Gene characterization and phylogenetic analysis of four mitochondrial genomes in Caenogastropoda

Caenogastropoda is a highly diverse group,containing~60%of all existing gastropods.Species in this subclass predominantly inhabit marine environments and have a high ecological and economic value.Owing to the increase in relevant phylogenetic studies,our understanding of between species relatedness in Caenogastropoda has improved.However,the biodiversity,taxonomic status,and phylogenetic relationships of this group remain unclear.In the present study,we performed next-generation sequencing of four complete mitochondrial genomes from three families(Buccinidae,Columbellidae,and Cypraeidae)and the four mitogenomes were classical circular structures,with a length of 16177 bp in Volutharpa ampullacea,16244 bp in Mitrella albuginosa,16926bp in Mauritia arabica asiatica and 15422 bp in Erronea errones.Base composition analysis indicated that whole sequences were biased toward A and T.Then compared them with 171 complete mitochondrial genomes of Caenogastropoda.The phylogenetic relationship of Caenogastropoda derived from Maximum Likelihood(ML)and Bayesian Inference(BI)trees constructed based on CDS sequences was consistent with the results of traditional morphological analysis,with all three families showing close relationships.This study supported Caenogastropoda at the molecular level as a separate clade of Mollusca.According to our divergence time estimations,Caenogastropoda was formed during the middle Triassic period(~247.2–237 Ma).Our novel mitochondrial genomes provide evidence for the speciation of Caenogastropoda in addition to elucidating the mitochondrial genomic evolution of this subclass.

Phylogenetic Analysis of Actinomycete Isolates from Iron Mine Tailings

[Objective]The aim was to discuss the actinomycete biodiversity of iron-mine tailings by phylogenetic analysis of 12 typical isolates. [Method]The genomic DNAs were extracted by phenol-chloroform method; phylogeny analysis was carried out based on 16S rDNA PCR amplification and sequencing. [Result]The results showed that all the 12 strains belong to the genus Streptomyces sharing 98.7%-99.9% similarities with their nearest known neighbors. [Conclusion]Streptomyces is the dominant culturable actinomycete group of iron mine tailings,in which there are many potential novel species.

Phylogenetic Analysis of Cystatin

[Objective] The molecular weight,isoelectric point,signal peptide,domain and other properties of the encoding protein of the known cystatin genes were analyzed.[Method] Cystatin genes were searched in NCBI and the related amino acids sequences were downloaded.SMART software was used to predict the domain.SingalP program was used to search signal peptide.TMHMM program was used to search and predict the transmembrane domain.CLUSTAL W program was used to make multiple sequence alignment.Using MEGA3.1 software,...

Isolation and Phylogenetic Analysis of Plant Pathogen-Inhibiting Strains from Southern Ocean

[Objective] The aim was to isolate the strains resistant to plant pathogenic fungi from Southern Ocean and study their phylogenetic relationship and antimicrobial spectrum. [Method] Agar diffusion method was adopted to screen antimicrobial strains and determine the antimicrobial spectrum. Phylogenetic relationship of the strains was analyzed by neighbor-joining method of the Mega 4.0 software. [Result] Twenty antimicrobial strains were screened from seawater of Southern Ocean collected during the 27^th Chinese Antarctic Scientific Expedition. Molecular identification and phyloge- netic analysis indicated that two antimicrobial strains were members of Pseu- domonas, two strains were members of Psychrobacter, and the other 16 trains were members of Pseudoalteromonas. The antimicrobial spectrum of four strains which had higher antimicrobial activity indicated that the strains 312, 83-1 and 195 greatly inhibited the growth of Fusarium oxysporum, Rhizoctonia solani K（Jhn, Phytophthora capsici Leonian, Verticillium dahliae, Alternaria solani, Thanatephoru scucumeris and Phomopsis asparagi （Sacc）; strain 312-1 had obvious antimicrobial effect on the six of the plant pathogens except R. solani. [Conclusion] Four strains which had higher antimicrobial effect were obtained and should be further studied for development and application.

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.

