇菜属的分子系统学研究

利用基于ITS序列的分子系统学对国产堇菜属(Viola L.)进行了系统发育重建,选择Hybanthus concolor和鳞隔堇(Scyphellandra pierrei)作为外类群,对国产堇菜属植物54种1亚种共66个序列进行分析。分子系统树中获得强烈支持的中国堇菜属属下组级分类群有Sect.Viola、Sect.Diffusae、Sect.Bilobatae、Sect.Vaginatae。Subgen.Melanium与Sect.Viola和Sect.Trigonocarpae聚在一起,说明它们的亲缘关系较近,但Sect.Trigonocarpae支获得的支持率较低。分子系统树证实了Subgen.Dischidium与Subgen.Chamaemelanium的近缘关系,但不支持根据距的长短将Subgen.Dischidium划分为Sect.Longicalcaratae和Sect.Brevicalcaratae的处理。而Pinnatae类群应该作为Sect.Adnatae下的一个亚组处理。根据分子系统发育和形态学特征对V.lucens、V.magnifica、V.dissecta、V.yunnanensis等的分类地位进行了重新评价。     

云南保山猪线粒体DNA D-loop区序列初步分析

采用低小牛血清、低叶酸、pH 值较高的培养基,对50例白血病患儿进行rJL色休脆性浑位分析。发 现染色体畸变率及脆性部位表达率明显高于正常对照组, 且表达之脆性部位与痛断裂点及;zEt基因座位 密切相关。本文就脆性部位与白血病类型关系进行了讨沱。     

云南保山猪线粒体DNA D-loop区序列初步分析 Primary Analysis of Mitochondrial DNA D-loop Region Sequence in Baoshan Pig

摘要：为了解云南保山猪(Baoshan pig)的遗传多样性及其遗传背景,我们测定了19个个体线粒体DNA D-loop高变区I 15 363～15 801片段序列438 bp。检测到10种单倍型,包括8个多态位点,其中5次T/C转换、1次G/A转换、1次G/C颠换和1次A/T颠换,其A、T、G、C碱基的平均含量分别为35.4%、26.9%、13.2%和24.5%,A+T含量(62.3%)明显高于G+C含量(37.7%)。对于保山猪的保种及其持续利用有着重要的理论指导意义。 Abstract:To investigate the genetic diversity and genetic data of Baoshan pig in Yunnan province,the mitochondrial DNA D-loop hypervariable segment I sequences 15 363～15 801 (438 bp) in 19 individuals of Baoshan pig were sequenced.Ten mitochondrial haplotypes were identified in the samples,with 8 sites showing polymorphism,which were 5 T/C and 1 G/A transitions,1 G/C and 1 A/T transversions.The contents of A,T,G and C were 35.4%,269%,13.2% and 24.5%,respectively.The content of A+T (62.3%) was significantly higher than that of G+C (37.3%).It will be of importance to conservation and sustainable utilization in Baoshan pig.     

现代罗布人群线粒体DNA D-loop区序列多态性研究

目的：研究新疆尉犁县的现代罗布人群线粒体DNAD-loop区序列遗传多态性,并初步探讨现代罗布人群和其他人群的亲缘关系。方法：应用PER扩增直接测序法,对23个所测定的个体序列采用ClustalX、Mega3．1、hrlequin等软件包进行分析。结果：23个个体中,共检测到47个变异位点,界定了22种不同的单倍型,计算出偶合概率P值为0．05482,变异度h值为0．99604。结论：现代罗布人与中亚各民族的亲缘关系很近,尤其是与新疆维吾尔族有很近的亲缘关系。     

Polymorphism in Nucleotide Sequence of Mitochondrial Intergenic Region in Scleractinian Coral (Galaxea fascicularis)

A region of 826 bp that is unlikely to code for a protein, ribosomal RNA, or transfer RNA was identified between the cytochrome b and NADH–ubiquinone oxidoreductase chain 2 loci in the mitochondrial DNA of the scleractinian reef coral Galaxea fascicularis. Nucleotide sequences were determined in a part (625 bp) of this intergenic region in 95 individuals collected at 9 sites in the Ryukyu Archipelago in southwestern Japan. A total of 8 haplotypes were found, and a deletion of 290 bp was found in 3 of them. Significant differences were found in frequencies of the haplotypes at 3 sampling sites. The presence or absence of the deletion was highly correlated with the hard or soft morphotype. The deletion was found in the majority of hard-type colonies, but in a small fraction of soft-type individuals.     

