1.Progress in research of norovirus.
Jia-Dong WANG ; Jun FANG ; Xiao-Hui HAN
Chinese Journal of Virology 2008;24(5):409-413
2.Genome structure and variation of Reynoutria japonica Houtt. chloroplast genome.
Mengtao SUN ; Junxin ZHANG ; Tiran HUANG ; Mingfeng YANG ; Lanqing MA ; Liusheng DUAN
Chinese Journal of Biotechnology 2022;38(5):1953-1964
Reynoutria japonica Houtt., belonging to Polygoneae of Polygonaceae, is a Chinese medicinal herb with the functions of draining dampness and relieving jaundice, clearing heat and detoxifying, dispersing blood stasis and relieving pain, and relieving cough and resolving phlegm. In this study, we carried out high-throughput sequencing for the chloroplast genome sequences of five cultivars of R. japonica and analyzed the genome structure and variations. The chloroplast genomes of the five R. japonica cultivars had two sizes (163 376 bp and 163 371 bp) and a typical circular tetrad structure composed of a large single-copy (LSC) region of 85 784 bp, a small single-copy (SSC) region of 18 616 bp, and a pair of inverted repeat (IR) regions (IRa/IRb) which are spaced apart. A total of 161 genes were obtained by annotation, which consisted of 106 protein-coding genes, 10 rRNA-coding genes, and 45 tRNA-coding genes. The total GC content was 36.7%. Specifically, the GC content in the LSC, SSC, and IR regions were 34.8%, 30.7%, and 42.7%, respectively. Comparison of the whole chloroplast genome among the five cultivars showed that trnk-UUU, rpoC1, petD, rpl16, ndhA, and rpl12 in coding regions had sequence variations. In the phylogenetic tree constructed for the 11 samples of Polygoneae, the five cultivars of R. japonica clustered into one clade near the root and was a sister group of Fallopia multiflora (Thunb.).
Base Composition
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Genome, Chloroplast/genetics*
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Open Reading Frames
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Phylogeny
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Reynoutria
3.The structure and function analysis of duplicate genes in Merlin strains of human cytomegalovirus.
Guang YANG ; Yue-Qin LI ; Yi ZOU ; Xin ZHANG ; Tian-Hong ZHOIU
Chinese Journal of Experimental and Clinical Virology 2011;25(3):194-196
OBJECTIVETo determine the genes in which exist overlapping ORF in Merlin strains of human cytomegalovirus, and to reveal their structure and functional characteristics.
METHODSWe search for overlapping genes of ORF in HCMV Merlin strains' whole genome by Bioinformatics methods, analyzing coding sequence CDS and starting and ending sites of ORF, calculating the length of CDS and ORF, analyzing the molecular weight of encoding protein, overlapping length and coding direction of protein, identifying overlapping sequences and overlapping types, analyzing the expression phase of overlapping genes and the function of proteins.
RESULTSThere were 39 overlapping ORF genes in HCMV Merlin strains, accounting for 23% of total genes. Among these 39 genes, there are 13 IE genes, 9 E genes and 17 L genes, which can be divided into 16 contigs. There are 11 contigs when two genes overlap, with 3 contigs in three genes overlapping, and 2 contigs in four genes overlapping. The functions of overlapping genes are widely.
CONCLUSIONWe found that there are a lot of complex overlapping genes in HCMV Merlin strains, which are basis for further study of the transcription and translation mechanism of overlapping genes.
Computational Biology ; Contig Mapping ; Cytomegalovirus ; genetics ; Genes, Duplicate ; genetics ; Humans ; Open Reading Frames ; genetics
4.Localization of functional domains of HEV ORF1 in cells.
Hui HUANG ; Zi-Zheng ZHENG ; Min ZHAO ; Jing-Xian LI ; Wang-Sheng LAI ; Ji MIAO ; Jun ZHANG ; Ning-Shao XIA
Chinese Journal of Virology 2011;27(3):195-201
To investigate the expression and localization of various functional domains of ORF1 polyprotein and ORF3 protein of hepatitis E virus in host cells, the coding sequences of the various functional domains (RdRp, HEL, MET, PLP, X) of ORF1 were separately cloned into pcDNA3. 1-GFP vectors for constructing the recombinant plasmids which were verified by enzyme digestion and sequencing. The exact expression of the fusion proteins were detected by Western Blot, and the distribution and localization were observed by the laser scanning confocal microscope(LSCM). In huh7 cells, GFP-RdRp proteins were found mainly in the nuclei, GFP-HEL proteins were distributed vesicularly around the nucleus, GFP-MET proteins were distributed granularly both in the nuclei and the cytoplasm, GFP-PLP proteins had polar distribution around the nucleus, and unknown GFP-X proteins were distributed uniformly both in the nuclei and the cytoplasm. Different localization of these proteins verified the previous data obtained from in vitro studies, providing a support for further research on the biological functions of various proteins coded by HEV genome.
Blotting, Western
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Cells, Cultured
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Hepatitis E virus
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genetics
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Humans
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Open Reading Frames
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Viral Proteins
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genetics
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physiology
5.Analysis of ANK1 gene mutation in a family with hereditary spherocytosis type Ⅰ.
