The integration and insertion site of GbVe1 gene in the genome of transgenic cotton (Gossypium hirsutum)

[Objective] The aim of this study was to obtain the flanking sequences of T-DNA in the transgenic cotton containing a GbVe1 over-expression cassette. [Method] The T-DNA insertion copy number in the transgenic GbVe1 cotton was analyzed by southern blot. Flanking sequences of the transgenic lines with putative single T-DNA insertion copy were obtained using high-efficiency Thermal asymmetric interlaced polymerase chain reaction (hiTAIL-PCR). The T-DNA insertion sites were further confirmed by PCR with specific primers. [Result] RB-flanking sequences (119-1 018 bp) and LB-flanking sequences (243-516 bp) were obtained from three transgenic lines with low copy number of T-DNA insertion. The AT content was more than 63% in these flanking sequences. A same single insertion site in the intron of Gohir.D01G157600.1 was found in the two transgenic lines 7/100826-152 and 12/100826-393, while two separated insertion sites, one also in the intron of Gohir.-D01G157600.1 and the other in the intergenic region of A12 chromosome, were found in the transgenic line 1/w-ch14. A deletion of 21 bp was found in the insertion site in the intron of Gohir.D01G157600.1. The T-DNA insertion in the intron of Gohir.D01G157600.1 was further confirmed by the specific PCR. [Conclusion] The flanking sequences of T-DNA in the transgenic GbVe1 cotton were obtained and the specific transformation event in the intron of Gohir.D01G157600.1 was further confirmed by PCR.     

禽腺病毒血清4型贵州株全基因序列分析

为了解禽腺病毒血清4型(FAdV-4)地方流行毒株的分子进化情况,基于实验室分离的2株FAdV-4贵州株GZ-BJ株和GZ-QL株,分别对2株FAdV-4毒株进行PCR分段扩增,扩增产物克隆至载体,提取质粒进行PCR和双酶切鉴定后筛选出重组质粒进行测序,将测序结果依次拼接得到病毒的全基因组,获得FAdV-4贵州株的全基因序列,并对其进行序列和遗传进化分析。结果显示,通过PCR分段扩增成功获得了2株FAdV-4贵州株(GZ-BJ株和GZ-QL株)的全基因序列,长度分别为43352、43723 bp,FAdV-4 GZ-BJ株全基因序列长度比FAdV-4 GZ-QL株短371 bp,少6个ORF(22K、putative 9.1 ku、u-exon、ORF17、ORF28、ORF42),二者的氨基酸同源性为57.1%。2株FAdV-4贵州株同国内外不同地区FAdV-4毒株核苷酸同源性在88.7%~100%,与FAdV-4经典毒株ON1比对,2株FAdV-4贵州株和国内FAdV-4分离株均缺失ORF19、ORF27、ORF30。系统进化树分析显示,2株FAdV-4贵州株GZ-BJ株和GZ-QL株仍属于Ⅰ群C种FAdV。研究结果表明,2株贵州株FAdV-4 GZ-BJ株和FAdV-4 GZ-QL株较国内外FAdV-4毒株均存在进化与突变,且FAdV-4 GZ-BJ株变化较大,但尚未改变其血清型,这为探索FAdV-4致病机理的分子机制研究提供依据。     

土耳其斯坦裂体吸虫23kDa蛋白基因的序列分析及抗原表位预测

为研究土耳其斯坦裂体吸虫23 kDa蛋白的生物学特性,以土耳其斯坦裂体吸虫cDNA为模版,利用PCR对23 kDa基因进行扩增,并将其克隆到T-easy载体后进行序列测定。利用生物信息学对其结构、抗原指数进行分析,并对其抗原表位进行预测。序列分析结果表明,该虫体的23 kDa基因长度为657 bp,A+T含量为57.38%,与曼氏血吸虫、埃及血吸虫和日本血吸虫的23 kDa基因的相似性分别为85.24%、83.71%和81.89%。蛋白二级结构分析表明,23 kDa蛋白经过4次跨膜,主要由6个α-螺旋、3个β-折叠、7个β转角和若干个无规则卷曲构成。抗原表位预测结果表明,该蛋白有3个B细胞抗原表位。综合分析土耳其斯坦裂体吸虫23 kDa蛋白是一种较好的抗原分子,是土耳其斯坦裂体吸虫疫苗的重要候选分子。     