美丽硬仆骨舌鱼mtDNA D-loop区遗传变异特征

采用直接测序法分析美丽硬仆骨舌鱼(Scleropages formosus)3个种群(金龙鱼、红龙鱼和青龙鱼)共24个个体的线粒体D-loop区的遗传变异特征。经序列比对、分析,金龙鱼、红龙鱼和青龙鱼的D-loop序列不仅在个体间存在位点序列的变异(17个简约性信息位点),而且还存在序列长度的多态性(长度为915-924 bp),这种长度的差异在于存在不同碱基长度的微卫星序列。3种龙鱼碱基组成基本一致,G含量偏低。定义了10种单倍型,但金龙鱼、红龙鱼和青龙鱼间没有共享单倍型,单倍型多样度较高(0.667-1.00),核苷酸多样度较低(0.001 09-0.003 23)。AMOVA分析显示,变异主要来自地理区内不同群体间,个体间遗传距离为0-0.008 7,显示遗传变异仍处于种内水平。NJ、MP和Bayesian构建的分子系统树拓扑结构基本一致,但不能有效地反映金龙鱼、红龙鱼和青龙鱼间的亲缘关系。     

Evolution of Repeated Sequence Arrays in the D-Loop Region of Bat Mitochondrial DNA

Analysis of mitochondrial DNA control region sequences from 41 species of bats representing 11 families revealed that repeated sequence arrays near the tRNA-Pro gene are present in all vespertilionine bats. Across 18 species tandem repeats varied in size from 78 to 85 bp and contained two to nine repeats. Heteroplasmy ranged from 15% to 63%. Fewer repeats among heteroplasmic than homoplasmic individuals in a species with up to nine repeats indicates selection may act against long arrays. A lower limit of two repeats and more repeats among heteroplasmic than homoplasmic individuals in two species with few repeats suggests length mutations are biased. Significant regressions of heteroplasmy, θ and π, on repeat number further suggest that repeat duplication rate increases with repeat number. Comparison of vespertilionine bat consensus repeats to mammal control region sequences revealed that tandem repeats of similar size, sequence and number also occur in shrews, cats and bighorn sheep. The presence of two conserved protein-binding sequences in all repeat units indicates that convergent evolution has occurred by duplication of functional units. We speculate that D-loop region tandem repeats may provide signal redundancy and a primitive repair mechanism in the event of somatic mutations to these binding sites.     

大趾鼠耳蝠线粒体DNA控制区结构及变异

采用PCR产物直接测序法首次测定大趾鼠耳蝠(Myotis macrodactylus)10个个体的线粒体DNA(mtDNA)控制区全序列,并进行了结构和变异分析。结果表明,大趾鼠耳蝠的控制区结构与其他哺乳动物相似,可分为一个中央保守区(包括F、E、D、C、B元件)和两个外围结构域:延伸的终止结合序列区(包括ETAS1和ETAS2元件)和保守序列区(包括CSB1、CSB2和CSB3元件),其中最为保守的是中央保守区(核苷酸变异度为1.8%)。大趾鼠耳蝠控制区核苷酸全序列具有丰富的长度多态性(1778～2048bp),主要是由在碱基组成、重复数目和排列方式上异质的串联重复序列造成的。在ETAS内发现了TACAT及其反向互补序列ATGTA,支持滑移错配模式(slipped mispairing model)。本研究为该物种的进一步研究和保护提供基础遗传数据。     