Cloning and Phylogenetic Analysis of NS1 Genes from Different Isolates of H9N2 Subtype Duck Influenza Virus

[ Objective] The study aimed to lay a foundation for the further studies on function mechanism of NS1 protein in the interspecies transmission of waterfowl influenza virus. [Method] Using the serologic assay and the specific RT-PCR method, some strains of H9 subtype waterfowl influenza virus were isolated from the 12 to 20 day-old muscovy duck flocks without any clinical symptoms in different areas of Guangdong Province. Four of these strains, including A/duck/ZQ/303/2007（H9N2） （A3 for short）, A/Duck/FJ/301/2007 （H9N2） （C1 for short）, A/Duck/NH/306/2007（H9N2） （ D6 for short）, A/duck/SS/402/2007（H9N2） （ E2 for short）, and a strain named A/duck/ZC/2007（H9N2） （L1 for short） from a muscovy duck died of avian influenza virus （AIV）, were used for NSl gene cloning and sequencing. Subsequently, the obtained NSl gene sequences were compared with other NS1 sequences registered in GenBank, and the phylogenetic analysis was also conducted. [Result] When compared with the H9N2 AIV NS1 sequences in GenBank, the NSl genes of the four AIV strains A3, C1, 136 and E2 displayed homologies ranging from 99% to 100% at nucleotide level, and 95% to 100% at amino acid level; while the NSl gene of L1 strain displayed homology ranging from 94% to 97% at nucleotide level, and 93% to 98% at amino acid level. The phylogenetic tree demonstrated that A3, C1, D6 and E2 were highly resemblant, and L1 was closest to AY66473 （chicken, 2003）. By comparison with the NS1 gene sequences of L1, AF523514 （duck）, AY664743 （chicken） and EF155262.1 （quail） using DNAstar, A3, C1, D6 and E.2 presented nucleotide variations at site 21 （ R→Q）, 70, 71 （ KE→EG）, 86 （ A→S）, 124 （V→M） and 225 （ S→N）, and amino acid variations at site 21,70, 71 and 86 in dsRNA- dependent protein kinase （PKR） binding domain of NSl gene, which induced the evident variations of antigenic determinant and surface proba- bility plot of NS1 protein. [ Conclusion] This study suggested that the amino acid sequence variation in PKR binding domain of NS1 protein had something to do with the virus pathogenicity.

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.

Identification and Phylogenetic Analysis of an Orf Virus Isolated from an Outbreak in Boer Goat in Shanxi Province

To identify and analyze the Orf virus in Shanxi Province, China, an Orf virus strain was successfully isolated from crust materials of boer goat with clinical sore mouth symptom from a goat farm of Shanxi Province by passaging in lamb testis （LT）. The Orf virus was identified by enzyme linked immunosorbent assay （ELISA） test, recurrent infection test, transmission electron microscopy, and PCR. The nucleotide and amino acid sequences of two genes of the Orf virus were analyzed. The results showed that under the electron microscopy the virus had a presence of typical parapoxvirus virions and there were many eosinophilic intracytoplasmic inclusions observed by hematoxylin-eosin （H＆E） stain. In ELISA test, optical density （OD） readings of the sample showed a positive result, and the rabbits infected with the virus showed a typically Orf virus-infected appearance. All these findings proved that the sample was an Orf virus. The phylogenetic studies of Orf B2L and Orf F1L genes showed that the virus clustered in different branches and were closer to the Orf virus Nantou （DQ904351） and the OV-SA00 isolates （AY386264）. Furthermore, the above results may provide some insight into the genotype of the etiological agent responsible for the Orf outbreak in Shanxi Province, and could also provide a comparative view of the B2L and F1L genes of parapoxvirus.

A survey on porcine circovirus type 2 infection and phylogenetic analysis of its ORF2 gene in Hangzhou,Zhejiang Province,China

Porcine circovirus type 2 (PCV2) is closely related to the postweaning multisystemic wasting syndrome (PMWS). In this study, the pig serum and tissue samples collected from different regions of Hangzhou District in Zhejiang Province of China between 2003 and 2005 were analyzed by enzyme-linked immunosorbent assay (ELISA) for PCV2 antibody and by polymerase chain reaction (PCR) for ORF2 gene. The results show that out of 1250 randomly collected serum samples, 500 sera (40%) were seropositive for PCV2. PCR results demonstrate that Hangzhou PCV2 with more than 50% Chinese PCV2 strains and French PCV2 formed Cluster A. Only one PCV2 from Hangzhou belonged to Cluster B with some other Chinese PCV2 and Netherlands’s isolates. Cluster C consisted of PCV2 isolates from China, US, Canada, UK and Germany. The results indicate that the PCV2 infection was widespread in Hangzhou.

Cloning and characterization of an actin gene of Chlamys farreri and the phylogenetic analysis of mollusk actins

An actin gene (CfACT1) was cloned by using RT-PCR, 3’and 5’RACE from hemocytes of the sea scallop Chlamys farreri. The full length of the transcript is 1 535 bp, which contains a long 3’ un-translated region of 436bp and 59bp of a 5’ un-translated sequence. The open reading frame encodes a polypeptide of 376 amino acids. Sequence comparisons indicated that CfACT1 is more closely related to vertebrate cytoplasmic actins than muscle types. Phylogenetic analysis showed that molluscan actins could be generally divided into two categories: muscle and cytoplasmic, although both are similar to vertebrate cytoplasmic actins. It was also inferred that different isotypes existed in muscle or cytoplasma in mollusks. The genomic sequence of CfACT1 was cloned and sequenced. Only one intron was detected: it was located between codons 42 and 43 and different from vertebrate actin genes.

