De-AMPylation of the small GTPase Rab1 by the pathogen Legionella pneumophila

The bacterial pathogen Legionella pneumophila exploits host cell vesicle transport by transiently manipulating the activity of the small guanosine triphosphatase (GTPase) Rab1. The effector protein SidM recruits Rab1 to the Legionella-containing vacuole (LCV), where it activates Rab1 and then AMPylates it by covalently adding adenosine monophosphate (AMP). L. pneumophila GTPase-activating protein LepB inactivates Rab1 before its removal from LCVs. Because LepB cannot bind AMPylated Rab1, the molecular events leading to Rab1 inactivation are unknown. We found that the effector protein SidD from L. pneumophila catalyzed AMP release from Rab1, generating de-AMPylated Rab1 accessible for inactivation by LepB. L. pneumophila mutants lacking SidD were defective for Rab1 removal from LCVs, identifying SidD as the missing link connecting the processes of early Rab1 accumulation and subsequent Rab1 removal during infection.     

Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis

We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.     

Incorporating genomic annotation into single-step genomic prediction with imputed whole-genome sequence data

Single-step genomic best linear unbiased prediction (ssGBLUP) is now intensively investigated and widely used in livestock breeding due to its beneficial feature of combining information from both genotyped and ungenotyped individuals in the single model. With the increasing accessibility of whole-genome sequence (WGS) data at the population level, more attention is being paid to the usage of WGS data in ssGBLUP. The predictive ability of ssGBLUP using WGS data might be improved by incorporating biological knowledge from public databases. Thus, we extended ssGBLUP, incorporated genomic annotation information into the model, and evaluated them using a yellow-feathered chicken population as the examples. The chicken population consisted of 1 338 birds with 23 traits, where imputed WGS data including 5 127 612 single nucleotide polymorphisms (SNPs) are available for 895 birds. Considering different combinations of annotation information and models, original ssGBLUP, haplotype-based ssG_HBLUP, and four extended ssGBLUP incorporating genomic annotation models were evaluated. Based on the genomic annotation (GRCg6a) of chickens, 3 155 524 and 94 837 SNPs were mapped to genic and exonic regions, respectively. Extended ssGBLUP using genic/exonic SNPs outperformed other models with respect to predictive ability in 15 out of 23 traits, and their advantages ranged from 2.5 to 6.1% compared with original ssGBLUP. In addition, to further enhance the performance of genomic prediction with imputed WGS data, we investigated the genotyping strategies of reference population on ssGBLUP in the chicken population. Comparing two strategies of individual selection for genotyping in the reference population, the strategy of evenly selection by family (SBF) performed slightly better than random selection in most situations. Overall, we extended genomic prediction models that can comprehensively utilize WGS data and genomic annotation information in the framework of ssGBLUP, and validated the idea that properly handling the genomic annotation information and WGS data increased the predictive ability of ssGBLUP. Moreover, while using WGS data, the genotyping strategy of maximizing the expected genetic relationship between the reference and candidate population could further improve the predictive ability of ssGBLUP. The results from this study shed light on the comprehensive usage of genomic annotation information in WGS-based single-step genomic prediction.     

辣椒炭疽病3病原核糖体基因ITS区的序列测定及分析

辣椒炭疽病(pepper anthracnose)是辣椒生产中的主要病害之一。利用真菌核糖体内转录间隔区(internal transcribed spac-er,ITS)序列通用引物对辣椒炭疽病3病原进行扩增,分别获得其rDNA-ITS序列,序列分析结果表明,病菌的5.8S rDNA序列高度保守,而ITS区的可变性则相对较高,其中ITS1区的差异大于ITS2区的差异,说明ITS1区的变异较丰富,可考虑将该区域作为病原鉴定的PCR检测特异引物的靶序列,为今后各病菌的特异性分子鉴定提供可靠的靶标。     

Human immunoglobulin D: genomic sequence of the delta heavy chain

The DNA coding for the human immunoglobulin D(IgD) heavy chain (delta, delta) has been sequenced including the membrane and secreted termini. Human delta, like that of the mouse, has a separate exon for the carboxyl terminus of the secreted form. This feature of human and mouse IgD distinguishes it from all other immunoglobulins regardless of species or class. The human gene is different from that of the mouse; it has three, rather than two, constant region domains; and its lengthy hinge is encoded by two exons rather than one. Except for the third constant region, the human and mouse genes are only distantly related.     

