Wolbachia Infection in Populations of Ostrinia furnacalis: Diversity,Prevalence, Phylogeny and Evidence for Horizontal Transmission

Wolbachia are maternally inherited endosymbiotic bacteria infecting a wide range of arthropods and filarial nematodes. They can induce various reproduction alterations in their hosts, including thelytokous parthenogenesis, cytoplasmic incompatibility (CI), feminization of genetic males and male killing. Here we investigated diversity and prevalence patterns of Wolbachia infection in 43 geographical populations of the Asian corn borer, Ostrinia furnacalis, in China and one population in North Korea. Based on Wolbachia surface protein gene (wsp) sequences, nine strains of Wolbachia (wFur1-wFur9), belonging to supergroups A and B, were identified in populations of O. furnacalis with an average infection rate of 10.5%. Superinfection commonly appeared in individuals of O. furnacalis and coinfection patterns were very complex. There was no specific pattern for the prevalence and distribution of the nine Wolbachia strains suggesting an intricate evolutionary history of Wolbachia infection in this species. The genetic similarity of the wFur1-wFur9 strains with those detected in two parasitoids of O. furnacalis, Macrocentrus cingulum and Lydella grisescens, strongly suggests host-parasitoid horizontal transmission.     

Population genetic structure of Sitobion miscanthi in China

The wheat aphid, Sitobion miscanthi, is one of the most destructive pests of wheat plants in the temperate regions of China. Little is known about the genetic structure evolution of the different geographic populations of S. miscanthi with its migration. In this study, we investigated the population genetic structure and demographic history of S. miscanthi by analysing 18 geographical populations across China using one mitochondrial gene, COI; one nuclear gene, EF-1α; and two endosymbiont Buchne...     

油松遗传结构与地理阻隔因素的相关性

油松(Pinus tabulaeformis)是我国特有广布树种。秦岭是我国亚热带和暖温带气候的重要分界线,贺兰山是我国西北干旱区与半干旱区的分界线。旨在以分布于秦岭、贺兰山和晋陕两省的10个天然油松种群为研究对象,通过对其线粒体DNA(nad1和matR内含子)的序列,探讨地理阻隔对油松遗传结构的影响。结果表明,10个天然油松种群的100个个体中共检测到27个单倍型,多态位点172个,简约信息位点35个,单一多态性位点137个。其中1个单倍型为全部种群共有,4个单倍型为2-5个种群共有,其余22个单倍型为各个种群所独有。在这10个种群中,有8个种群分别具有1-4个独有单倍型。尽管秦岭南侧种群和北侧种群分别具有两个和一个独有单倍型; 贺兰山东侧种群和西侧种群均具有3个独有单倍型;但是与晋陕种群(即油松分布区中心种群)相比,其种群独有单倍型平均数目则明显较少。与此同时,不仅秦岭南北两侧或贺兰山东西两侧种群的独有单倍型的进化关系往往较近,而且秦岭北侧或贺兰山东侧种群的独有单倍型与油松分布区中心种群的某些独有单倍型的关系亦较近。从而导致秦岭南北两侧或贺兰山东西两侧种群与油松分布区中心种群之间表现出比较复杂的聚类关系。由此可见,油松的遗传结构与山脉屏障的存在没有明显关系。     

Investigation of mitochondrial DNA genetic diversity and phylogeny of goats worldwide

