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ABSTRACT A portion of the 18S ribosomal DNA (rDNA) gene, the internal transcribed spacers (ITS1 and ITS2), and the 5.8S rDNA gene were polymerase chain reaction-amplified from strains and field populations of Venturia inaequalis and assessed for genetic variation. A previously reported optional group I intron in the 18S rDNA gene of V. inaequalis was detected in 75.0% of 92 strains collected worldwide and in 61.1 and 71.2% of 54 and 59 strains from two Michigan orchards, respectively. Sequence and restriction analysis of rDNA revealed four intron alleles, three of which were present both in worldwide strains and in each field population. Two ITS1 alleles were detected and found to be linked to specific intron alleles. The ITS1-5.8S-ITS2 sequences from V. asperata V. carpophila, V. cerasi, V. inaequalis, V. nashicola, V. pyrina, and Cladosporium caryigenum were compared using phylogenetic analysis. Strains of the Venturia species were placed in three distinct monophyletic groups in a phylogenetic tree. The first group comprised V. inaequalis; the second, V. pyrina and V. nashicola; and the third, V. cerasi, V. carpophila, and V. asperata. The described intron and ITS1 alleles in V. inaequalis provide genetic markers for subdividing populations of V. inaequalis, and the ITS1-5.8S-ITS2 sequences are valuable in determining the relationship of the species from tree-fruit crops with other Venturia species. 相似文献
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This paper sums up the results of light microscopical, ultrastructural and molecular studies of five strains of amoeboid organisms isolated as endocommensals from coelomic fluid of sea urchins, Sphaerechinus granularis (Lamarck), collected in the Adriatic Sea. The organisms are reported as Didymium-like myxogastrids. Of the life-cycle stages, the attached amoeboids, flagellated trophozoites, cysts and biflagellated swarmers are described. Formation of fruiting bodies was not observed. Although phylogenetic analyses of SSU rDNA sequences indicated a close relationship with Hyperamoeba dachnaya, our sea-urchin strains have not been assigned to the genus Hyperamoeba Alexeieff, 1923. The presence of either one or two flagella reported in phylogenetically closely related organisms and mutually distant phylogenetic positions of strains declared as representatives of the genus Hyperamoeba justify our approach. Data obtained in this study may be useful in future analyses of relationships of the genera Didymium, Hyperamoeba, Physarum and Pseudodidymium as well as in higher-order phylogeny of Myxogastrea. 相似文献
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We studied amoebae associated with nodular gill disease (NGD) outbreaks in rainbow trout Oncorhynchus mykiss (Walbaum) in fish farms in South-Western Germany. Gills of 12 diseased rainbow trout were examined in fresh, by isolation attempts, histologically and using in situ hybridisation (ISH). A total of nine amoeba strains of the genera Acanthamoeba (1), Hartmannella (2), Naegleria (1), Protacanthamoeba (1) and Vannella (4) were isolated and determined using light microscopical, ultrastructural and molecular methods. Specific molecular probes designed from the SSU rDNA sequences of individual amoeba strains were used for non-radioactive ISH in histological sections. Association of Naegleria sp. with NGD and a direct ISH proof of Naegleria trophozoites attached to hyperplastic gill epithelium are novel findings, expanding the number of possible agents of NGD and supporting the hypothesis on multicausal aetiology of this disease. 相似文献
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Francesca De Luca Aurelio Reyes Alberto Troccoli Pablo Castillo 《European journal of plant pathology / European Foundation for Plant Pathology》2011,130(3):415-426
Sequence comparisons and molecular phylogenetic analyses were used to describe the nucleotide variability of the ITS containing
regions of eighteen Pratylenchus species and several populations. Comparative analysis of nucleotide sequences of the rDNA internal transcribed spacers (ITS1
and ITS2) among Pratylenchus species used in the present study demonstrates that ITS sequences can widely vary in primary sequence and length. Alignment
of eighty-seven Pratylenchus sequences and one outgroup taxon reveals the presence of ambiguous regions that have the greatest effect on phylogeny reconstruction.
Phylogenetic analyses using Bayesian Inference, Neighbour Joining-LogDet, Maximum Likelihood and Maximum Parsimony, distinguished
twelve highly or moderately supported major clades within Pratylenchus. Our results support the taxonomic usefulness of the ITS region to identify root-lesion nematode species of the genus Pratylenchus but the high nucleotide variability, sometimes, can preclude its use to resolve relationships among all members of the genus.