一株鸭坦布苏病毒的分离鉴定及全基因组序列分析

2010年我国爆发了使蛋鸭产蛋量急剧下降、由一种鸭黄病毒引起的疾病,通过对来自山东某发病鸭场的病料进行分离,得到实验室分离株Du/CH/LSD/110128。对其进行全基因组序列测定分析,确定该株病毒全基因组含有一个开放阅读框,编码一个由3 426个氨基酸组成的多聚蛋白。将试验测得株Du/CH/LSD/110128株与黄热病毒(Yellow fever virus)、登革热病毒(Dengue virus)、伊利乌斯脑炎病毒(Ilheus virus)、西尼罗病毒(West Nilevirus)、巴格扎病毒(Bagaza virus)和其他一些已公布序列的坦布苏病毒进行核酸同源性比较和遗传进化树分析,发现Du/CH/LSD/110128株与巴格扎病毒亲缘关系较近但介于病毒种的水平上,与其他株坦布苏病毒核酸同源性在87%以上,可以确定Du/CH/LSD/110128株属于新型鸭坦布苏病毒(Duck Tembusu virus)。     

Direct cloning and sequence analysis of enzymatically amplified genomic sequences

A method is described for directly cloning enzymatically amplified segments of genomic DNA into an M13 vector for sequence analysis. A 110-base pair fragment of the human beta-globin gene and a 242-base pair fragment of the human leukocyte antigen DQ alpha locus were amplified by the polymerase chain reaction method, a procedure based on repeated cycles of denaturation, primer annealing, and extension by DNA polymerase I. Oligonucleotide primers with restriction endonuclease sites added to their 5' ends were used to facilitate the cloning of the amplified DNA. The analysis of cloned products allowed the quantitative evaluation of the amplification method's specificity and fidelity. Given the low frequency of sequence errors observed, this approach promises to be a rapid method for obtaining reliable genomic sequences from nanogram amounts of DNA.     

芦笋枯萎病菌的鉴定及rDNA ITS序列分析

为准确鉴定芦笋枯萎病致病菌并确定其分类地位,通过形态学观察和核糖体DNA内转录间区(rDNA ITS)序列比对方法,对该病菌进行形态学和分子生物学鉴定,比较其与近缘真菌rDNA ITS序列的差异,并进行系统发育分析。鉴定结果表明,芦笋枯萎病的致病菌为尖孢镰刀菌天门冬专化型Fusarium oxysporum f.sp.asparagi。芦笋枯萎病菌F.oxysporumf.sp.asparagi及其同属近缘种木贼镰刀菌F.equiseti和变红镰刀菌F.incarnatum的rDNA ITS序列比对结果表明,其序列在76~80、104~115、129~138、151~158、175~178、382~402、438~445和473~479bp等rDNA ITS区段上存在差异性碱基。芦笋枯萎病菌及其近缘真菌系统发育分析结果表明,6属真菌大致聚为2个组群2个亚群,芦笋枯萎病菌F.oxysporum f.sp.asparagi与木贼镰刀菌F.equiseti和变红镰刀菌F.incarnatum亲缘关系最近。     

