基于线粒体基因分析的中华血吸虫分子种系发生研究

目的 测定中华血吸虫线粒体细胞色素 C氧化酶亚基 1(CO1)和 NADH脱氢酶亚基 1(ND1)基因序列 ,并根据这些序列构建分子系统发生树 ,探讨中华血吸虫在裂体属内的系统发生位置。 方法 以 GNT- K法抽提虫体基因组 DNA,用特异引物 PCR扩增目的基因。PCR扩增产物经纯化后克隆于质粒载体 ,以纯化后的阳性质粒 DNA作为模板 ,M13(F/ R)为引物于 L icor测序仪测序。检索 Gen Bank,查找曼氏血吸虫等相关血吸虫两线粒体基因序列 ,作基因排序及比较分析后 ,用 PHYL IP和 MEGA以邻接法和最大简约法绘制系统发生树。 结果 克隆了中华血吸虫的 CO1和 ND1基因片段 ,并测定了两基因片段的核苷酸序列 ,根据这些序列构建了系统发生树。 结论 中华血吸虫 CO1和ND1基因的系统发生树结果一致。

雄激素受体基因动态突变及线粒体基因分析诊断Kennedy病1例报告

目的通过对一例肌肉活检提示线粒体肌病的患者进行雄激素受体基因（androgen receptor gene，AR）进行动态突变分析和全线粒体（mtDNA）基因扫描明确诊断。方法使用PCR方法分析患者雄激素受体（androgen receptor gene，AR）基因的CAG重复序列数，使用Touch Down PCR方法分析患者全线粒体基因突变。结果该患者雄激素受体基因第一个外显子（Xqll-12）上存在46个三核普酸（CAG）重复，确诊Kennedy病。全线粒体（mtDNA）基因分析未显示线粒体疾病的相关致病突变。结论AR基因CAG动态突变分析和全mtDNA基因扫描是KD与线粒体脑肌病鉴别诊断或KD并发线粒体脑肌病诊断的重要依据。

Complete Sequence and Gene Organization of the Mitochondrial Genome of Tokay (Gekko gecko)

Long-PCR amplification, clone and primer-walking sequencing methods were employed in determine the complete sequence of mitochondrial genome of tokay (Gekko gecko). The genome is 16 435 bp in size, contains 13 protein-coding, 2 ribosomal and 22 transfer RNA genes. The mt genome of Gekko is similar to most of the vertebrates in gene components, order, orientation, tRNA structures, low percentage of guanine and high percentage of thymine, and skews of base GC and AT. Base A was preferred at third codon positions for protein genes is similar to amphibians and fishes rather than amnion vertebrates. The standard stop codes (TAA) present only in three protein genes, less than those of most vertebrates. Transfer RNA genes range in length from 63 to 76 nt, their planar structure present characteristic clover leaf, except for tRNA-Cys and tRNA-Ser (AGY) because of lacking the D arm.

Application of Mitochondria DNA Hypervariable Region in Identification of Genetic Relationships among Different Varieties in Musa paradisiaca

[Objective] The aim was to establish an effective method for the identification of genetic relationships among different varieties in Musa paradisaca. [Method] Based on the diversity of mitochondria DNA intron sequence among different varieties of M. paradisaca,an intron of cytochrome oxidase subunit II gene in mitochondria DNA genome was amplified and sequenced. And then the cluster analysis was used to classify 16 varieties of M. paradisaca,which belonged to five genotypes （AAA,AA,AAB,ABB and BB）. [Result] The 16 varieties of M. paradisaca could be divided to three classes：the first class contained one variety,the genotype of which was BB; the second class contained seven varieties,the genotype of which was ABB; the third class contained eight varieties,the genotypes of which included AA,AAA,AAB and BB. The new varieties YiXian 1,2 and 3 showed the nearest relationship with FenZa. [Conclusion] The result of classification was consistent with the genotypes,thus verified the feasibility and effectiveness of the new method in the genetic relationship identification of M. paradisaca germplasm.

Cloning,Sequencing and Molecular Phylogenetic Analysis of the Mitochondrial Cytochrome Oxidase Ⅰ Gene of Chilo suppressalis

[Objective] The research aimed at cloning and analyzing mitochondrial cytochrome oxidase I gene（cox 1）of C.suppressalis.[Method] The mitochondrial cox 1 gene of C.suppressalis was cloned with PCR method and sequenced.Then,cox1 sequences of other 21 Lepidopteran species were obtained by blasting the GenBank with cox 1 gene sequence of C.suppressalis.Finally,homology comparison and molecular phylogenitic analysis among the 22 Lepidopteran species were conducted.[Result] The open reading frame of cox 1 gene from C.suppressalis contained 1 531 nucleotides encoding a putative protein of 510 amino acids.The cox1 gene used a start codon CGA,and an incomplete termination codon composed of only T.Based on the amino acid sequences of cox 1,the molecular phylogenetic tree of Lepidoptera was reconstructed using the maximum likelihood（ML）method.The molecular phylogenetic tree was similar to the morphological phylogenetic tree mainly,but also showed some differences.[Conclusion] The result will provide reference for further research on expression and application of cox 1 gene.