In addition, the phylogenetic groupings are not congruent with those defined by characters derived by lip patterns and numbers
of lip annuli. 相似文献
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Free-living amoebae infecting freshwater and marine fish include those described thus far as agents of fish diseases, associated with other disease conditions and isolated from organs of asymptomatic fish. This survey is based on information from the literature as well as on our own data on strains isolated from freshwater and marine fish. Evidence is provided for diverse fish-infecting amphizoic amoebae. Recent progress in the understanding of the biology of Neoparamoeba spp., agents responsible for significant direct losses in Atlantic salmon and turbot industry, is presented. Specific requirements of diagnostic procedures detecting amoebic infections in fish and taxonomic criteria available for generic and species determination of amphizoic amoebae are analysed. The limits of morphological and non-morphological approaches in species determination are exemplified by Neoparamoeba, Vannella and Platyamoeba spp., which are the most common amoebae isolated from fish gills, Acanthamoeba and Naegleria spp. isolated from various organs of freshwater fish, and by other unique fish isolates of the genera Nuclearia, Thecamoeba and Filamoeba. Advances in molecular characterisation of SSU rRNA genes and phylogenetic analyses based on their sequences are summarised. Attention is particularly given to specific diagnostic tools for fish-infecting amphizoic amoebae and ways for their further development. 相似文献
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海南一品红细菌性叶斑病病原菌的分离与鉴定研究 总被引:1,自引:0,他引:1
为明确海南省近几年发生的一品红细菌性叶部病害的病原菌特别是该病原菌的分子特征,为该病害的治理提供可行的依据,本文描述了2005年海南省部分花圃一品红植株上发生的细菌性叶斑病症状,并通过致病性测定、BIOLOG分析和16SrDNA序列比较将分离的病原菌鉴定为黄单胞菌属(Xanthomonas);部分碳源利用测定进一步显示2005年海南分离的菌株与2004年海南报道的细菌性疫病病原菌存在差异,但与杭州地区报道的一品红细菌性叶斑病菌基本一致。利用黄单胞菌模式种典型菌株的核糖体DNA内转录间隔区(internal transcribed spacer,ITS)序列构建系统发育树,结果显示3个海南菌株与巴豆黄单胞菌(Xanthomonas codiaei)和地毯草黄单胞菌(X.axonopodis)单独聚合成群,其中与巴豆黄单胞菌亲缘关系最近。 相似文献
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浙江西兰花花球头腐病的病原鉴定 总被引:2,自引:0,他引:2
为明确近年来浙江省宁波市部分地区发生的西兰花花球头腐病的病原,通过田间症状观察、致病性测定、Biolog和脂肪酸(fatty acid methyl ester,FAME)分析将分离到的病原菌鉴定为荧光假单胞菌Pseudomonas fluorescens.利用16S rDNA和核糖体DNA内转录间隔区(internal transcribed spacer,ITS)序列构建的系统发育树也都显示分离的西兰花菌株与假单胞菌聚合成群,其中与荧光假单胞菌的亲缘关系最近,序列同源性分别为99%和98%.表明浙江省西兰花花球上发生的细菌性头腐病由荧光假单胞菌引起. 相似文献
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Jankovics T Bai Y Kovács GM Bardin M Nicot PC Toyoda H Matsuda Y Niks RE Kiss L 《Phytopathology》2008,98(5):529-540
Previous works indicated a considerable variation in the pathogenicity, virulence, and host range of Oidium neolycopersici isolates causing tomato powdery mildew epidemics in many parts of the world. In this study, rDNA internal transcribed spacer (ITS) sequences, and amplified fragment length polymorphism (AFLP) patterns were analyzed in 17 O. neolycopersici samples collected in Europe, North America, and Japan, including those which overcame some of the tomato major resistance genes. The ITS sequences were identical in all 10 samples tested and were also identical to ITS sequences of eight previously studied O. neolycopersici specimens. The AFLP analysis revealed a high genetic diversity in O. neolycopersici and indicated that all 17 samples represented different genotypes. This might suggest the existence of either a yet unrevealed sexual reproduction or other genetic mechanisms that maintain a high genetic variability in O. neolycopersici. No clear correlation was found between the virulence and the AFLP patterns of the O. neolycopersici isolates studied. The relationship between O. neolycopersici and powdery mildew anamorphs infecting Aquilegia vulgaris, Chelidonium majus, Passiflora caerulea, and Sedum alboroseum was also investigated. These anamorphs are morphologically indistinguishable from and phylogenetically closely related to O. neolycopersici. The cross-inoculation tests and the analyses of ITS sequences and AFLP patterns jointly indicated that the powdery mildew anamorphs collected