黄瓜霜霉病和白粉病病原菌的rDNA-ITS序列分析

为了应用分子特征确定黄瓜霜霉病和白粉病的病原菌种类,扩增、测定了上海地区黄瓜霜霉病菌和白粉病菌的核糖体DNA内转录间隔区(rDNA-ITS)序列,依据rDNA-ITS序列特征分析了两种病原菌种类,以及与近缘种的差异性。结果显示,黄瓜霜霉病菌的rDNA-ITS1和rDNA-ITS2长度分别为141和406 bp,rDNA-ITS1 GC含量为41.13%,rDNA-ITS2 GC含量为46.80%(闵行区株和金山区株)或46.55%(浦东新区株),rDNA-ITS序列在种内保守性很高,种间差异性与亲缘关系呈正相关,分子特征证实研究的黄瓜霜霉病病原菌为古巴拟霜霉菌;黄瓜白粉病菌的rDNA-ITS1和rDNA-ITS2长度分别为136和89 bp,GC含量分别为59.56%和66.29%,rDNA-ITS序列在研究材料中保守,与瓜类单囊壳(Sphaerotheca cucurbitae)完全相同,但与形态鉴别的结果Sphaerotheca fuliginea差异高达4.5%,提示黄瓜白粉病病原菌的种类需进一步澄清和确定。     

高羊茅炭疽病病菌的生物学特性及其ITS序列分析

通过2006—2008年6～8月份的观察发现,上海地区高羊茅的炭疽病症状为叶片上形成梭形病斑,中央灰白色．边缘黄褐色或者黑褐色,中后期在病斑中央形成黑色小点即分生孢子盘。分生孢子为单胞、香蕉形、无色、3～0μm×20～28μm。高羊茅炭疽病病菌在PSA上菌落灰褐色。病菌菌丝生长适宜温度24～28℃,单糖和双糖、硝态氮有利于病菌菌丝的生长。通过病菌核糖体DNAITS序列的测定及GenBank的BLAST比对．与禾生炭疽病菌（Colletotrichum graminicola）相似性最高,达98％。形态和分子鉴定表明：上海地区高羊茅炭疽病病原菌为禾生炭疽病菌。室内药剂筛选试验表明：咪鲜胺、苯醚甲环唑等5种药剂对高羊茅禾生刺盘孢菌菌丝生长有强烈的抑制作用。     

Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes

We report the genome sequence of Theileria parva, an apicomplexan pathogen causing economic losses to smallholder farmers in Africa. The parasite chromosomes exhibit limited conservation of gene synteny with Plasmodium falciparum, and its plastid-like genome represents the first example where all apicoplast genes are encoded on one DNA strand. We tentatively identify proteins that facilitate parasite segregation during host cell cytokinesis and contribute to persistent infection of transformed host cells. Several biosynthetic pathways are incomplete or absent, suggesting substantial metabolic dependence on the host cell. One protein family that may generate parasite antigenic diversity is not telomere-associated.     

油茶叶枯病原的形态及ITS序列分析鉴定

对一株引起油茶落叶的叶枯病菌进行分离鉴定,为防治该病菌奠定基础。从油茶叶枯病斑中分离得到一株优势菌,通过对其形态特征的观察及rDNA的转录间隔区(ITS)序列测定,并与Genbank中同源性较高的菌株构建系统发育树,最后确定该菌株为拟盘多毛孢属菌,且与小孢拟盘多毛孢菌亲缘关系最近。     

猪圆环病毒Ⅱ型的分离与全基因组序列分析

从福建省表现为断奶猪多系统衰竭综合征的猪群中分离到两株猪圆环病毒Ⅱ型(PCV2),分别命名为FUQING0401和PUTIAN0401。通过对这两个分离株的全基因组序列测定,并同GenBank登录的12个代表毒株进行了遗传进化分析,结果表明：福建省两分离株的ORF1核苷酸同源率为97.5％,rep蛋白之间有6个氨基酸的差别,ORF2的核苷酸同源率为99.7％,而两者氨基酸同源率为98.7％。福建省两分离株与加拿大、美国、欧洲以及中国其他地方毒株之间的同源性很高,遗传进化分析表明这两毒株与其他代表毒株可分为几个小分支,但它们之间的核苷酸同源率在91.6％～99.9％,并没有发现福建的两个毒株之间存在地区特异性。     