Dongliang LI ; Bolun LI ; Suxin LI ; Wenjing LI ; Youjun WANG ; Xiao GUO
Chinese Journal of Medical Genetics 2019;36(10):999-1001
OBJECTIVE:
To detect the disease-causing mutation in a family with hereditary spherocytosis type Ⅰ.
METHODS:
Genomic DNA was extracted from peripheral blood samples of the proband and his relatives. Next-generation sequencing was used to detect the mutations of relevant genes. Suspected pathogenic mutation was verified by Sanger sequencing.
RESULTS:
The proband was found to harbor a novel frameshifting mutation in the coding region of ANK1 gene, which has resulted in abnormal structure or function of the protein. The mutation was confirmed by Sanger sequencing, with both his father and brother found to have carried the same mutation.
CONCLUSION
The c.247delG mutation of proband hereditary spherocytosis typeⅠin this family due to mutation of the ANK1 gene..
Ankyrins
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genetics
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High-Throughput Nucleotide Sequencing
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Humans
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Male
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Mutation
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Open Reading Frames
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Spherocytosis, Hereditary
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genetics
6.Analysis of the chloroplast genome characteristics of Rhus chinensis by de novo sequencing.
Ruihua ZUO ; Ping JIANG ; Chuanbo SUN ; Cunwu CHEN ; Xinjian LOU
Chinese Journal of Biotechnology 2020;36(4):772-781
Rhus chinensis is an important economic species, which could provide raw materials for pharmaceutical and industrial dyes. Rhus chinensis is famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. We report here Rhus chinensis chloroplast genomes by de novo sequencing. The results show that the length of Rhus chinensis was 159 082 bp, exhibiting a typical four-part structure with two single-copy regions (long single copy [LSC] and short single copy [SSC] sections) separated by a pair of inverted repeats (IRs). The length of LSC and SSC was 85 394 bp and 18 663 bp, respectively. The genomes contained 126 genes, including 88 protein encoding genes, 8 rRNA and 30 tRNA genes. In the chloroplast genome, 61.97% of the sequence were gene coding region. In the sequence of gene encoding region, the vast majority of sequences were protein encoding region, accounting for 86.65%, followed by rRNA (10 620 bp, 10.77%) and tRNA (2 540 bp, 2.58%). In Rhus chinensis chloroplast genome, only 8 genes contain introns, all containing 1 intron except ycf3 gene (2 introns). The Rhus chinensis chloroplast genome contains 755 SSR locies. SSR mainly consists of dinucleotide and mononucleotide, accounting for 60% (453) and 28.74% (217) respectively. The clustering results show that Anacardiaceae were closest to Rhus chinensis, followed by Aceraceae and Sapindaceae. This study provides a molecular basis for the classification of Rhus chinensis.
Genome, Chloroplast
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genetics
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Open Reading Frames
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Phylogeny
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Rhus
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classification
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genetics
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Sequence Analysis, DNA
7.Exploration of IRES Elements within the ORF of the Coxsackievirus B3 Genome.
Qin Qin SONG ; Xiao Nuan LUO ; Bing Tian SHI ; Mi LIU ; Juan SONG ; Dong XIA ; Zhi Qiang XIA ; Wen Jun WANG ; Hai Lan YAO ; Jun HAN
Biomedical and Environmental Sciences 2022;35(4):322-333
Objective:
This study aimed to identify internal ribosome entry sites (IRESs) in the open reading frame (ORF) of the Coxsackievirus B3 (CVB3) genome.
Methods:
The sequences of P1, P2, or P3 of the CVB3 genome or the truncated sequences from each antithymocyte globulin (ATG) to the end of the P1, P2, or P3 gene were inserted into the pEGFP-N1 vector. After transfection, possible IRES-dependent green fluorescent protein (GFP)-fused proteins were detected by anti-GFP western blotting. The sequences of possible IRESs were inserted into specific Fluc/Rluc bicistronic vectors, in which the potential IRESs were determined according to the Fluc/Rluc activity ratio. Expression of Fluc and Rluc mRNA of the bicistronic vector was detected by RT-qPCR.
Results:
After transfection of full length or truncated sequences of the P1, P2, or P3 plasmids, six GFP-fused protein bands in P1, six bands in P2 and nine bands in P3 were detected through western blotting. Two IRESs in VP2 (1461-1646 nt) and VP1 (2784-2983 nt) of P1; one IRES in 2C (4119-4564 nt) of P2; and two IRESs in 3C (5634-5834 nt) and 3D (6870-7087 nt) of P3 were identified according to Fluc/Rluc activity ratio. The cryptic promoter was also excluded by RT-qPCR.
Conclusion
Five IRESs are present in the CVB3 coding region.
Internal Ribosome Entry Sites/genetics*
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Open Reading Frames
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RNA, Messenger/genetics*
8.Full sequence analysis and characterization of the Shenzhen Norovirus strain SZ2010422.