from the above mentioned plant species all represent distinct, but closely related species according to the phylogenetic species recognition. All these species were pathogenic only to their original host plant species, except O. neolycopersici which infected S. alboroseum, tobacco, petunia, and Arabidopsis thaliana, in addition to tomato, in cross-inoculation tests. This is the first genome-wide study that investigates the relationships among powdery mildews that are closely related based on ITS sequences and morphology. The results indicate that morphologically indistinguishable powdery mildews that differed in only one to five single nucleotide positions in their ITS region are to be considered as different taxa with distinct host ranges. 相似文献
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昆虫病原线虫rDNA多态性分析 总被引:1,自引:0,他引:1
本文对国内外昆虫病原线虫斯氏属和异小杆属的47个品系进行rDNA—ITS PCR—RFLP分析,研究其DNA多态性,并构建了分子系统发育树状图。各品系的ITS区无明显的长度差异,PCR—RFLP分析将47个品系分为斯氏属和异小杆属两大类,两属线虫又分别分为11组和4组。所得结果丰富了ITS PCR—RFLP图谱库,为弄清我国的昆虫病原线虫与国外种类的分子系统发育关系及未定名线虫的鉴定提供重要依据,同时为筛选适合的线虫种类防治害虫奠定基础。 相似文献
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Eric V VIRTUDAZO Hitoshi NAKAMURA Makoto KAKISHIMA 《Journal of General Plant Pathology》2001,67(1):28-36
Phylogenetic analysis of sugarcane rusts based on sequences of ITS and the 5.8 S rDNA revealed two highly divergent ITS groups
among isolates of Puccinia sp. sensu Muta, 1987 and P. kuehnii specimens. Although there is sufficient divergence (exceeding normal intraspecific variation) between the ITS regions of the
two groups to support separation into different species, unusually high homology of the ITS group I sequences with those of
members of Cronartium and identical sequences of the D1/D2 regions of the LSU rDNA for all the isolates of “Puccinia sp.” and P. kuehnii that otherwise exhibited different ITS sequences, suggest that the two highly divergent sequences may have resulted from abnormal
genetic events leading to non-orthologous, intraspeciflc polymorphisms. The other sugarcane rust, P. melanocephala and the grass rusts, P. miscanthi and P. rufipes, were separated from “Puccinia sp.” and P. kuehnii and from each other in D1/D2 region analyses, indicating that D1/D2 region sequences may more correctly reflect phylogenetic
relationships in these rusts than do the ITS regions. Further studies to examine differences in patho-genicity or finer morphological
features within P. kuehnii that may be correlated with the high divergence in ITS sequences and experiments to determine if these two sequence types
represent intraspeciflc polymorphism are necessary.
Received 11 October 2000/ Accepted in revised form 24 November 2000 相似文献
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The small subunit ribosomal RNA gene (SSU rDNA) of two freshwater and one marine species of the genus Chloromyxum Mingazzini, 1890 were sequenced. The SSU rDNA trees obtained show the phylogenetic position of the marine species Chloromyxum leydigi Mingazzini, 1890 to be at the base of the freshwater clade, being well supported by a high bootstrap value. Chloromyxum cyprini Fujita, 1927 is closely related to Chloromyxum truttae Léger, 1906 and they represent a sister branch to raabeia sp., Myxidium sp. and Myxidium truttae Léger, 1930. Chloromyxum legeri Tourraine, 1931 is in a position ancestral to Myxidium lieberkuehni Bútschli, 1882 and Sphaerospora oncorhynchi Kent, Whitaker et Margolis, 1993. Three newly sequenced species of the genus Chloromyxum represent three separate lineages within the myxosporean tree and do not support the monophyly of this genus. 相似文献
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根据曼陀罗属核糖体基因转录间隔区(ITS)序列设计通用引物,得到33个不同来源的曼陀罗属植物的ITS序列,并以小天仙子(Hyoscyamus bohemicus)为外群,应用遗传距离与系统树分析法对曼陀罗属植物之间的分类进行了初步探讨。结果表明:在供试样品中,紫花曼陀罗(Datura tatula)和曼陀罗(Daturastramonium)的ITS序列完全相同;多刺曼陀罗(Datura ferox)、栎叶曼陀罗(Datura quercifolia)和曼陀罗(Datura stramonium)之间的亲缘关系很近;紫花曼陀曼(Datura tatula)、曼陀罗(Datura stramonium)、无刺曼陀罗(Datura inermis)和光滑曼陀罗(Datura laevis)4个种间不存在遗传距离;传统分类中曼陀罗属的Dutra亚属内除光曼陀罗(Datura leichhardtii)和异色曼陀罗(Datura discolor)在ITS序列表现为比较独立的2个种外,其他各种间的亲缘关系也较近;在ITS序列上湿地曼陀罗(Datura ceratocaula)与曼陀罗(Daturastramonium... 相似文献