Complete Mitochondrial Genome of the Red Fox (Vuples vuples) and Phylogenetic Analysis with Other Canid Species

The whole mitochondrial genome sequence of red fox （Vuples vuples） was determined. It had a total length of 16 723 bp. As in most mammal mitochondrial genome, it contained 13 protein coding genes, two ribosome RNA genes, 22 transfer RNA genes and one control region. The base composition was 31.3% A, 26.1% C, 14.8% G and 27.8% T, respectively. The codon usage of red fox, arctic fox, gray wolf, domestic dog and coyote followed the same pattern except for an unusual ATT start codon, which initiates the NADH dehydrogenase subunit 3 gene in the red fox. A long tandem repeat rich in AC was found between conserved sequence block 1 and 2 in the control region. In order to confirm the phylogenetic relationships of red fox to other canids, phylogenetic trees were reconstructed by neighbor-joining and maximum parsimony methods using 12 concatenated heavy-strand protein-coding genes. The result indicated that arctic fox was the sister group of red fox and they both belong to the red fox-like clade in family Canidae, while gray wolf, domestic dog and coyote belong to wolf-like clade. The result was in accordance with existing phylogenetic results.

The first complete mitogenome of Cyclommatus stag beetles(Coleoptera: Lucanidae) with the phylogenetic implications

The first complete mitogenome of Cyclommatus stag beetles, Cyclommatus vitalisi（Coleoptera： Lucanidae） is sequenced using the next generation sequening. The genomic structure is a closed circular molecule with 17,853 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes（t RNAs）, 2 ribosomal RNAs（r RNAs） and a control region. The sequence has neither a gene rearrangement nor a non-coding region. The nucleotide composition is A（36. 31%）, C（21. 48%）, T（31. 20%） and G（11. 01%）, with overall AT content of 73. 61%. The phylogenetic analysis of 13 stag beetles and another three scarab beetles show that Cyclommatus vitalisi shares a close ancestry with Lucanus mazama and Lucanus fortunei.

The Complete Sequence of Mitochondrial COII Gene of Fenneropenaeus chinensis and Its Applicability as a Marker for Phylogenetic Analysis

The complete mitochondrial cytochrome oxidase subunit Ⅱ （COⅡ） gene of Penaeinae shrimp Fenneropenaeus chinensis was cloned and sequenced. The gene is 688 bp in length and codes for 229 amino acids. It shows 83.2%, 87.0% and 83.8% sequence similarity to Marsupenaeus Japonicus, Penaeus monodon and Farfantepenaeus notialis, respectively. The A＋T content of the whole gene and that at the third position of codons are 64.7% and 78.2%, respectively. The phylogenetic relationship between F. chinensis and three other species representing genera Farfanatepenaeus, Marsupenaeus and Penaeus was analyzed. Results showed that the genetic distances among the four taxa ranged from 0.144 0 to 0.200 5, exceeding those estimated with COⅠ and partial 16S rRNA gene sequences among Marsupenaeus, Litopenaeus and Melicertus, and being therefore larger than the value among subgenera. It has been suggested that the COⅡ gene has a faster evolutionary rate than that of the COⅠ gene and partial 16S rRNA gene and could be used for phylogenetic analysis at genus or species level. The results of the present study indicated that Farfantepenaeus, Fenneropenaeus, Marsupenaeus and Penaeus are at a higher phylogenetic level than subgenus, which supports the opinion of the elevation of phylogenetic status of the four subgenera to genus level.

Species identification and phylogenetic analysis of genus Nassarius(Nassariidae)based on mitochondrial genes

Genus Nassarius contains many subgenera, such as Zeuxis, Telasco, Niotha, Varicinassa, Plicarcularia, Nassarius s. str. and Reticunassa. On the basis of morphological characteristics of the shell and radula and sequences of mitochondrial cytochrome oxidase subunit I (COI) and 16S rRNA genes, Nassarius specimens collected from the South China Sea were identified and phylogenetically analyzed. Although Nassarius sp. and Nassarius (Varicinassa) variciferus were morphologically different in their shells, few variations were found among their radular teeth and sequences of mtCOI and mt16S RNA genes. Therefore, Nassarius sp. should be classified as N. (Varicinassa) variciferus. Nassarius (Zeuxis) sp. has only a subtle difference from Nassarius (Zeuxis) algidus on the shell, but it shows obvious differences in radular teeth and DNA sequence, indicating that they are two distinct species. Sequence divergence of mtCOI and mt16S RNA genes within Nassarius species was much lower than that between species, suggesting that these two genes are suitable for Nassarius species identification. Phylogenetic analysis (neighbor-joining and maximum parsimony) based on mtCOI and mt16S rRNA genes revealed the presence of two groups in genus Nassarius and a closest relationship between subgenera Zeuxis and Telasco. Species of subgenus Plicarcularia did not form a single clade. The molecular phylogeny was not congruent with the previous morphological phylogeny. The subgeneric divisions of genus Nassarius appear to be uncertain and unreliable.