Genetic diversity, population structure, and population expansion of goats worldwide (4 165 individuals from 196 breeds) were analyzed using published mitochondrial DNA (mtDNA) D_loop hypervariable region sequences. Results showed that 2 409 haplotypes and 301 polymorphic sites were present within the 401-bp length D_loop region, the nucleotide diversity (Pi) was 0.03471, and the haplotype diversity (Hd) was 0.9983. Phylogenetic analysis revealed that 98.92% of haplotypes were divided into six obvious clusters, consistent with the classification of the known mitochondrial haplogroups of goats. Haplogroup A accounted for the largest proportion (86%). Interestingly, two unknown divisions (Unknown I and Unknown II) were discovered from goats in Southwest China, suggesting that Southwest China has unique maternal haplogroups. Analysis of molecular variance (AMOVA) and the average number of pairwise differences between populations (PiXY) indicated that geographical variation was small but significant. Neutrality tests (Tajima's D and Fu's F_S tests) and mismatch distribution showed that haplogroups B, C, and G had expansion histories. In addition, the phylogenetic relationship between domestic and wild goats suggested that Capra aegagrus is the most likely wild ancestor and may have participated in the domestication of ancestral populations of A, B, C, and F haplogroups. A meta-analysis on the mtDNA sequences of goats from international databases was conducted to analyze goats’ genetic diversity, population structure, and matrilineal system evolution worldwide. The results may help further understand the domestication history and gene flow of goats worldwide.     

东北狍mtDNA D-loop序列多态性分析

采用聚合酶链式反应(PCR)技术对东北狍(Capreolus capreolus)mtDNA D-loop序列进行扩增,所得PCR产物经纯化后克隆测序,得到622bp的核苷酸片段,多态位点数(S)为351,核苷酸多样性(Pi)为0．3492,平均核苷酸差异数(K)为166．238。狍的mtDNA D-loop区序列个体变异程度大,适合于群体内及群体间不同个体的遗传多样性分析。     

基于线粒体DNA分析青鱼养殖群体的遗传多样性

为了解安徽省养殖青鱼群体的遗传多样性变化,基于线粒体Cytb基因与D-loop区采用直接测序的方法,分析了安徽省滁州、怀远和无为3个青鱼养殖群体的遗传多样性和群体分化,并评估突变、环境选择和基因流等因素对遗传多样性的影响。结果显示:3个群体具有丰富的遗传多样性(Hd 0.5,Pi 0.05);群体间出现了高度分化(Fst 0.15),但是仍有遗传背景交叉;Cytb基因与D-loop区分别检出9个和41个变异位点;群体间基因交流明显(Nm 1);受到纯化选择作用(Ka/Ks=0～0.099)。     

基于线粒体DNA控制区序列的珠江和长江水系光倒刺鲃群体遗传变异分析

【目的】明确珠江和长江水系不同光倒刺鲃地理群体的遗传变异及进化关系,为其种质资源保护和可持续开发利用提供科学依据。【方法】从珠江水系（增江、流溪河、北江、连江、漓江、柳江和郁江）和长江水系（阊江、赣江和湘江）的10个支流（群体）采集347尾光倒刺鲃样本,扩增并测定其线粒体DNA（mtDNA）控制区序列;通过MEGA 6.0、DnaSP 6.10和Arlequin 3.5等在线软件统计序列碱基组成、变异位点、遗传距离、核苷酸多样性（π）、单倍型多样性（H_d）及遗传分化系数（F_st）,并进行分子变异分析（AMOVA）、核苷酸错配分布分析、中性检验,以及构建单倍型的系统发育进化树和网络结构图。【结果】光倒刺鲃mtDNA控制区序列长度为519 bp,其中T、C、A、G占比平均值分别为32.57%、19.16%、32.16%和16.11%。在所有mtDNA控制区序列中共检测到62个变异位点,34个单倍型;10个光倒刺鲃群体的H_d平均为0.917,π平均为0.0359,遗传距离为0.0018~0.0790,F_st为-0.0007~0.9978。光倒刺鲃mtDNA控制区序列63.46%的分子遗传变异来自各地理分组间;单倍型网络结构图和系统发育进化树均显示,10个光倒刺鲃群体聚类为三大支系,除了有个别交集外,东江水系、西江水系、赣江水系+湘江水系的光倒刺鲃群体分布在3个不同的独立分支上,而北江+流溪河水系群体分别与东江水系群体和西江水系群体有较多交集。10个光倒刺鲃群体的Fu’s Fs为-1.339~23.759,平均为9.857,但P均大于0.05;Tajima’s D为-2.613~2.824,仅有3个群体的Tajima’s D为显著性负值（P<0.05）;其核苷酸错配分布图谱呈多峰形式,即珠江和长江水系光倒刺鲃群体尚未发生过种群扩张。【结论】珠江和长江水系光倒刺鲃群体遗传多样性总体上偏低,应加强其种质资源保护,尤其是北江水系群体野生资源相对较丰富宜作为重点保护单元。复杂的地形地貌导致珠江和长江水系光倒刺鲃群体形成明显的地理隔离,群体间已发生明显分化,且受各种人为活动干扰导致其种群收缩,因此亟待采取有效防护措施以保证光倒刺鲃种质资源的可持续利用。     