人癌细胞线粒体DNA控制区序列特征分析

为了探讨癌细胞mtDNA控制区序列的变化特征, 采用PCR产物限制性片段长度多态性(PCR-RFLP)分析与直接测序相结合的方法,对比分析6株人癌细胞系、 6例癌患者及4例健康成人白细胞mtDNA控制区序列。发现第16519位T→C、16 534位A→G、46位T→G和49位A→C突变, 在癌细胞系和癌患者白细胞mtDNA中分别占50%(3/6)和33.3%(2/6), 健康成人白细胞mtDNA中未见此类型突变;第16 278位C→T突变,在癌细胞系mtDNA中占50%(3/6),显著高于正常人群mtDNA中此位点的多态性变异。表明癌细胞和癌患者白细胞mtDNA重链复制起点及其 相邻D环区的特征性突变可能与细胞癌变/或癌的易感性有关。 Abstract：　To explore the sequence feature of mitochondrial DNA(mtDNA) control region in human carcinoma cells, polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP) and direct sequence techniques were used to analyze the sequence of mtDNA control region of 6 human carcinoma cell lines versus white blood cells which from 6 tumor patients and 4 normal adults. The T to C mutation at np 16 519, A to G mutation at np 16 534, T to G mutation at np 46, and A to C mutation at np 49 was found in 50% (3/6 cases) of carcinoma cell lines and in 33.3%(2/6 cases) of tumor patients, but it was not found in normal adults. The C to T mutation at np 16 278 was found in 50%(3/6 cases) of carcinoma cell lines, it was significantly higher than that of the polymorphism of normal population. These findings suggest that the typical mutation in the starting area of heavy-strand replication and the first half of D-loop region might probably be associated with carcinogenesis or susceptibility of carcinoma.     

人癌细胞线粒体DNA控制区序列特征分析

为了探讨癌细胞mtDNA控制区序列的变化特征, 采用PCR产物限制性片段长度多态性(PCR-RFLP)分析与直接测序相结合的方法,对比分析6株人癌细胞系、 6例癌患者及4例健康成人白细胞mtDNA控制区序列。发现第16519位T→C、16 534位A→G、46位T→G和49位A→C突变, 在癌细胞系和癌患者白细胞mtDNA中分别占50%(3/6)和33.3%(2/6), 健康成人白细胞mtDNA中未见此类型突变;第16 278位C→T突变,在癌细胞系mtDNA中占50%(3/6),显著高于正常人群mtDNA中此位点的多态性变异。表明癌细胞和癌患者白细胞mtDNA重链复制起点及其 相邻D环区的特征性突变可能与细胞癌变/或癌的易感性有关。 Abstract：　To explore the sequence feature of mitochondrial DNA(mtDNA) control region in human carcinoma cells, polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP) and direct sequence techniques were used to analyze the sequence of mtDNA control region of 6 human carcinoma cell lines versus white blood cells which from 6 tumor patients and 4 normal adults. The T to C mutation at np 16 519, A to G mutation at np 16 534, T to G mutation at np 46, and A to C mutation at np 49 was found in 50% (3/6 cases) of carcinoma cell lines and in 33.3%(2/6 cases) of tumor patients, but it was not found in normal adults. The C to T mutation at np 16 278 was found in 50%(3/6 cases) of carcinoma cell lines, it was significantly higher than that of the polymorphism of normal population. These findings suggest that the typical mutation in the starting area of heavy-strand replication and the first half of D-loop region might probably be associated with carcinogenesis or susceptibility of carcinoma.     

Mitochondrial DNA variation of Salvelinus species found in Finland

Mitochondrial DNA (mtDNA) was purified from the Arctic charr, Salvelinus alpinus , the brook charr, Salvelinus fontinalis , and the lake charr, Salvelinus namaycush , and digested with restriction enzymes Ava II, Hinf I, Eco R V, Pst I and Xba I. Two Arctic charr samples were from natural populations and they represented two different morphotypes of Arctic charr. All other studied populations were hatchery maintained. Eight additional restriction enzymes and double digestions were employed to study morphotypes of Arctic charr. We distinguished two morphotypes with restriction enzyme Nci I. Sequence divergence among mtDNA types was 2.9–3.8% between S. alpinus and S. fontinalis , 3.4–4.6% between S. alpinus and S. namaycush , and 4.7–5.3% between S. fontinalis and S. namaycush . lntraspecific variation was lowest in Arctic charr, the average of nucleon diversity for three populations being 0.179, while for brook charr and for lake charr nucleon diversity was 0.334 and 0.550, respectively. According to the number of mtDNA types, it is obvious that introduction to Finland and hatchery propagation have not greatly affected the mtDNA variation of brook charr or lake charr.