2株猪圆环病毒2型的分离鉴定及全基因组序列分析

【目的】对河南部分地区疑似猪圆环病毒2型(Porcine circovirus type 2,PCV2)感染猪进行病毒分离鉴定,并对分离株的全基因组序列进行分析。【方法】对郑州、焦作两地疑似PCV2感染的猪淋巴结、脾脏和肺脏组织进行PCR检测,对检测为阳性的病料进行PCV2的分离,利用间接免疫荧光试验和PCR扩增进行初步鉴定。用PCR扩增PCV2全基因,经克隆、测序后,用MEGA5.1软件对克隆的序列与GenBank上获取的其他PCV2全基因组进行序列比对。【结果】分离到2株病毒,分别命名为ZHENGZ-12株和JIAOZ-12株。间接免疫荧光试验结果显示,感染病毒的细胞出现了特异的亮绿色荧光。2个分离株全基因组长度均为1 767bp,与国内外PCV2参考毒株核苷酸序列同源性为92.6%~99.9%,2个毒株之间的核苷酸序列同源性为96.0%,与PCV1核苷酸序列同源性分别为74.6%和77.7%。系统进化树分析结果显示,2个PCV2分离株同国内外分离株的亲缘关系很近;PCV2核苷酸序列比较稳定,其进化不存在明显的地域相关性。【结论】初步证实分离病毒为PCV2,ZHENGZ-12株基因型为PCV-2a,JIAOZ-12株基因型为PCV-2b。     

鲤白细胞介素-8基因组DNA的克隆及序列分析

在白细胞介素-8(IL-8)cDNA全长序列的两侧——非翻译区设计一对引物,以提取的鲤脾脏基因组DNA为模板进行PCR扩增,并将扩增产物回收、纯化,连接到pMD18-T载体上,再转化到DH5α大肠杆菌感受态细胞中,并对插入片段进行测序,获得了鲤IL-8基因组DNA的全长序列。结果表明:鲤IL-8DNA全长为943 bp,由4个外显子和3个内含子组成,与已知其它物种的排列非常相近,说明在进化过程中其拼接位点非常保守,符合GT-AG规则;对系统发生的分析证明,鲤与斑马鱼的亲缘关系较近,与哺乳动物亲缘关系较远;将鲤的IL-8基因组结构与人、猪、狗、虹鳟的基因组结构进行比较,发现IL-8基因在由鱼类到哺乳动物的分子进化过程中较为保守,外显子基本保持稳定,而内含子的变化较大。     

鲤白细胞介素-8基因组DNA的克隆及序列分析

在白细胞介素-8(IL-8)cDNA全长序列的两侧--非翻译区设计一对引物,以提取的鲤脾脏基因组DNA为模板进行PCR扩增,并将扩增产物回收、纯化,连接到pMD18-T载体上,再转化到DH5α大肠杆菌感受态细胞中,并对插入片段进行测序,获得了鲤IL-8基因组DNA的全长序列.结果表明:鲤IL-8DNA全长为943 bp,由4个外显子和3个内含子组成,与已知其它物种的排列非常相近,说明在进化过程中其拼接位点非常保守,符合GT-AG规则;对系统发生的分析证明,鲤与斑马鱼的亲缘关系较近,与哺乳动物亲缘关系较远;将鲤的IL-8基因组结构与人、猪、狗、虹鳟的基因组结构进行比较,发现IL-8基因在由鱼类到哺乳动物的分子进化过程中较为保守,外显子基本保持稳定,而内含子的变化较大.     