大别山牛mtDNA D-loop区遗传多样性和系统进化分析

通过PCR扩增技术对46头大别山母牛mtDNA D-loop区进行测序并得到其全序列,再从GenBank上下载中外部分黄牛品种mtDNA D-loop区的全序列,运用生物学软件对大别山牛的遗传进化进行分析。结果发现,46头大别山牛mtDNA D-loop序列长度在955～1 101 bp之间,有176个变异位点,约占核苷酸总数的16.18%,其中单一信息位点120个,简约信息位点56个。共有25种单倍型,单倍型多样性（Hd）为0.877,核苷酸多样性（Pi）为0.023 96,平均核苷酸差异数（k）为21.544,A、T、C和G 4种碱基含量所占比例分别为32.72%、28.46%、25.19%和13.63%,表明大别山牛有较为丰富的遗传多样性。遗传距离分析结果表明,大别山牛与吉安牛、雷州牛、鲁西牛、闽南牛、皖南牛和湘西牛的遗传距离最小,与欧洲野牛亲缘关系最远,由系统发育树可推测大别山牛属南方牛种,属普通牛和瘤牛的混合母系起源。     

基于线粒体控制区的中部太平洋黄鳍金枪鱼种群遗传结构的研究

根据2010年9月-2012年1月,我国远洋捕捞船在太平洋中部(16°S~8°N;160°W~155°E)的7个采样点采集到的101个样本,利用线粒体DNA控制区(mtDNA D-loop)基因的585 bp序列,分析了它们的遗传多样性和遗传结构。结果显示,585 bp片段中发现23个变异位点,80个单倍型;序列多样性分析结果显示,7个采样群体单倍型多样性指数h=0.994±0.002和核苷酸多样性指数π=0.00892±0.00038。分子方差分析揭示98.18%的遗传变异来自种群内,群体间的Fst分析揭示黄鳍金枪鱼7个采样群体内部不存在显著的遗传分化。Fu’s Fs呈负值和核苷酸不配对呈单峰,显示了黄鳍金枪鱼大约在335~544万年前经历了种群扩张;基因交流与遗传分化分析表明,该7个采样点的黄鳍金枪鱼群体之间存在强烈的基因交流,种群遗传分化水平较低。黄鳍金枪鱼种群遗传多样性低,为单一种群,应采用合理的有效措施进行管理,确保黄鳍金枪鱼产业的可持续发展。     

稀有白甲鱼西江种群mtDNA D环区的结构及遗传多样性

采用PCR扩增和DNA直接测序技术,测定分析了采自珠江水系西江的30尾稀有白甲鱼(Onychostoma rara)mtDNA D环约467 bp的序列。结果显示,该序列的长度为467～470 bp,共计发现了16个变异位点,占分析总位点数的3.40%,其碱基组成A+T的平均含量(67.6%)高于C+T(32.3%)。稀有白甲鱼西江种群mtDNA D环区在结构上可分为终止序列区、中央保守区和保守序列区,存在着与终止相关的序列ETAS以及保守序列CSB-F、CSB-E、CSB-D和CSB1。定义了11种单倍型,单倍型多样性指数(Hd)为0.733 3,单倍型之间平均遗传距离(P)为0.010 2,核苷酸多样性(Pi)为0.005 79,平均核苷酸差异数(K)为2.705 75。11个单倍型构建的非加权分组平均法(UPGMA)系统树聚为2个分支。该研究表明稀有白甲鱼西江种群存在着较丰富的遗传多样性。研究亮点:(1)有关濒危鱼类稀有白甲鱼西江种群mtDNA D环测序及遗传多样性研究尚未见报道;(2)本研究揭示了稀有白甲鱼西江种群尚保存有较丰富的遗传多样性;(3)对稀有白甲鱼西江种群遗传学研究具有理论价值,并对开展该种群的保护和资源利用具有现实指导意义。     