Characterization and phylogenetic analysis of a phenanthrene-degrading strain isolated from oil-contaminated soil

Bacterium strain EVA17 was isolated from an oil-contaminated soil, and identified as Sphingomonas sp. based on analysis of 16S rDNA sequence,cellular fatty acid composition and physiological-chemical tests. The salicylate hydroxylase and catechol 2,3-dioxygenase(C23O) were detected in cell-free lysates, suggesting a pathway for phenanthrene catabolism via salicylate and catechol. Alignment showed that both of the C23O and GST genes of the strain EVA17 had high similarity with homologues of strains from genus Sphingomonas. The phylogenetic analysis based on 16S rDNA and C23O gene sequence indicated that EVA17 should be classified into genus Sphingomonas, although the two phylogenetic trees were slightly different from each other. The results of co-amplification and sequence determination indicated that GST gene should be located upstream of the C23O gene.

Phylogenetic Analysis and Expression Patterns of the MAPK Gene Family in Wheat (Triticum aestivum L.)

Mitogen activated protein kinases （MAPK） cascades based on protein phosphorylation play an important role in plant growth and development. In this study, we have identified 15 putative members of the wheat MAPK gene （TaMPK） family through an in silico search of wheat expressed sequence tags （EST） databases based on the presence of amino acid sequence of Arabidopsis and rice MAPKs. Phylogenetic analyses of MAPKs from wheat, rice and Arabidopsis genomes have classified them into seven subgroups （A, B, C, D, E, F, and G）. Using the available EST information as a source of expression data, the MAPK family genes from Triticum aestivum were detected in diverse tissues. Further expression analysis of the MAPKs in NCBI EST database revealed that their transcripts were most abundant in callus （20%）, followed by leaf （12%） and inflorescence （12%）. Most MAPK family genes showed some tissue specificity.

Cloning and Phylogenetic Analysis of Ubiquitinconjugating Enzyme Gene TaUBC4 in Different Wheat Cultivars

[Objective] This study aimed to clone ubiquitin-conjugating enzyme gene TaUBC4 from different wheat cultivars and thus analyze their phylogenetic relationship.[Method] The UBC4 coding sequences were cloned through reverse transcription PCR （RT-PCR） from 21 wheat varieties.After sequencing,the UBC4 sequence in wheat cultivar Zhongguochun （GenBank accession No：M28059） was selected as the reference gene,to analyze the mutation frequency and evolutionary distance in the CDSs and corresponding amino acid sequences of the different wheat cultivars.Moreover,the phylogenetic tree based on the amino acid sequences of these TaUBC4 genes were constructed,involving the homologous sequences of TaUBC4 in eight other monocots.[Result] TaUBC4 sequence was highly conserved because the similarity in DNA sequences of the wheat varieties was over 94％,while that in amino acid sequence was over 96％.And the amino acid sequence difference only can be seen at two sites among some varieties.Phylogenetic tree constructed revealed the evolutionary relationships among these wheat varieties.[Conclusion] This study reveals the polymorphism and evolutionary characteristics in the nucleotide and amino acid sequences in different wheat varieties,which lays foundation for investigating the evolution and biological function of TaUBC4 gene.In addition,the phylogenetic tree constructed provides theoretical references for the classification of the wheat varieties with complicated background.

Sequence and phylogenetic analysis of hemagglutinin genes of H9N2 influenza viruses isolated from chicken in China from 2013 to 2015

H9N2 avian influenza virus（AIV） infection is a major problem in poultry industry worldwide. In this study, molecular characterizations and phylogenetic relationships of hemagglutinin（HA） gene sequences of H9N2 AIV of 5 Chinese isolates in 2014 recently available in Gen Bank, 3 widely used vaccine strains, and 52 novel isolates in China from 2013 to 2015 were analyzed. The homology analysis showed that the nucleotide sequences of HA gene of these recent Chinese H9N2 AIV isolates shared homologies from 94.1 to 99.9%. Phylogenetic analysis showed that all isolates belonged to AIV lineage h9.4.2.5. Fifty-six out of the 57 recent Chinese H9N2 AIV isolates had the motifs PSRSSR↓GLF at the cleavage sites within the HA protein, while one isolate PWH01 harbored LSRSSR↓GLF. Remarkably, all of the recent Chinese H9N2 AIV strains had the Q216 L substitution in the receptor binding site, which indicated that they had potential to infect humans. Most of recent Chinese H9N2 AIV isolates lost the potential N-linked glycosylation site at residues 200–202 compared with vaccine strains. This present study demonstrated that AIV lineage h9.4.2.5 was more predominant in China than other lineages as it harbored all the H9N2 AIV isolated between 2013 and 2015. Also we showed the importance of continuous surveillance of emerging H9N2 AIV in China and update of vaccine formulation accordingly in order to prevent and control H9N2 AIV.

