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...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.展开更多
[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 sequenc...[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.展开更多
[Objective] The sequences of mitochondrial DNA D-loop region of Xinjiang Goose with three different colors of plumage were analyzed in order to study the genetic diversity of Xinjiang Goose, as well as the phylogeny a...[Objective] The sequences of mitochondrial DNA D-loop region of Xinjiang Goose with three different colors of plumage were analyzed in order to study the genetic diversity of Xinjiang Goose, as well as the phylogeny and evolution. [Method] Ten geese were selected randomly from the core populations of grey-, mosaic- and white-plumaged Xinjiang Goose respectively with a total number of thirty as experi- mental materials, of which the blood samples were collected from the largest vein under the wing (brachial vein) for DNA extraction. Sequences of mitochondrial DNA D-loop regions were determined using DNA sequencing technology to analyze the polymorphism. In addition, the genetic distances among different populations were estimated through the comparison with the reference sequences. [Resull] The con- tents of A, G, C and T nucleotides in the D-loop region of Xinjiang Goose were 28.85%, 17.05%, 25.38% and 28.72%, respectively. The average haplotype diversity and nucleotide diversity of Xinjiang Goose were 0.583 and 0.056. Xinjiang Goose and Greylag Goose were clustered into the same group. [Conclusion] The results showed that Xinjiang Geese with three different colors of plumage all descend from Greylag Goose (Anser anser).展开更多
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 g...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.展开更多
AIM: To design a novel method to rapidly detect the quantitative alteration of mtRNA in patients with tumors.METHODS: Oligo 6.22 and Primer Premier 5.0 bio-soft were used to design 15 pairs of primers of mtRNA cDNA pr...AIM: To design a novel method to rapidly detect the quantitative alteration of mtRNA in patients with tumors.METHODS: Oligo 6.22 and Primer Premier 5.0 bio-soft were used to design 15 pairs of primers of mtRNA cDNA probes in light of the functional and structural property of mtDNA, and then RT-PCR amplification was used to produce 15 probes of mtRNA from one normal gastric mucosal tissue. Total RNA extracted from 9 gastric cancers and corresponding normal gastric mucosal tissues was reverse transcribed into cDNA labeled with fluorescein. The spotted mtDNA microarrays were made and hybridized. Finally,the microarrays were scanned with a GeneTACTM laser scanner to get the hybridized results. Northern blot was used to confirm the microarray results.RESULTS: The hybridized spots were distinct with clear and consistent backgrounds. After data was standardized according to the housekeeping genes, the results showed that the expression levels of some mitochondrial genes in gastric carcinoma were different from those in the corresponding non-cancerous regions.CONCLUSION: The mtDNA expression microarray can rapidly, massively and exactly detect the quantity of mtRNA in tissues and cells. In addition, the whole expressive information of mtRNA from a tumor patient on just one slide can be obtained using this method, providing an effective method to investigate the relationship between mtDNA expression and tumorigenesis.展开更多
Superoxide dismutase (SOD) is one of the most important antioxidant defense enzymes, and is considered as the first line against oxidative stress. In this study, we cloned a mitochondrial manganese (Mn) SOD (mMn...Superoxide dismutase (SOD) is one of the most important antioxidant defense enzymes, and is considered as the first line against oxidative stress. In this study, we cloned a mitochondrial manganese (Mn) SOD (mMnSOD) cDNA from the ridgetail white prawn Exopalaemon carinicauda by using rapid amplification of cDNA ends (RACE) methods. The fulMength cDNA for mMnSOD was 1 014-bp long, containing a 5'-untranslated region (UTR) of 37-bp, a 3'-UTR of 321-bp with a poly (A) tail, and included a 657-bp open reading frame encoding a protein of 218 amino acids with a 16-amino-acid signal peptide. The protein had a calculated molecular weight of 23.87 kDa and a theoretical isoelectric point of 6.75. The mMnSOD sequence included two putative N-glycosylation sites (NHT and NLS), the MnSOD signature sequence 18~DVWEHAYY^87, and four putative Mn binding sites (H48, H96, D180, and