Cloning and Sequence Analysis of PTTG1 Gene in Luchuan Pig

This experiment was aimed to clone PTTG1 gene CDS sequence of Luchuan pig,and was analyzed by bioinformatics methods.A pair of special primers was designed according to predicted sequence of porcine PTTG1 in GenBank.The coding sequence of PTTG1 in Luchuan pig was amplified by RT-PCR,its gene sequence characteristics and protein structure was systemically analyzed by bioinformatics techniques.The results showed that the cloned PTTG1 fragment included a 609 bp CDS (coding 202 amino acids).The sequence multi-aligned results showed that Luchuan pig shared 90.15%,87.85%,87.52%,87.03%,76.03%,74.38%,55.74% and 44.48% of similar nucleotide sequence with that of Bos,Pan troglodytes,Homos,Macaca,Rattus,Mus,Gallus and Danio retio,respectively.The protein structure analysis results showed that the protein attributed hydrophilic protein without signal peptide,localized in cell cytoplasm and had 16 phosphorylation sites.The phylogentic tree of amino acid indicated that PTTG1 was highly conserved in the process of evolution of different species.The cloning and analysis of PTTG1 gene provided an important foundation for further study biological function of porcine PTTG1 during early embryonic development.     

油桐LEC1基因的cDNA克隆与序列分析

为了解LEC1(Leafy Cotyledon 1)基因对油桐油脂合成过程的调控机理,以油桐种仁转录组数据库中基因的部分c DNA序列为基础,采用RT-PCR技术从油桐种子中克隆LEC1基因的全长c DNA,并对其进行序列分析。油桐LEC1基因全长c DNA为1 152 bp,编码区为729 bp(142~870),编码243个氨基酸,5′端非编码区和3′端非编码区分别为141 bp和263 bp。该基因编码蛋白质的相对分子质量为27 025.4 Da,理论等电点为6.97;蛋白二级结构以不规则卷曲和α螺旋为主,是不具有跨膜结构的膜外蛋白。经对比发现,油桐LEC1具有典型的HAP3结构特点,在不保守的N端和C端中间有1个十分保守的结构域,与拟南芥、玉米、麻风树、黄连木等的LEC1氨基酸序列高度同源。     

杨树抗黑斑病相关基因表达谱分析

利用黑斑病的高抗无性系美洲黑杨I-69及黑斑病的高感无性系欧美杨I-45为材料建立的2个cDNA文库,随机挑取cDNA克隆进行5'端EST序列测序,共获得有效序列20 023条.序列经聚类分析和拼接后,共获得10 816个Unigene,其中包括3 734个Contig,7 082个独立的Singleton.被注释的8 853个具有同源性匹配序列基因中,按照GO的分子功能、生物过程和细胞组分3个不同分类角度进行分类.在具有功能注释的8 853个Unigene中,选出330个与完成全基因组测序的毛果杨序列进行BLAST分析,结果发现有177个抗病相关候选基因出现在282个Unigene中,其中135个分布于杨树的18个不同连锁群上,其他42个基因位于还没定位的scaffolds上.所测定的这些EST序列为后期在基因组水平上研究杨树黑斑病的水平抗性遗传机制及进一步的相关基因发现奠定基础.

Abstract：

In an attempt to elucidate the molecular mechanism for resistance of black spot disease in poplar,gene expression profiles in leaves of Populus deltoides'Lus'(I-69/55)and P.euramericana'I-45/51',which were inoculated with the pathogen Marssonina brunnea f.sp.brunnea,were analyzed based on expressed sequence tags (ESTs).A total of 20 023 valid ESTs from the 5'terminal ends derived from corresponding cDNA libraries of the two poplar species were sequenced.Cluster analysis of the 20 023 sequences yielded 10 816 tentative unigenes,including 3 734 contigs and 7 082 singletons.All tentative unigenes were classified by Gene Ontology functional categories.To find resistance-associated candidate genes and locate them on poplar genome,330 unigenes was chosen from 8 853 annotated tentative unigenes,and their BLAST alignment was conducted with Populus trichocarpa assembly,1 77 related candidate resistant genes were found,and they presented in 282 unigenes.Among these genes,there were 1 35 genes located on 18 different linkage groups of poplar genome,and 42 genes located on the different scaffolds.This study supplied a resource of candidate genes for further exploring the genetic mechanism for the host horizontal resistance to the pathogen Marssonina brunnea at the whole genome range,and provided important information for further gene discovery.     