基于线粒体Cytb序列的3个宽体金线蛭群体遗传多样性分析

对江苏省扬州高邮、苏州张家港、泰州海陵3个地区宽体金线蛭自然群体的线粒体Cytb基因全序列进行了测定和分析。结果显示:宽体金线蛭Cytb基因全长1 146 bp,样本的A、G、T、C平均含量分别为27.57%、15.77%、43.49%、13.17%,A+T含量(71.06%)明显高于G+C含量(28.94%)。在77个宽体金线蛭样本中,共检测到96个多态位点,其中有58个简约信息位点,获得47个单倍型,共享单倍型数目1个。3个宽体金线蛭群体的平均单倍型多样性、核苷酸多样性、平均核苷酸差异数分别为0.9781、0.0133、15.20,其中泰州海陵群体的单倍型多样度(0.987 7)和核苷酸多样度(0.013 1)最高。3个群体间的遗传分化指数F_(st)为0.065 1～0.175 6,且差异显著(P0.05),不同群体间存在一定的遗传分化。分子方差分析(AMOVA)表明,11.13%的变异来自群体间,88.87%的变异来自群体内。用邻接法构建的单倍型系统发育进化树显示,不同地理群体的个体呈交错分布,没有形成明显的地理谱系。中性检验和核酸不配对分布结果表明,3个宽体金线蛭野生群体总体大小保持相对稳定,没有发生明显的种群扩张。     

樱桃谷鸭线粒体控制区的遗传多样性分析

[目的]探究樱桃谷鸭的遗传背景。[方法]通过线粒体D—loop区测序对樱桃谷鸭19个个体进行测序。[结果]结果表明,樱桃谷鸭群体内的核苷酸多样性（Pi）、单倍型多样度（Hd）和平均核苷酸差异数（K）分别为0．01434、0．982和10．140,存在4种单倍型,可以将樱桃谷鸭分为2个较大的类群,同时樱桃谷鸭与绿头野鸭、建昌鸭和野生斑嘴鸭有较高的亲缘性。鸭种群线粒体D—loop区序列个体变异程度很小,但种群的遗传多样性水平很高,可用于群体内及群体间不同个体的遗传多样性分析。[结论]该研究结果为樱桃谷鸭的多态性位点和单倍型的深入分析提供参考。     

Population Genetic Analysis of Blumeria graminis f. sp. tritici in Qinghai Province,China

To gain more precise information about molecular genetic variation for wild populations of Blumeria graminis f. sp. tritici from Qinghai Province, China, 38 single-colony isolates were purified from samples collected from Haidong District, Xining City and Hainan Tibetan Autonomous Prefecture in 2010. The virulence of 21 isolates among them was tested at seedling stage on 34 wheat cultivars (lines) carrying known powdery mildew (Pm) resistant genes. The results showed that V1a, V3a, V3c, V3e, V5a, V6, V7, V8 and V19 had high virulence frequencies (>75%), indicating a wide distribution; and V1c, V5b, V12, V13, V16, V21, VXBD, V2+6, V2+Mld and V4+8, with less distribution, appeared to be lower in frequencies (0-20%). The Nei's gene diversity (H), Shannon's information index (I) and the percentage of polymorphic loci (P) were 0.23, 0.35 and 67.65%, respectively, which revealed a virulent diversity. The results from single nucleotide polymorphisms (SNPs) of 38 isolates showed that three housekeeping genes were found to contain a total of 9 SNP sites. 10 haplotypes (H1-H10) were inferred from the concatenated sequences, with 1 haplotype (H1) comprising of over 55% of Qinghai population. Phylogenic analysis did not show obvious geographical subdivision between the isolates. A multilocus haplotype network presented a radial structure, with H1 in the central as an inferred ancestor. Using analysis of molecular variance (AMOVA), we found 1.63% of the total variation was among populations and 98.37% within populations, with a low fixations index (F_ST=0.01634, P<0.05). This revealed a relatively high genetic diversity but a low genetic divergence in Qinghai population. Moreover, the molecular data on gene flow (Nm=6.32) confirmed the migration of pathogen populations among areas in Qinghai Province.     