H184). Sequence comparison showed that the mMnSOD deduced amino acid sequence of E. carinicauda shared 97%, 95%, 89%, 84%, 82%, 72%, and 69% identity with that ofMacrobrachium rosenbergii, Macrobrachium nipponense, Fenneropeneaus chinensis, Callinectes sapidus, Perisesarma bidens, Danio rerio, and Homo sapiens, resectively. Quantitative real-time RT-PCR analysis showed that mMnSOD transcripts were present in all E. carinicauda tissues examined, with the highest levels in the hepatopancreas. During an ammonia stress treatment, the transcript levels of mMnSOD and cMnSOD were up-regulated at 12 h in hemocytes and at 24 h in the hepatopancreas. As the duration of the ammonia stress treatment extended to 72 h, the transcript levels of mMnSOD and cMnSOD significantly decreased both in hemocytes and hepatopancreas. These findings indicate that the SOD system is induced to respond to acute ammonia stress, and may be involved in environmental stress responses in E. carinicauda.展开更多
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 17,8...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.展开更多
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 sequen...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.展开更多
AIM:To investigate the effect of α-mangostin on the growth and apoptosis induction of human colon cancer cells.METHODS:The three colorectal adenocarcinoma cell lines tested (COLO 205,MIP-101 and SW 620) were treated ...AIM:To investigate the effect of α-mangostin on the growth and apoptosis induction of human colon cancer cells.METHODS:The three colorectal adenocarcinoma cell lines tested (COLO 205,MIP-101 and SW 620) were treated with α-mangostin to determine the effect on cell proliferation by MTT assay,cell morphology,chromatin condensation,cell cycle analysis,DNA fragmentation,phosphatidylserine exposure and changing of mitochondrial membrane potential.The molecular mechanisms of α-mangostin mediated apoptosis were further investigated by Western blotting analysis including activation of caspase cascade,cytochrome c release,Bax,Bid,p53 and Bcl-2 modifying factor.RESULTS:The highest inhibitory effect of α-mangostin on cell proliferation of COLO 205,MIP-101 and SW 620 were 9.74 ± 0.85 μg/mL,11.35 ± 1.12 μg/mL and 19.6 ± 1.53 μg/mL,respectively.Further study showed that α-mangostin induced apoptotic cell death in COLO 205 cells as indicated by membrane blebbing,chromatin condensation,DNA fragmentation,cell cycle analysis,sub-G1 peak (P < 0.05) and phosphatidylserine exposure.The executioner caspase,caspase-3,the initiator caspase,caspase-8,and caspase-9 were expressed upon treatment with α-mangostin.Further studies of apoptotic proteins were determined by Western blotting analysis showing increased mitochondrial cytochrome c release,Bax,p53 and Bmf as well as reduced mitochondrial membrane potential (P < 0.05).In addition,up-regulation of tBid and Fas were evident upon treatment with α-mangostin (P < 0.01).CONCLUSION:α-Mangostin may be effective as an anti-cancer agent that induced apoptotic cell death in COLO 205 via a link between extrinsic and intrinsic pathways.展开更多
AIM: To evaluate the effect of mitochondrial tumor ne- crosis factor receptor-associated protein-1 (TRAP-l) on the lymph node metastasis (LNM) in Chinese colorectal cancer (CRC) patients, and develop potential ...AIM: To evaluate the effect of mitochondrial tumor ne- crosis factor receptor-associated protein-1 (TRAP-l) on the lymph node metastasis (LNM) in Chinese colorectal cancer (CRC) patients, and develop potential LNM- associated biomarkers for CRC using quantitative real- time polymerase chain reaction (RT-PCR) analysis. METHODS: Differences in mitochondrial TRAP-1 gene expression between primary CRC with LNM (LNM CRC) and without LNM (non-LNM CRC) were assessed in 96 Chinese colorectal carcinoma samples using quantita- tive RT-PCR analysis, Western blotting, and confirmed with immunohistochemical assay. The relationship between clinicopathological parameters and potential diaclnostic biomarkers was also examined.RESULTS: TRAP-1 was significantly upregulated in LNM CRC compared with non-LNM CRC, which was confirmed by RT-PCR, Western blotting and immuno- histochemical assay. The expression of TRAP-1 in two different metastatic potential human colorectal cancer cell lines, LoVo and HT29, was analyzed with Western blotting. The expression level of TRAP-1 was dramati- cally higher in LoVo than in HT29. Overexpression of TRAP-1 was significantly associated with LNM (90.2% in LNM group vs 22% in non-LNM