Cui-Hong ZHANG ; Jia-Jian QIN ; Ya-Qing HE ; Hai-Long ZHANG ; Hui-Ying LI ; Miao JIN ; Ke-Na CHEN ; Shao-Long FENG ; Zhao-Jun DUAN
Chinese Journal of Experimental and Clinical Virology 2013;27(3):181-183
OBJECTIVETo obtain information on viral molecular structural and evolutionary characteristics, we conducted the SZ2010422 full-length genomic analysis.
METHODSPrimers were designed by New Orleans full sequence, SZ2010422 full genome was amplified by RT-PCR, the whole genome sequence and the capsid domain amino acid sites was analysised after cloned and sequenced.
RESULTSThe genome of G II-4 Norovirus SZ2010422 strain was consist of 7559 bp, it revealed three ORFs composites of the whole genome, ORF1 (5100 bp), ORF2 (1623 bp), ORF3 (807 bp) respectively, ORF1 and ORF2 had 19 nucleotide overlap. By evolutionary comparative analysis found SZ2010422 genomic nucleotide sequences with reference strains of G II-4 New Orleans1805 strains the highest homology with a total length of homology was 99.3%, of ORF1 (99.5%), ORF2 (99.2%), ORF3 (98.6%). Phylogenetic analyses showed SZ2010422 belonging to G II-4 New Orleans variant. Date of 541 amino acid analyses showed: New Orleans variant strains of popular sites: aa310N or K, --> S aa341D --> of N, aa359T--> S, aa396H --> P, aa460H --> Y.
CONCLUSIONNorovirus SZ2010422 belonged to the G II-4 New Orleans variant. In This study, SZ2010422 full sequence can be used not only as a full-length NoV variant sequence standard for future comparison studies, but also as useful material for the public health field by enabling the diagnosis, vaccine development, and prediction of new emerging variants. Noroviruses; Genes; Sequence analysis
China ; Genome, Viral ; Norovirus ; classification ; genetics ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA
9.Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04).
Shengli BI ; E'de QIN ; Zuyuan XU ; Wei LI ; Jing WANG ; Yongwu HU ; Yong LIU ; Shumin DUAN ; Jianfei HU ; Yujun HAN ; Jing XU ; Yan LI ; Yao YI ; Yongdong ZHOU ; Wei LIN ; Hong XU ; Ruan LI ; Zizhang ZHANG ; Haiyan SUN ; Jingui ZHU ; Man YU ; Baochang FAN ; Qingfa WU ; Wei LIN ; Lin TANG ; Baoan YANG ; Guoqing LI ; Wenming PENG ; Wenjie LI ; Tao JIANG ; Yajun DENG ; Bohua LIU ; Jianping SHI ; Yongqiang DENG ; Wei WEI ; Hong LIU ; Zongzhong TONG ; Feng ZHANG ; Yu ZHANG ; Cui'e WANG ; Yuquan LI ; Jia YE ; Yonghua GAN ; Jia JI ; Xiaoyu LI ; Xiangjun TIAN ; Fushuang LU ; Gang TAN ; Ruifu YANG ; Bin LIU ; Siqi LIU ; Songgang LI ; Jun WANG ; Jian WANG ; Wuchun CAO ; Jun YU ; Xiaoping DONG ; Huanming YANG
Genomics, Proteomics & Bioinformatics 2003;1(3):180-192
Beijing has been one of the epicenters attacked most severely by the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) since the first patient was diagnosed in one of the city's hospitals. We now report complete genome sequences of the BJ Group, including four isolates (Isolates BJ01, BJ02, BJ03, and BJ04) of the SARS-CoV. It is remarkable that all members of the BJ Group share a common haplotype, consisting of seven loci that differentiate the group from other isolates published to date. Among 42 substitutions uniquely identified from the BJ group, 32 are non-synonymous changes at the amino acid level. Rooted phylogenetic trees, proposed on the basis of haplotypes and other sequence variations of SARS-CoV isolates from Canada, USA, Singapore, and China, gave rise to different paradigms but positioned the BJ Group, together with the newly discovered GD01 (GD-Ins29) in the same clade, followed by the H-U Group (from Hong Kong to USA) and the H-T Group (from Hong Kong to Toronto), leaving the SP Group (Singapore) more distant. This result appears to suggest a possible transmission path from Guangdong to Beijing/Hong Kong, then to other countries and regions.
Genome, Viral
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Haplotypes
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Humans
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Mutation
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Open Reading Frames
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Phylogeny
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SARS Virus
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genetics
10.Research progress in functions of coronavirus accessory genes.
Chinese Journal of Virology 2014;30(3):325-332
In addition to the structural genes of the coronavirus genome, S, E, M, and N, there are several additional genes called "group-specific or accessory genes". Their gene products are designated as "accessory proteins", as reports to date make it clear that these proteins are not essential for virus replication in vitro. Nevertheless, many of these genes are still maintained in the virus genome under selective pressure, suggesting that they might play a very important role in the survival of the virus in the natural environment of the infected host. This review will summarize the research progress in the functions of coronavirus accessory genes.
Animals
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Coronavirus
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genetics
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metabolism
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Coronavirus Infections
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virology
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Humans
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Open Reading Frames
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Viral Proteins
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metabolism