Population genetic structure of Chinese Puccinia triticina races based on multi-locus sequences

Puccinia triticina, the causal agent of wheat leaf rust, is one of the most devastating rust fungi attacking wheat worldwide. Seventy-six isolates of the wheat leaf rust pathogen from Yunnan, Sichuan, Gansu and Henan provinces, China, were tested on wheat leaf rust differentials and the population structure was analyzed using four presumably neutral partial sequence markers such as elongation factor-1α(EF-1α), glyceraldehyde-3-phosphate dehydrogenase(GAPDH), β-tubulin(TUB) and the second largest RNA polymerase subunit(RPB2). The phenotypic diversity of Yunnan and Sichuan populations was higher than that of Gansu and Henan populations. The four populations were separated into two clusters based on the pathogenic data. A total of 12 single nucleotide polymorphisms(SNPs) and 32 haplotypes were identified among the four sequences. The 32 haplotypes were divided into two clusters in a neighbor-joining tree. Bayesian analyses also identified two clusters. Pairwise FST between populations in different regions were significantly different(P0.05). Analysis of molecular variance(AMOVA) indicated that 68% of the total genetic variation was within populations.     

基于线粒体Cyt b基因的南海北部金钱鱼种群遗传结构分析

【目的】分析南海北部金钱鱼（Scatophagus argus）遗传多样性,明确其群体演化历史和分布动态,为金钱鱼养殖育种及其种质资源的合理开发利用提供科学依据。【方法】以采自福建东山（DS）、广东阳江（YJ）、海南海口（HK）、广西北海涠洲岛（BH）、广西钦州（QZ）、广西防城港（FC）及越南清化（TH）等南海北部的7个金钱鱼地理群体为研究对象,基于线粒体DNA细胞色素b基因（Cyt b）序列分析,利用DnaSP 5.10统计南海北部金钱鱼群体的单倍型、单倍型多样性指数（H_d）和遗传多样性指数（π）,通过邻接法（NJ）构建单倍型的系统发育进化树,以Network 4.6中的中介连接网络法构建单倍型网络图,并综合Tajima’s D检验、Fu’s Fs检验及核苷酸错配分布等方法分析金钱鱼群体的历史动态。【结果】7个金钱鱼地理群体的291条Cyt b基因序列定义为33个单倍型（Hap1~Hap33）,其中单倍型Hap1、Hap2和Hap7是南海北部金钱鱼在长期进化过程中形成的稳定优势基因型。7个金钱鱼地理群体的H_d为0.54103~0.77436,π为0.00112~0.00171,群体内遗传距离为0.00113~0.00171,遗传分化系数（F_st）为-0.01734~0.00364,基因流（Nm）为137.03888~inf。不同地理群体的单倍型均无规律地散布在单倍型系统发育进化树上,不存在与地理群体明显对应的系统分支,也未表现出明显的地理聚群分布特征。金钱鱼群体内个体间的遗传变异为100.74%,说明遗传变异全部来源于群体内个体间,即南海北部金钱鱼群体既无群体分化,也无以琼州海峡分隔的组群分化。Tajima’s D检验和Fu’s Fs检验结果均为显著负值,且核苷酸错配分布呈单峰分布,推测南海北部金钱鱼群体发生过群体扩张,且扩张事件约发生在3.4万年前,属于更新世晚期。【结论】南海北部7个金钱鱼地理群体的遗传多样性符合高单倍型多样性低核苷酸多样性类型,群体间遗传距离较小,亲缘关系较近,遗传分化不明显,且群体间存在频繁的基因交流,具有高度的遗传同质性,符合南海北部金钱鱼是一个随机交配种群的假设。     

