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Docynia longiunguis is a plant uniquely present in China and is of high edible and medicinal value. The analysis of its chloroplast genome will help clarify the phylogenetic relationship among Docynia and facilitate the development and utilization of D. longiunguis resources. Based on the alignment of chloroplast genome sequences of related species, the phylogeny and codon preference were analyzed. The total length of D. longiunguis chloroplast genome sequence was 158 914 bp (GenBank accession number is MW367027), with an average GC content of 36.7%. The length of the large single-copy (LSC), the small single-copy (SSC), and inverted repeats (IRs) are 87 020 bp, 19 156 bp, and 26 369 bp, respectively. A total of 102 functional genes were annotated, including 72 protein-coding genes, 26 tRNA genes, and 4 rRNA genes. The best model for constructing phylogenetic tree was TVM+F+R2. D. longiunguis and Docynia indica were clustered into a single group, while Docynia and Malus were clustered into a single group. Comparison of the chloroplast genome sequences of D. longiunguis and its five related species revealed that trnY (GUA)-psbD, ndhC-trnV (UAC), accD-psaI, psbZ-trnfM (CAU), ndhF-trnL gene regions varied greatly. The nucleic acid diversity analysis showed that there were 11 high variation areas with nucleotide variability > 0.01, all were located in the LSC and SSC regions. Except for D. longiunguis, the trnH genes in other sequences were located at the IRs/LSC junction and did not cross the boundary. Codon preference analysis showed that D. longiunguis chloroplast genome has the largest number of isoleucine (Ile) codons, up to 1 205. D. longiunguis has the closest genetic relationship with Malus baccata, Malus sieboldii, Malus hupehensis and Chaenomeles sinensis. Its chloroplast genome codon prefers to end with A/T. The chloroplast genome of D. longiunguis and other Rosaceae chloroplast genomes showed great differences in gene distribution in four boundary regions, while relatively small differences from the chloroplast genomes of Docynia delavayi and D. indica of the same genus were observed. The genome annotation, phylogenetic analysis and sequence alignment of chloroplast genome of D. longiunguis may facilitate the identification, development and utilization of this species.
Subject(s)
Codon Usage , Genome, Chloroplast , Genomics , Phylogeny , RosaceaeABSTRACT
Objective To study the diagnostic and epidemiological features of the first two HIV-2 indigenous cases in Hunan province.Methods Blood samples from two individuals with "HIV antibody indeterminate" and HIV-2 specific band showed by HIV-1/2 western blotting method,were repeatedly collected and detected under HIV 1 + 2 strip immunoassay and PCR,in Changsha city,Hunan province,through March to November,2017.An epidemiological survey was carried out at the same time.Results Our findings showed that the two cases were sex partners,without histories of sexual contact with foreigners and the source of infection was unknown.Results from the HIV 1 + 2 antibody confirmation test showed that they were "HIV-2 antibody positive".Through amplifying and sequencing the gag area of HIV-2 and BLAST,the similarity of HIV-2 strains presented as 98％.The results also showed that there were HIV-2 specific fragments in the two cases.Conclusion HIV-2 indigenous cases had never been reported in China.These cases had brought new challenge on prevention,diagnosis and treatment of HIV/AIDS in China.
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Objective To study the diagnostic and epidemiological features of the first two HIV-2 indigenous cases in Hunan province.Methods Blood samples from two individuals with "HIV antibody indeterminate" and HIV-2 specific band showed by HIV-1/2 western blotting method,were repeatedly collected and detected under HIV 1 + 2 strip immunoassay and PCR,in Changsha city,Hunan province,through March to November,2017.An epidemiological survey was carried out at the same time.Results Our findings showed that the two cases were sex partners,without histories of sexual contact with foreigners and the source of infection was unknown.Results from the HIV 1 + 2 antibody confirmation test showed that they were "HIV-2 antibody positive".Through amplifying and sequencing the gag area of HIV-2 and BLAST,the similarity of HIV-2 strains presented as 98％.The results also showed that there were HIV-2 specific fragments in the two cases.Conclusion HIV-2 indigenous cases had never been reported in China.These cases had brought new challenge on prevention,diagnosis and treatment of HIV/AIDS in China.