group, P 〈 0.001), the advanced tumor node metastasis stage (89.1% in LNM group vs 26.9% in non-LNM group, P 〈 0.001), the increased 5-year recurrence rate (82.7% in LNM group vs 22.6% in non-LNM group, P 〈 0.001) and the decreased 5-year overall survival rate (48.4% in LNM vs 83.2% in non-LNM group, P 〈 0.001). Univariate and multivariate analyses indicated that TRAP-1 expression was an independent prognostic factor for recurrence and survival of CRC patients (Hazard ratio of 2.445 in recurrence, P = 0.017; 2.867 in survival, P = 0.028). CONCLUSION: Mitochondria TRAP-1 affects the lymph node metastasis in CRC, and may be a potential bio- marker for LNM and a prognostic factor in CRC. Over- expression of TRAP-1 is a predictive factor for the poor outcome of colorectal cancer patients. 2012 Baishideng. All rights reserved展开更多
AIM: To study genetic difference of mitochondrial DMA (mtDNA) between two hepatocarcinoma cell lines (Hca-F and Hca-P) with diverse metastatic characteristics and the relationship between mtDNA changes in cancer cells...AIM: To study genetic difference of mitochondrial DMA (mtDNA) between two hepatocarcinoma cell lines (Hca-F and Hca-P) with diverse metastatic characteristics and the relationship between mtDNA changes in cancer cells and ttieir oncogenic phenotype. METHODS: Mitochondrial DMA D-loop, tRNAMet+Glu+Ile and ND3 gene fragments from the hepatocarcinoma cell lines with 1100,1126 and 534 bp in length respectively were analysed by PCR amplification and restriction fragment length polymorphism techniques. The D-loop 3′ end sequence of the hepatocarcinoma cell lines was determined by sequencing. RESULTS: No amplification fragment length polymorphism and restriction fragment length polymorphism were observed in tRNAMet+Glu+Ile, ND3 and D-loop of mitochondrial DNA of the hepatocarcinoma cells. Sequence differences between Hca-F and Hca-P were found in mtDNA D-loop. CONCLUSION: Deletion mutations of mitochondrial DNA restriction fragment may not play a significant role in carcinogenesis. Genetic difference of mtDNA D-loop between Hca-F and Hca-P, which may reflect the environmental and genetic influences during tumor progression, could be linked to their tumorigenic phenotypes.展开更多
Japanese butterfly ray Gymnura japonica from twinspot butterfly ray G. bimaculata based on a pair of white spots behind eyes or not, which was not reliable. To clarify the taxonomic status of G. japonica and G. bimacu...Japanese butterfly ray Gymnura japonica from twinspot butterfly ray G. bimaculata based on a pair of white spots behind eyes or not, which was not reliable. To clarify the taxonomic status of G. japonica and G. bimaculata, the nucleotide variation between the two butterfly rays was examined using mitochondrial DNA sequence comparisons. Approximately 585 bp of 16S ribosomal RNA (rRNA) and 1,128 bp cytochrome b (cyt b) genes were sequenced from representatives of two butterfly rays species in East China Sea. The results showed that there were the same sequences of 16S rRNA gene between two butterfly rays; six sites were variable among two butterfly rays of cyt b genes, the proportion of polymorphie loci was 0.53%, and two haplotypes were defined which genetic distance was 0.5%. Combined with the morphological character and the analysis of mtDNA sequence indicated that twinspot butterfly ray G. bimaculata was a synonym of Japanese butterfly ray G. japonica.展开更多
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 an...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 .展开更多
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 sys...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.展开更多
Seoul virus(SEOV), which is predominantly carried by Rattus norvegicus, is one of the major causes of hemorrhagic fever with renal syndrome(HFRS) in China. Hubei province, located in the central south of China, has ex...Seoul virus(SEOV), which is predominantly carried by Rattus norvegicus, is one of the major causes of hemorrhagic fever with renal syndrome(HFRS) in China. Hubei province, located in the central south of China, has experienced some of the most severe epidemics of HFRS. To investigate the mitochondrial DNA(mt DNA)-based phylogenetics of wild rats in Hubei, and the relationship with SEOV infection, 664 wild rats were captured from five trapping sites in Hubei from2000–2009 and 2014–2015. Using reverse-transcription(RT)-PCR, 41(6.17%) rats were found to be positive for SEOV infection. The SEOV-positive percentage in Yichang was significantly lower than that in