Phylogenetic analysis and arsenate reduction effect of the arsenic-reducing bacteria enriched from contaminated soils at an abandoned smelter site

Microbial reduction of As(V)(i.e.,arsenate)plays an important role in arsenic(As)mobilization in aqueous environment.In this study,we investigated As(V)reduction characteristics of the bacteria enriched from the arsenic-contaminated soil at an abandoned smelter site.It was found that As(V)was completely reduced to As(III)(i.e.,arsenite)in 21 h.After 3-d incubation,a yellow solid was precipitated and the concentration of As(III)decreased sharply.After 150 h incubation,ca.65%of soluble arsenic was removed fro...

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.

Confirmed Diagnosis by RT-PCR and Phylogenetic Analysis of Peste des Petits Ruminants Viruses in Tibet, China

This paper reports the confirmed diagnosis by nested RT-PCR of PPR cases in Tibet, China in 2007, and results of phylogenetic analysis. Results showed that the 11 tested samples were PPRV positive by nested RT-PCR, of which 2 samples were genetically close to the X7443 strain (Nigeria 75/1) of lineage I, and 3 samples close to the strain AY560591 (Sungri96) of linage IV with 96.6%、97.3%、97.6% and 98% nucleotide sequence homogeneity respectively, based on partial sequencing of the F gene from 5 samples and complete sequencing of the N/M/F/H genes from one sample. This study suggested that there are at least 2 origins of PPRV in China.

Characterization of the Complete Mitochondrial Genome of the Hybrid Epinephelus moara♀ × Epinephelus lanceolatus♂,and Phylogenetic Analysis in Subfamily Epinephelinae

This study presents the complete mitochondrial genome of the hybrid Epinephelus moara♀× Epinephelus lanceolatus♂. The genome is 16886 bp in length, and contains 13 protein-coding genes, 2 r RNA genes, 22 t RNA genes, a light-strand replication origin and a control region. Additionally, phylogenetic analysis based on the nucleotide sequences of 13 conserved protein-coding genes using the maximum likelihood method indicated that the mitochondrial genome is maternally inherited. This study presents genomic data for studying phylogenetic relationships and breeding of hybrid Epinephelinae.

Phylogenetic Analysis of Citrus tristeza virus Isolates of Wild Type Citrus in China

The genetic variation and phylogenetic relationships of Citrus tristeza virus （CTV） isolates collected from Chinese wild type citrus were analyzed by comparing the sequences of nine genomic regions （p23, p20, p13, p18, p25, p27, POL, HEL and k17） with the CTV isolates of cultivated citrus from different countries. The results showed that the divergence pattern of genomic RNA of the CTV isolates from wild type citrus was similar to that of other isolates from cultivated citrus, the 3′ proximal region was relatively conserved, and the 5′ proximal region had greater variability. The nine genomic regions of CTV isolates analyzed were found to have been under purifying selection in the evolution process. Phylogenetic analysis showed that the eleven Chinese wild CTV isolates were located at different clades and did not relfect their geographical origins, suggesting genetic diversity among the Chinese wild CTV populations. These results will aid in the understanding of molecular evolution of the Chinese CTV populations.

Properties study and phylogenetic analysis of a bacterial strain with high de-emulsification efficiency

For further practical application, the phylogenetic analysis and de-emulsification properties study of strain XH1 with high de-emulsification efficiency isolated from crude oil contaminated soil in Daqing oil field were conducted with a surfactant-stabilized water-kerosene model emulsion. The factors influencing the de-emulsification efficiency and the generation site of de-emulsification active component of the strain were also investigated. The similarity of 16SrDNA sequences between strain XH1 and Bacillus mojavensis （DQ993678）was 99%. According to the physiological biochemical test, strain XH1 was preliminarily identified as Bacillus mojavensis. The logarithmic growth, stable phase and decline phase of strain XHI were determined as 14, 18 and 28 h, respectively. The best de-emulsification activity emerged after cultivating for 18h, and the complete de-emulsification was achieved at 24 h. The most favorable incubation conditions for de-emulsification occurred with pH of 6. 0 at 30 ℃. The de-emulsification capability of strain XH1 was mainly resulted from extracellular metabolites. The above results indicate that strain XH1 has high de-emulsification efficiency and is potential as a commercial de-emulsifier.