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M. P. A. Coetzee B. D. Wingfield † T. Kirisits D. B. Chhetri P. Bloomer M. J. Wingfield 《Plant pathology》2005,54(1):36-45
Armillaria root rot is a serious disease in fir and mixed conifer forests of Bhutan, Eastern Himalayas. The species causing this disease have, however, never been identified. The aim of this study was to identify field isolates collected at four localities in Bhutan. Identification was based on RFLP analysis of the IGS-1 region, comparisons of ITS and IGS-1 sequence data with those available on GenBank, cladistic analyses and sexual compatibility studies. Isolates were found to reside in two distinct RFLP groups. RFLP group 1 isolates from Pinus wallichiana at Yusipang had RFLP profiles and IGS-1 sequences similar to those of Armillaria mellea ssp. nipponica . Although ITS sequence data are not available for A. mellea ssp. nipponica , sequences from this DNA region were most similar to the closely related A. mellea from Asia. The RFLP profile and IGS-1 sequences for RFLP group 2 isolates from Abies densa at Changaphug, Tsuga dumosa at Chimithanka as well as Picea spinulosa and T. dumosa in the Phobjikha valley were similar to those published for Armillaria borealis , Armillaria cepistipes , Armillaria gemina and Armillaria ostoyae . Distance analysis based on IGS-1 and ITS sequence data indicated that these isolates are closely related to A. cepistipes , Armillaria gallica and Armillaria sinapina . The isolates were, however, sexually incompatible with tester strains of A. cepistipes , A. gallica and A. sinapina . Although closely related to these species, they appear to represent a distinct taxon that will be referred to as Bhutanese phylogenetic species I (BPS I) until basidiocarps are found and the species can be described. 相似文献
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西瓜细菌性果斑病菌的16S rDNA序列分析及特异性引物的设计 总被引:2,自引:0,他引:2
利用细菌16S rDNA基因的通用引物对16个供试菌株进行PCR扩增,把扩增产物进行核苷酸序列测定。将获得的序列与GenBank中相关菌株的16S rDNA序列进行同源性分析。以此设计出检测A.a.c的特异性引物,并利用最大简约法构建了16S rDNA系统演化树。系统演化关系分析表明,6~9号供试菌株的16S rDNA序列与A.a.c标准菌株仅有3个位点的差异,其同源性均在99.8%以上,在构建的系统演化树上,它们聚为同一个族群。利用设计的一对特异性引物(BFB64/65),对各供试菌株进行PCR检测,结果只有A.a.c相关菌株产生扩增条带,产物大小与预期一致。 相似文献
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P. Sarris M. Abdelhalim M. Kitner N. Skandalis N. Panopoulos A. Doulis A. Lebeda 《Plant pathology》2009,58(5):933-943
Molecular genetic polymorphisms within Pseudoperonospora cubensis isolates of different geographic origins were investigated to establish their phylogenetic relationships and to assess genetic variability between two distant pathogen populations. Thirty isolates originating from Greece (Crete; 15), the Czech Republic (13), the Netherlands (one) and France (one) were analysed by AFLP fingerprinting and ITS 5·8S rDNA sequence analysis. All isolates were obtained from cucumber ( Cucumis sativus ) plants showing typical downy mildew symptoms. Four AFLP primer combinations produced a total of 288 high-quality bands of which 45% were polymorphic, allowing isolates to be grouped into two separate clusters: one including the Central European (Czech Republic) and Western European (the Netherlands and France) and the other the Cretan isolates. Within each AFLP cluster there was some variation, which could be accounted for by geographic origin or pathogenicity. The two populations (Cretan vs. Central and Western European) exhibited a high degree of genetic isolation. There was no clear AFLP grouping of isolates on the basis of pathotypes. No variability was detected in the ITS1 region; however, ITS2 sequences grouped P. cubensis isolates in two subclusters: one with all investigated European and the other with Asian isolates. The two subclusters formed a larger P. cubensis cluster which was differentiated from the cluster of the neighbouring species Pseudoperonospora humuli . Within P. cubensis , AFLP fingerprints could resolve genetically isolated populations, even on small or medium geographic scales, while ITS2 sequence showed differences on a global scale, being only suitable for phylogenetic analyses. 相似文献