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Objective@#To investigate the HCV genotypes distribution of 107 HIV/HCV co-infection individuals in Hunan province.@*Methods@#HCV antibodies positive plasma samples were collected from HIV-1 antibodies positive plasma bank in Hunan Provincial Center for Disease Control and Prevention and carried out the nucleic acid amplification, the PCR products were used for the HCV genotypes analysis.@*Results@#For 107 samples, 77.5%(83/107) were from intravenous drug users and 25.2%(27/107) were underwent spontaneous clearance of HCV. The HCV genotypes distribution varied greatly in different routes of HIV infection. The non-1/non-2 types exceeded 70% in intravenous drug use and unknown route of transmitted infection populations, while the types 1 and 2 mainly occurred in blood transfusion or aphaeresis plasma populations, accounted for 83.3%. There was no statistical significant differences of immune and liver function among the three groups.@*Conclusions@#Among 107 HIV/HCV co-infection individuals in Hunan province, most of them were intravenous drug users and the distribution of HCV genotypes varied greatly in different routes of HIV infection.
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Objective To explore the association between interleukin 28B (IL-28B),equilibrative nucleoside transporters 1 (ENT1) gene polymorphisms and spontaneous clearance of HCV in HIV/HCV co-infectors in Hunan province.Methods Genotypes of IL-28B and ENT1 (rs12980275,rs12979860,rs8099917 and rs760370) were analyzed in 107 HIV/HCV co-infectors in Hunan province and the distributions of gene polymorphisms were compared between chronic hepatitis and spontaneous clearance groups.Results The major genotypes in rs12980275,rs12979860 and rs8099917 of IL-28B were AA,CC and TT in HIV/HCV co-infectors,which accounted for 84.1％ of each.The three single nucleotide polymorphisms were highly linkage disequilibrium (r2＞0.94) and the differences of genotype distribution were statistically significant between chronic hepatitis and the spontaneous clearance groups (P＜0.05).Infectors which carrying the major genotypes were more susceptible to spontaneous clearance of HCV.Differences of the genotype distributions in rs760370 of ENT1 were not statistically significant between the two groups.Conclusion Genotypes AA,CC and TT of IL-28B were related to spontaneous clearance of HCV in HIV/HCV co-infectors.
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0bjective To establish a standard curve method with more accuracy employed in fluorescence real-time PCR(RT-PCR)as a alternation of the general method.Methods β-actin and KLK11 plasmid DNA for quantitative standard curve were constructed in our study,and Plasmids of β-actin was employed as a internal control.After serial dilution these plasmid were used as DNA standard to obtained slope.Expression of these two genes in malignant prostate cancer cell line LNCAP were tested by real-time PCR,and we analyzed the RT-PCR results with two different methods and compared their accuracy.Results Thestandards curves made from these linear DNA standards showed good linearity (R2=0.991 and 0.992 for β-actin and KLK11 standards graphs),but also displayed a discrepancy in their PCR efficiency(β-actin 123% and KLK11 99%).There were different results after two different stand curve analytical method:the expression of KLK11 mRNA in LNCAP was downregulated in general standard curve method.In the new analytical method,howerer,KLK11 upregnlated for 4.46-fold.And there was a significant difference between aplification efficiency of targt gene and internal control gene(t=4.829,P<0.05).Conclusions Compared with general standard curve method,the new advanced standard curve method described here avoids an error which considers there is identical amplification efficiency between target gene and internal reference gene.It is considered to be a more correct analytical method in fluorescence real-time PCR.
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Objective:To explore the relationship between polymorphism of endothelial nitric oxide synthase(eNOS)gene G894T and coronary heart disease(CAD)in Han Nationlity.Methods:Polymerase chain reaction-restricted fragments length polymorphism(PCR-RFLP)was used to determine the genotype of the eNOS gene G894T in 103 patients with CAD and 104 controls.Results:There was significant difference in frequencies of allele in G894T polymorphism of eNOS gene between CAD and control groups(P=0.029),but there was no significant difference in genotype distribution between two groups.Logistic regression analysis revealed that hypertension,diabete mellitus and smoking history were independent risk factors for the incidence of CAD,but T allele was not.Conclusion:The frequency of eNOS gene G894T mutation in the CAD group is higher than that in the control group and T allele may be related to with the development of CAD.