other areas. The mt DNA D-loop and cytochrome b(cyt-b) genes of 103 rats were sequenced.Among these animals, 37 were SEOV-positive. The reconstruction of the phylogenetic relationship(based on the complete D-loop and cyt-b sequences) allowed the rats to be categorized into two lineages, R. norvegicus and Rattus nitidus, with the former including the majority of the rats. For both the D-loop and cyt-b genes, 18 haplotypes were identified. The geographic distributions of the different haplotypes were significantly different. There were no significant differences in the SEOVpositive percentages between different haplotypes. There were three sub-lineages for the D-loop,and two for cyt-b. The SEOV-positive percentages for each of the sub-lineages did not significantly differ. This indicates that the SEOV-positive percentage is not related to the mt DNA D-loop or cyt-b haplotype or the sub-lineage of rats from Hubei.展开更多
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 4...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].展开更多
Nineteen taxa representing 10 genera of Sisoridae were subjected to phylogenetic analyses of sequence data for the nuclear genes Plagl2 and ADNP and the mitochondrial gene cytochrome b. The three data sets were analyz...Nineteen taxa representing 10 genera of Sisoridae were subjected to phylogenetic analyses of sequence data for the nuclear genes Plagl2 and ADNP and the mitochondrial gene cytochrome b. The three data sets were analyzed separately and combined into a single data set to reconstruct phylogenetic relationships among Chinese sisorids. Both Chinese Sisoridae as a whole and the glyptosternoid taxa formed monophyletic groups. The genus Pseudecheneis is likely to be the earliest diverging extant genus among the Chinese Sisoridae. The four Pareuchiloglanis species included in the study formed a monophyletic group. Glaridoglanis was indicated to be earliest diverging glyptosternoid, followed by Glyptosternon maculatum and Exostoma labiatum. Our data supported the conclusion that Oreoglanis and Pseudexostoma both formed a monophyletic group. On the basis of the fossil record and the results of a molecular dating analysis, we estimated that the Sisoridae diverged in the late Miocene about 12.2 Mya. The glyptosternoid clade was indicated to have diverged, also in the late Miocene, about 10.7 Mya, and the more specialized glyptosternoid genera, such as Pareuchiloglanis, originated in the Pleistocene (within 1.9 Mya). The speciation of glyptosternoid fishes is hypothesized to be closely related with the uplift of the Qinghai-Tibet Plateau.展开更多
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...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.展开更多
文摘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.
文摘[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.
基金Supported by the Fond for Open Projects of Xinjiang Key Laboratory of Herbivore Nutrition for Meat&Milk Production~~
文摘[Objective] The sequences of mitochondrial DNA D-loop region of Xinjiang Goose with three different colors of plumage were analyzed in order to study the genetic diversity of Xinjiang Goose, as well as the phylogeny and evolution. [Method] Ten geese were selected randomly from the core populations of grey-, mosaic- and white-plumaged Xinjiang Goose respectively with a total number of thirty as experi- mental materials, of which the blood samples were collected from the largest vein under the wing (brachial vein) for DNA extraction. Sequences of mitochondrial DNA D-loop regions were determined using DNA sequencing technology to analyze the polymorphism. In addition, the genetic distances among different populations were estimated through the comparison with the reference sequences. [Resull] The con- tents of A, G, C and T nucleotides in the D-loop region of Xinjiang Goose were 28.85%, 17.05%, 25.38% and 28.72%, respectively. The average haplotype diversity and nucleotide diversity of Xinjiang Goose were 0.583 and 0.056. Xinjiang Goose and Greylag Goose were clustered into the same group. [Conclusion] The results showed that Xinjiang Geese with three different colors of plumage all descend from Greylag Goose (Anser anser).
基金National Natural Science Foundation of China (30370218)the program for New Century Excellent Talents in University (NCET-07-0507)+1 种基金 the Project of Science and Technology Development Plan in Shandong Province (2007GG2009011)Shandong Science Fund for Distinguished Young Scholars (2005BS02005)
文摘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.