不同来源花生品种的ISSR分析及亲缘关系研究

利用13对ISSR引物对28个栽培种花生品种进行PCR扩增,研究这些品种的DNA多态性及其亲缘关系。结果表明,有7对引物检测到明显的多态性,从28个花生品种中扩增出90条带,其中多态性带达到79条,多态性比率为87.8%,平均每个引物可扩增出12.86条带,11.29条为多态性条带。品种间的遗传相似系数值在0.411~0.800之间,平均为0.620。在UPGMA聚类分析简单匹配系数值为0.57处,可把28个花生品种分成3个品种群。由此表明,这些不同来源的花生品种具有较高的DNA多态性,亲缘关系不同。     

普通羊肚菌密码子偏好性分析

采用CodonW1.4.2软件和CUSP程序,以普通羊肚菌(Morchella conica)全基因组蛋白质编码序列(coding sequence,CDS)为对象,解析了该菌的有效密码子数(effective number of codon,ENC)、密码子3个位点的 GC含量、相对同义密码子使用度(relative synonymous codon usage,RSCU)和高表达优越密码子。结果表明：普通羊肚菌全基因组密码子第2位密码子的 GC含量明显低于第1位和第3位,第3位密码子与第1位含量差异不大,分别为57.8%和56.8%,RSCU 值大于等于1的密码子总共35个,其中以 G 或 C 结尾的25个,占71.4%,确定了25个高表达优越密码子。     

Sequence Analysis and Prokaryotic Expression of NSP1 Gene of Bovine Rotavirus UK Strain

Rotavirus is a major cause of acute diarrhea in both many kinds of young animals and children under 5 years old.Rotavirus NSP1, a 55 ku RNA binding protein, is the product of gene 5, which can subvert innate immune responses and be one of virulent determinant factors.According to the sequence in GenBank, specific primers targeting to NSP1 gene were designed and the gene was amplified by RT-PCR, following by being cloned into the pET-28a(+) vector.It showed that the full length of NSP1 gene was 1 473 bp, encoding 491 amino acids.The NSP1 shared the highest identity with WC3 strain.The recombinant protein was induced in E.coli Rosetta(DE3) by IPTG and was analyzed by SDS-PAGE and Western blotting.The results revealed that NSP1 recombinant protein existed in the form of inclusion body with the molecular weight of 55 ku.The purified recombinant protein could be recognized by His-tag antibody.This study laid the foundation for further research on the relationship between the intracytoplasmic location of NSP1 protein and its activity.     

Whole-genome sequence of a novel Chinese cyprinid herpesvirus 3 isolate reveals the existence of a distinct European genotype in East Asia

Cyprinid herpesvirus 3 (CyHV3), also known as koi herpesvirus (KHV), can be subdivided primarily into European and Asian genotypes, which are represented by CyHV3-U or CyHV3-I and CyHV3-J, respectively. In this study, the whole genome sequence of a novel Chinese CyHV3 isolate (GZ11) was determined and annotated. CyHV3-GZ11 genome was found to contain 295,119 nucleotides with 52.9% G/C content, which is highly similar to those of published CyHV3-U, CyHV3-I, and CyHV3-J strains. With reference to CyHV3-U, CyHV3-I, and CyHV3-J, CyHV3-GZ11 was also classified into 164 open reading frames (ORF), which include eight repeated ORFs. On the basis of the 12 alloherpeviruses core genes, results from phylogenetic analysis showed that CyHV3-GZ11 had closer evolutionary relationships with CyHV3-U and CyHV3-I than with CyHV3/KHV-J, which were also supported by genome wide-based single nucleotide substitution analysis and the use of a series of developed molecular markers. This study was the first to reveal the presence of a distinct European CyHV3 genotype in East and Southeast Asia at a whole genome level, which will evoke new insights on exploring the origin, evolution, and epidemiology of the virus.