鸭病毒性肝炎病毒NA株全基因序列测定及分析

应用RT-PCR方法分段扩增DHV-NA株cDNA,并进行基因组全序列测定及同源性等分析。结果显示DHV-NA株基因组全长7 692 bp(不包括PolyA),5'和3'非编码区长度分别为626 bp和316 bp,有1个单一开放阅读框架(ORF,627~7 376 nt),编码2 249个氨基酸;与I型DHV(DHV-Ⅰ)参考株比较,其核苷酸和氨基酸同源性分别为94.3%~96.9%和97.8%~98.8%;与新型DHV(N-DHV)90D株比较,其核苷酸和氨基酸同源性分别为72.6%和82.3%。表明NA株与DHV-Ⅰ参考株遗传进化关系较密切,而与N-DHV遗传关系较远。     

甘肃省苹果树腐烂病菌ITS序列分析及潜育期研究

为了明确甘肃省苹果树腐烂病菌的种类及其优势种的潜育期,通过ITS序列比对和离体枝条接种法对采自甘肃省不同地区的苹果树腐烂病菌进行了ITS序列测定、分析及潜育期研究.结果表明:甘肃省苹果树腐烂病菌有2个种,分别为Valsa mali和Valsa malicola,其中Valsa mali有2个变种,分别为Valsa mali var.mali和Valsa mali var.pyri.甘肃省苹果树腐烂病菌优势种Valsa mali的潜育期随保湿时间增加而缩短,保湿时间为72h时潜育期为74.3h;温度30℃时潜育期最短,为64.3h;潜育期随枝龄的增加而增加,嫩梢的潜育期为46.3h;光暗交替下潜育期最短,为45.3h.     

山西西葫芦花叶病病原鉴定与部分序列分析

利用双链RNA(double-stranded RNA,dsRNA)技术和非序列依赖PCR扩增(sequence-independent amplification,SIA)方法对感病西葫芦进行了分子鉴定。序列测定及分析发现,具有明显花叶和斑驳症状的西葫芦受到黄瓜花叶病毒(Cucumber mosaic virus,CMV)的侵染。为进一步明确黄瓜花叶病毒山西西葫芦分离物(CMV-XHL)的分类地位,克隆了CMV-XHL RNA3的外壳蛋白和移动蛋白基因全序列。通过序列比对分析,发现CMV-XHL CP核苷酸序列和氨基酸序列与CMV亚组ⅠB中CMV烟草分离物(CMV-SG)的相似性最高,分别为98.6%和99.5%;MP核苷酸序列和氨基酸序列与CMV亚组Ⅰ分离物的相似性最高,为93.2%~94.6%。MP和CP氨基酸序列系统进化分析表明,CMV-XHL与中国大多数CMV分离物聚为一类,属于CMV亚组Ⅰ中的成员。研究结果对西葫芦病毒病的防治提供一定的理论依据。     

番茄叶霉菌CfHNNI1基因5'端序列的功能分析

番茄叶霉菌(Cladosporium fulvum)CfHNNI1是一种寄主和非寄主抗病性的广谱激发子.但CfHNNI1cDNA序列是否为全长序列尚不明确.本研究构建了两个缺失不同长度5端序列的CfHNNI1序列结构,并研究了这些缺失型序列与坏死诱导功能之间的关系.研究结果表明,缺失包括ATG3在内的5端100bp序列,使缺失型CfHNNI1的翻译起始于ATG101,形成一个新的开读框,导致对番茄、烟草(Nicotiana tabacum)和N.clevelandii植株坏死诱导能力的完全丧失.而缺失所有在ATG273以前的4个ATG、长度为272bp的序列,但与ATG3处于同一密码框架中的缺失型CfHNNI1,丧失了诱发番茄、N.clevelandii以及N.paniculata产生坏死反应的能力,却仍能诱发N.tabacum,N.benthamiana,N.langsdorfii,N.glutinosa及N.solanifolia等5个Nicotiana种的植株产生明显坏死反应.这些结果说明,以ATG3为起始密码子的开读框是CfHNNI1真正开读框;5端272bp序列在诱导产生坏死反应中的作用因植物对象而异.