基金Supported by the National Natural Science Foundation of China,No.30371607
文摘AIM: To design a novel method to rapidly detect the quantitative alteration of mtRNA in patients with tumors.METHODS: Oligo 6.22 and Primer Premier 5.0 bio-soft were used to design 15 pairs of primers of mtRNA cDNA probes in light of the functional and structural property of mtDNA, and then RT-PCR amplification was used to produce 15 probes of mtRNA from one normal gastric mucosal tissue. Total RNA extracted from 9 gastric cancers and corresponding normal gastric mucosal tissues was reverse transcribed into cDNA labeled with fluorescein. The spotted mtDNA microarrays were made and hybridized. Finally,the microarrays were scanned with a GeneTACTM laser scanner to get the hybridized results. Northern blot was used to confirm the microarray results.RESULTS: The hybridized spots were distinct with clear and consistent backgrounds. After data was standardized according to the housekeeping genes, the results showed that the expression levels of some mitochondrial genes in gastric carcinoma were different from those in the corresponding non-cancerous regions.CONCLUSION: The mtDNA expression microarray can rapidly, massively and exactly detect the quantity of mtRNA in tissues and cells. In addition, the whole expressive information of mtRNA from a tumor patient on just one slide can be obtained using this method, providing an effective method to investigate the relationship between mtDNA expression and tumorigenesis.
基金Supported by the National High Technology Research and Development Program of China(863 Program)(No.2012AA10A409)the Modern AgroIndustry Technology Research System(No.CARS-47)+1 种基金the Special Fund for Independent Innovation of Shandong Province(No.2013CX80202)the Special Fund for Agro-Scientific Research in the Public Interest(No.201103034)
文摘Superoxide dismutase (SOD) is one of the most important antioxidant defense enzymes, and is considered as the first line against oxidative stress. In this study, we cloned a mitochondrial manganese (Mn) SOD (mMnSOD) cDNA from the ridgetail white prawn Exopalaemon carinicauda by using rapid amplification of cDNA ends (RACE) methods. The fulMength cDNA for mMnSOD was 1 014-bp long, containing a 5'-untranslated region (UTR) of 37-bp, a 3'-UTR of 321-bp with a poly (A) tail, and included a 657-bp open reading frame encoding a protein of 218 amino acids with a 16-amino-acid signal peptide. The protein had a calculated molecular weight of 23.87 kDa and a theoretical isoelectric point of 6.75. The mMnSOD sequence included two putative N-glycosylation sites (NHT and NLS), the MnSOD signature sequence 18~DVWEHAYY^87, and four putative Mn binding sites (H48, H96, D180, and H184). Sequence comparison showed that the mMnSOD deduced amino acid sequence of E. carinicauda shared 97%, 95%, 89%, 84%, 82%, 72%, and 69% identity with that ofMacrobrachium rosenbergii, Macrobrachium nipponense, Fenneropeneaus chinensis, Callinectes sapidus, Perisesarma bidens, Danio rerio, and Homo sapiens, resectively. Quantitative real-time RT-PCR analysis showed that mMnSOD transcripts were present in all E. carinicauda tissues examined, with the highest levels in the hepatopancreas. During an ammonia stress treatment, the transcript levels of mMnSOD and cMnSOD were up-regulated at 12 h in hemocytes and at 24 h in the hepatopancreas. As the duration of the ammonia stress treatment extended to 72 h, the transcript levels of mMnSOD and cMnSOD significantly decreased both in hemocytes and hepatopancreas. These findings indicate that the SOD system is induced to respond to acute ammonia stress, and may be involved in environmental stress responses in E. carinicauda.
基金supported by the National Natural Science Foundation of China(31201745,31071954 and 31572311)
文摘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.
基金Supported by the Youth Science Foundation of the State Oceanic Administration (No. 2009106)the Directorate Foundation of South China Sea Branch, the State Oceanic Administration (No. 0815)
文摘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.
基金Supported by The Thailand Research Fund,Grant No. RMU 4980043
文摘AIM:To investigate the effect of α-mangostin on the growth and apoptosis induction of human colon cancer cells.METHODS:The three colorectal adenocarcinoma cell lines tested (COLO 205,MIP-101 and SW 620) were treated with α-mangostin to determine the effect on cell proliferation by MTT assay,cell morphology,chromatin condensation,cell cycle analysis,DNA fragmentation,phosphatidylserine exposure and changing of mitochondrial membrane potential.The molecular mechanisms of α-mangostin mediated apoptosis were further investigated by Western blotting analysis including activation of caspase cascade,cytochrome c release,Bax,Bid,p53 and Bcl-2 modifying factor.RESULTS:The highest inhibitory effect of α-mangostin on cell proliferation of COLO 205,MIP-101 and SW 620 were 9.74 ± 0.85 μg/mL,11.35 ± 1.12 μg/mL and 19.6 ± 1.53 μg/mL,respectively.Further study showed that α-mangostin induced apoptotic cell death in COLO 205 cells as indicated by membrane blebbing,chromatin condensation,DNA fragmentation,cell cycle analysis,sub-G1 peak (P < 0.05) and phosphatidylserine exposure.The executioner caspase,caspase-3,the initiator caspase,caspase-8,and caspase-9 were expressed upon treatment with α-mangostin.Further studies of apoptotic proteins were determined by Western blotting analysis showing increased mitochondrial cytochrome c release,Bax,p53 and Bmf as well as reduced mitochondrial membrane potential (P < 0.05).In addition,up-regulation of tBid and Fas were evident upon treatment with α-mangostin (P < 0.01).CONCLUSION:α-Mangostin may be effective as an anti-cancer agent that induced apoptotic cell death in COLO 205 via a link between extrinsic and intrinsic pathways.