Phylogeny and species differentiation of Mollitrichosiphum spp. （Aphididae, Greenideinae） based on mitochondrial CO1 and Cyt b genes

Phylogenetic analyses based on mitochondrial genes were conducted to reconstruct species relationships within the aphid genus MoUitrichosiphum （Aphididae, Greenideinae）. MP and Bayesian analysis results using COI and Cyt b datasets, and combined MP, ML and Bayesian analysis of both were consistent with a morphologically supported monophyly. Subdivision of the genus into two subgenera was strongly supported. Samples of each included species form monophyletic clade, respectively; and the result implied the valid status of related species in this genus. These results suggest some surprising hypotheses regarding the phylogeography of the genus： the uplift of the Tibetan Plateau, reorganization of major fiver catchments and the isolation of Hainan Island were probably important factors contributing to the diversification of species in this genus .

Genealogy and phylogeography of Cyprinid fish Labeo rohita （Hamilton, 1822） inferred from ATPase 6 and 8 mitochondrial DNA gene analysis

ATPase 6/8 gene （842 bp） of mitochondrial DNA was sequenced in Labeo rohita samples （n = 253） collected from nine rivers belonging to four river basins; Indus, Ganges, Brahmaputra and Mahanadi. Analysis revealed 44 haplotypes with high haplotype diversity （Hd） 0.694 and low nucleotide diversity （π） 0.001. The within population variation was larger （83.44%） than among population differences （16.56%）. The mean Fsv value （0.166; P 〈 0.05） for overall populations revealed moderate level of genetic structuring in the wild L. rohita populations. The haplotype network presented a single clade for wild L. rohita population, from different rivers. Negative values for Fu＇s index （Fs）, mismatch distribution analysis indicated period of expansion in L. rohita population. The time after recent expansion was estimated for each population, between 0.042 to 0.167 mya. The pattern of Isolation by Distance （IBD） was not significant （r = -0.113, P 〈 0.287）, when all the sampling locations were compared （Mantel test）, however, when an outlier （Indus, Brahmaputra and Mahanadi） was removed from the whole population set, a clear positive correlation between pairwise Fsv and geographic distance （Km） was seen. The analysis of data demonstrated that ATPase6/8 gene polymorphism is a potential marker to understand genetic population structure of wild L. rohita existing in different rivers. The study identified population substructure in wild L. rohita with common ancestral origin [Current Zoology 60 （4）： 460--471, 2014].

Diversification of Sisorid catfishes(Teleostei: Siluriformes)in relation to the orogeny of the Himalayan Plateau

Abstract Sisorid catfishes are primarily limited in distribution to rivers of the Himalayan region and Tibetan Plateau. These species have external morphologies that are adapted for extremely fast-flowing riverine systems. Given the diversity of the group and the above qualities of these catfishes, this lineage serves as an ideal group for inferring the geological history of this region based on their phylogenetic relationships reflecting evolu- tionary history. We sequenced the complete mitochondrial genome and four nuclear genes of representative sisorids distributed across river systems in China. Phylogenetic analyses strongly support the monophyly of the Sisoridae and the glyptosternoids. An analysis of the reconstructed ancestral states derived from inferred genealogical relationships suggests that the evolution of this lineage was accompanied by convergent evolution in morphological traits that were presumably in response to environmental pressure involving the rapid flowing river system that were generated during the uplift of the Tibetan Plateau （UTP）. Molecular dating indicates that the Chinese sisorids and the glyptosternoids originated at the later Miocene （~ 10.9-9.8 Mya）, and with further biogeographic analyses indicates that the species of Sisoridae likely originated from a widely distributed ancestor. Moreover, the divergence of the Sisoridae in China can be divided into two phases consis- tent with the UTP. All of these results indicate that the diversification and dispersal events in this lineage occurred as a result of drainage systems formed during and after the UTP in the late Miocene and Quaternary periods.

Progress in the Researches on Insect Mitochondrial Genome and Analysis of Gene Order

Insect mitochondrial genome is a double-stranded circular genomes which range from 14 503 bp to 19 571 bp in size.Nearly all the sequenced insect mitochondrial genomes encode 37 genes:two for rRNAs,13 for proteins and 22 for tRNAs.This review compares and summarizes the features of complete mitochondrial genomes from 175 sequenced species of insects in 22 orders.The genomic organization, contents,gene order,and rearrangements of gene order are analyzed.