安徽长江水系黄鳝的群体遗传结构分析

为研究安徽长江水系黄鳝(Monopterus albus)的遗传多样性和群体遗传结构,测定了其6个地理群体(当涂、无为、繁昌、贵池、怀宁和望江)共178尾个体的线粒体DNA控制区部分序列.对其长度为556～558 bp的控制区同源序列进行分析,共检测到变异位点41个(变异率7.35％),单倍型56种.平均单倍型多样性和核苷酸多样性分别为0.694～0.954、0.00237～0.01382.群体分化指数(Fst)和基因流(Nm)分别为0.01974～0.87529、0.07124～24.82928,分子变异分析(AMOVA)中,群体间遗传变异占61.72％,表明黄鳝群体间具有明显的遗传分化.基于单倍型或群体间遗传距离的分子系统进化树均显示,6个地理群体分为两支:当涂与繁昌群体聚为一支,其余4群体聚为另一支.     

广东地区犬瘟热病毒血凝素基因的克隆与序列分析

【目的】对广州和东莞市宠物犬感染犬瘟热病毒(CDV)的情况进行病原鉴定和分析,为监测CDV的遗传变异情况和防治犬瘟热(CD)提供数据基础。【方法】从表现CD症状的犬只中鉴定了17份CDV阳性样本,采用RT-PCR的方法克隆得到这些野毒株的血凝素(H)基因序列,采用生物信息学方法进行序列比对分析。【结果】17株CDV的H基因核苷酸与氨基酸序列的相似性分别为97.4%～100.0%和97.5%～100.0%,与Onderstepoort、Lederle和Convac等疫苗株相比,其核苷酸与氨基酸序列相似性分别为90.3%～91.5%和89.4%～90.8%。进化树分析结果显示,17株CDV野毒株均属于AsiaⅠ型,与疫苗株的分支较远;本研究鉴定的野毒株已进化形成9个潜在的N-糖基化位点。【结论】AsiaⅠ型CDV仍为该地区的流行基因型,基因型较稳定,但与疫苗株相比形成了一定的进化距离和出现了大量的变异。因此,继续监控CDV在犬群中的进化,掌握其遗传变异状况具有重要意义。     

太湖鲢鱼mtDNA D-loop区遗传多样性

为深入研究太湖鲢鱼的种群遗传结构及进化过程,有效的保护和利用太湖鲢鱼种质资源,作者采用聚合酶链式反应(PCR)技术对太湖鲢鱼的mtDNA D-loop序列进行扩增,获得了大小约为500 bp的扩增产物.PCR产物经纯化后克隆到pMD19-T Vector进行序列鉴定测序,得到了520 bp的核苷酸片段(除去引物及部分端部序列).用CLUSTAL X(1.83)软件进行排序比较,在30个个体中,共检测到52个变异位点,包括1个碱基缺失、36个转换位点、15个颠换位点及1个转换与颠换同时存在的位点.运用MEGA软件计算出不同个体间的遗传距离,并据此构建了NJ系统树.用DNASP软件计算出的多态位点数(S)为52、核苷酸多样性(Pi)和平均核苷酸差异数(k)分别为1.24%0.35%和6.368.研究结果表明,太湖鲢鱼的mtDNAD-loop个体序列变异程度较大,遗传多样性较为丰富.     

元江鲤种群遗传多样性

选择12对微卫星标记检测了于2011年采集自元江(红河上游中国江段)5个样点192尾鲤的群体遗传多样性。共检测到201个等位基因,每个位点等位基因2-27个。各群体各位点平均等位基因(N_A)12.25-14.67个,平均有效等位基因(N_E)8.28-9.73个,平均观察杂合度(H_O) 0.7765-0.8037,平均期望杂合度(H_E)0.7761-0.8080,平均多态信息含量(PIC) 0.7534-0.7843。元江鲤种群192个个体各位点N_A、N_E、H_O、H_E、PIC分别为16.50、11.26、0.7927、0.8049、0.7966,种群遗传多样性水平高。元江鲤群体之间遗传分化小,可作为一个种群管理单元进行管理。增殖放流要防止遗传多样性丧失。