基金Supported by The Grants from Shanghai Health Bureau,No.JG1103
文摘AIM: To evaluate the effect of mitochondrial tumor ne- crosis factor receptor-associated protein-1 (TRAP-l) on the lymph node metastasis (LNM) in Chinese colorectal cancer (CRC) patients, and develop potential LNM- associated biomarkers for CRC using quantitative real- time polymerase chain reaction (RT-PCR) analysis. METHODS: Differences in mitochondrial TRAP-1 gene expression between primary CRC with LNM (LNM CRC) and without LNM (non-LNM CRC) were assessed in 96 Chinese colorectal carcinoma samples using quantita- tive RT-PCR analysis, Western blotting, and confirmed with immunohistochemical assay. The relationship between clinicopathological parameters and potential diaclnostic biomarkers was also examined.RESULTS: TRAP-1 was significantly upregulated in LNM CRC compared with non-LNM CRC, which was confirmed by RT-PCR, Western blotting and immuno- histochemical assay. The expression of TRAP-1 in two different metastatic potential human colorectal cancer cell lines, LoVo and HT29, was analyzed with Western blotting. The expression level of TRAP-1 was dramati- cally higher in LoVo than in HT29. Overexpression of TRAP-1 was significantly associated with LNM (90.2% in LNM group vs 22% in non-LNM group, P 〈 0.001), the advanced tumor node metastasis stage (89.1% in LNM group vs 26.9% in non-LNM group, P 〈 0.001), the increased 5-year recurrence rate (82.7% in LNM group vs 22.6% in non-LNM group, P 〈 0.001) and the decreased 5-year overall survival rate (48.4% in LNM vs 83.2% in non-LNM group, P 〈 0.001). Univariate and multivariate analyses indicated that TRAP-1 expression was an independent prognostic factor for recurrence and survival of CRC patients (Hazard ratio of 2.445 in recurrence, P = 0.017; 2.867 in survival, P = 0.028). CONCLUSION: Mitochondria TRAP-1 affects the lymph node metastasis in CRC, and may be a potential bio- marker for LNM and a prognostic factor in CRC. Over- expression of TRAP-1 is a predictive factor for the poor outcome of colorectal cancer patients. 2012 Baishideng. All rights reserved
基金Supported by the National Natural Science Foundation of China, No. 39900173
文摘AIM: To study genetic difference of mitochondrial DMA (mtDNA) between two hepatocarcinoma cell lines (Hca-F and Hca-P) with diverse metastatic characteristics and the relationship between mtDNA changes in cancer cells and ttieir oncogenic phenotype. METHODS: Mitochondrial DMA D-loop, tRNAMet+Glu+Ile and ND3 gene fragments from the hepatocarcinoma cell lines with 1100,1126 and 534 bp in length respectively were analysed by PCR amplification and restriction fragment length polymorphism techniques. The D-loop 3′ end sequence of the hepatocarcinoma cell lines was determined by sequencing. RESULTS: No amplification fragment length polymorphism and restriction fragment length polymorphism were observed in tRNAMet+Glu+Ile, ND3 and D-loop of mitochondrial DNA of the hepatocarcinoma cells. Sequence differences between Hca-F and Hca-P were found in mtDNA D-loop. CONCLUSION: Deletion mutations of mitochondrial DNA restriction fragment may not play a significant role in carcinogenesis. Genetic difference of mtDNA D-loop between Hca-F and Hca-P, which may reflect the environmental and genetic influences during tumor progression, could be linked to their tumorigenic phenotypes.
文摘Japanese butterfly ray Gymnura japonica from twinspot butterfly ray G. bimaculata based on a pair of white spots behind eyes or not, which was not reliable. To clarify the taxonomic status of G. japonica and G. bimaculata, the nucleotide variation between the two butterfly rays was examined using mitochondrial DNA sequence comparisons. Approximately 585 bp of 16S ribosomal RNA (rRNA) and 1,128 bp cytochrome b (cyt b) genes were sequenced from representatives of two butterfly rays species in East China Sea. The results showed that there were the same sequences of 16S rRNA gene between two butterfly rays; six sites were variable among two butterfly rays of cyt b genes, the proportion of polymorphie loci was 0.53%, and two haplotypes were defined which genetic distance was 0.5%. Combined with the morphological character and the analysis of mtDNA sequence indicated that twinspot butterfly ray G. bimaculata was a synonym of Japanese butterfly ray G. japonica.
文摘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 .
基金supported by the National Natural Science Foundation of China (31090254, 30770300 and U1036603)the Chinese Academy of Sciences (KSCX2-EW-Q-12)the endowment of William S. Barnickle, Saint Louis University, St. Louis, Missouri, USA
文摘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.
基金supported by grants from the National Natural Science Foundation of China(81402728,81371865)
文摘Seoul virus(SEOV), which is predominantly carried by Rattus norvegicus, is one of the major causes of hemorrhagic fever with renal syndrome(HFRS) in China. Hubei province, located in the central south of China, has experienced some of the most severe epidemics of HFRS. To investigate the mitochondrial DNA(mt DNA)-based phylogenetics of wild rats in Hubei, and the relationship with SEOV infection, 664 wild rats were captured from five trapping sites in Hubei from2000–2009 and 2014–2015. Using reverse-transcription(RT)-PCR, 41(6.17%) rats were found to be positive for SEOV infection. The SEOV-positive percentage in Yichang was significantly lower than that in other areas. The mt DNA D-loop and cytochrome b(cyt-b) genes of 103 rats were sequenced.Among these animals, 37 were SEOV-positive. The reconstruction of the phylogenetic relationship(based on the complete D-loop and cyt-b sequences) allowed the rats to be categorized into two lineages, R. norvegicus and Rattus nitidus, with the former including the majority of the rats. For both the D-loop and cyt-b genes, 18 haplotypes were identified. The geographic distributions of the different haplotypes were significantly different. There were no significant differences in the SEOVpositive percentages between different haplotypes. There were three sub-lineages for the D-loop,and two for cyt-b. The SEOV-positive percentages for each of the sub-lineages did not significantly differ. This indicates that the SEOV-positive percentage is not related to the mt DNA D-loop or cyt-b haplotype or the sub-lineage of rats from Hubei.
文摘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].
基金supported by the National Natural Science Foundation of China (Grant No. 31090254)
文摘Nineteen taxa representing 10 genera of Sisoridae were subjected to phylogenetic analyses of sequence data for the nuclear genes Plagl2 and ADNP and the mitochondrial gene cytochrome b. The three data sets were analyzed separately and combined into a single data set to reconstruct phylogenetic relationships among Chinese sisorids. Both Chinese Sisoridae as a whole and the glyptosternoid taxa formed monophyletic groups. The genus Pseudecheneis is likely to be the earliest diverging extant genus among the Chinese Sisoridae. The four Pareuchiloglanis species included in the study formed a monophyletic group. Glaridoglanis was indicated to be earliest diverging glyptosternoid, followed by Glyptosternon maculatum and Exostoma labiatum. Our data supported the conclusion that Oreoglanis and Pseudexostoma both formed a monophyletic group. On the basis of the fossil record and the results of a molecular dating analysis, we estimated that the Sisoridae diverged in the late Miocene about 12.2 Mya. The glyptosternoid clade was indicated to have diverged, also in the late Miocene, about 10.7 Mya, and the more specialized glyptosternoid genera, such as Pareuchiloglanis, originated in the Pleistocene (within 1.9 Mya). The speciation of glyptosternoid fishes is hypothesized to be closely related with the uplift of the Qinghai-Tibet Plateau.
基金supported by grants from the National Natural Science Foundation of China (Nos.30825006,30970394)the Doctoral Program of Higher Education of China(No. 200800190015)
文摘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.