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1.
Based on morphological and molecular characterisation, four amoeba strains isolated from organs of freshwater fish were identified as Hartmannella vermiformis Page, 1967. Small subunit rRNA gene sequences of these strains expand the set of corresponding complete and almost complete sequences of this species to twelve. A new species-specific oligonucleotide probe inferred from recently available SSU rRNA gene sequences was designed and successfully tested in tissue lesions produced by one strain of H. vermiformis in experimentally infected fish. 相似文献
2.
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
3.
Shesh Kumari Sergei A. Subbotin 《European journal of plant pathology / European Foundation for Plant Pathology》2012,133(4):923-933
Longidorus helveticus was found at two out of 285 sampling sites for the first time in the Czech Republic. Females, males and juvenile stages were analyzed morphologically and morphometrically. The morphological identification of samples was verified by polymerase chain reaction using a species specific primer. Four markers of ribosomal DNA (18S, ITS1, ITS2, D2-D3 expansion segments of 28S rRNA) and two markers of mitochondrial DNA (cox1 and nad4) were sequenced and analyzed and compared with published gene sequences of other populations of L. helveticus. The partial mitochondrial cytochrome c-oxidase subunit 1 gene and partial nicotinamide dehydrogenase subunits 4 gene showed relatively high genetic variation within the species compared with ribosomal DNA markers. 相似文献
4.
ABSTRACT The evolutionary relationships of fungi in the Fusarium redolens-F. hostae clade were investigated by constructing nuclear and mitochondrial gene genealogies for 37 isolates representing the known genetic and pathogenic diversity of this lineage, together with 15 isolates from putative sister groups that include the Gibberella fujikuroi and F. oxysporum species complexes and related species. Included in the analyses were 29 isolates of F. redolens from Asparagus, Convallaria, Dianthus, Fritillaria, Hebe, Helleborus, Hordeum, Linum, Pisum, Pseudotsuga, and Zea spp., and from soil. Isolates of F. hostae analyzed included two reference isolates from Hosta spp. and six isolates from Hyacinthus spp. that originally were classified as F. oxysporum f. sp. hyacinthi. DNA sequences from a portion of the nuclear translation elongation factor 1alpha (EF-1alpha) gene and the mitochondrial small subunit (mtSSU) ribosomal RNA (rRNA) were analyzed individually and as a combined data set based on results of the nonparametric Wilcoxon signed ranks Templeton combinability test. Maximum parsimony analysis of the combined data set identified the F. redolens-F. hostae clade as a sister group to a phylogenetically diverse clade in which the G. fujikuroi species complex formed the most basal lineage. Also included in this latter clade were two unnamed Fusarium spp. that are morphologically similar to F. oxysporum and putative sister taxa comprising the F. oxysporum complex and a F. nisikadoi-F. miscanthi clade. Phylogenetic diversity in F. redolens was small; all isolates were represented by only three EF-1alpha and two mtSSU rDNA haplotypes. Both the isolates of F. redolens f. sp. asparagi and those of F. redolens f. sp. dianthi were nearly evenly distributed in the combined molecular phylogeny between the two major subclades within F. redolens. 相似文献
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6.
Nucleospora salmonis (Hedrick, Groff et Baxa, 1991), an intranuclear microsporidian parasite of marine and freshwater fish, causes diseases mainly in salmonid species. Losses have been reported in stocks of salmonid fish reared in the region of Auvergne (France). The cause of chronic mortalities in the local host species raised in aquaculture and destined for supplementation of the river system Loire-Allier was examined. The presence of N. salmonis was confirmed by PCR and histology in Salmo salar L. previously and in newly investigated salmonid species, Salmo salar, Salmo trutta fario L., Thymallus thymallus (L.) and Salvelinus alpinus (L.), present in European streams. The infection by N. salmonis was consistent in all cases with characteristic symptoms of the disease in deceased or moribund fish. The small subunit ribosomal DNA from N. salmonis was partially sequenced and compared to previously characterised N. salmonis isolates. As a result, a genotype, or clonal entity, was attributed to N. salmonis among Atlantic salmon found along the Northern Atlantic coastal lines and other salmonid species co-inhabiting or co-cultivated in the Auvergne region. 相似文献
7.
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
8.
A new species of amphizoic amoeba, Nuclearia pattersoni sp. n., isolated from gills of Rutilus rutilus L. is described. It is characterised by elongate flattened trophozoites of irregular shape. The longer dimension of their bodies is 13.2 (11.0-15.7) microm. Filopodia radiating mostly from the poles are 2 to 2.5 times longer than the body. The diameter of less frequently observed spherical trophozoites is 8.2-10.8 microm; their filopodia radiate to all directions. Cyst-like stages have shorter pseudopodia that arise from one pole only. The surface of locomotive forms from agar plate cultures has a thin amorphous glycocalyx, while most cells are covered by two layers of extracellular matrix. Mitochondria have flattened cristae, dictyosomes are located in the perinuclear zone. A conspicuous ultrastructural feature of the morphologically similar N. simplex, perinuclear striated band, is not present. Light microscopic and ultrastructural data are completed with the sequence of SSU rRNA gene and phylogenetic analysis including sequences of related taxa. The bacterial endosymbiont found in N. pattersoni type strain RR2G2 is assigned to the genus Rickettsia. 相似文献
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10.
The pathogenicity of Alternaria spp. isolated from wheat leaves collected in regions where alternaria leaf blight has been reported was compared with that of IMI reference isolates of A. triticina and A. alternata using two durum and two bread wheat genotypes. To identify isolates putatively corresponding to A. triticina , morphological and DNA sequence analyses based on ribosomal DNA from the internal transcribed spacer (ITS) region (ITS1, 5·8S rRNA gene, ITS2) and toxicity bioassays of culture filtrate were combined. Glasshouse inoculations provided reliable information to assess the pathogenicity of A. triticina isolates on wheat. Alternaria leaf blight symptoms were produced by the A. triticina isolates only on durum wheat cv. Bansi, while A. alternata , A. tenuissima and A. arborescens isolates were found to be nonpathogenic on the wheat cultivars tested. Alternaria triticina isolates were distinguished from other Alternaria species by Simmons and Roberts' sporulation pattern 6 and two to three conidia per sporulation unit associated with primary conidia bearing long (> 7 µ m) apical secondary conidiophores. Phylogenetic analysis also proved effective at discriminating wheat-pathogenic A. triticina from other nonpathogenic Alternaria species. Alternaria triticina isolates yielded longer ITS sequences than A. alternata , A. tenuissima and A. arborescens isolates, leading to clear-cut differences as visualized with agarose gel electrophoresis. Additionally, only culture filtrates of A. triticina isolates caused nonspecific necrotic lesions on leaves of 3-week-old wheat plants. 相似文献
11.
A sterile white fungus was isolated from the healthy looking roots of buffalo grass (Stenotaphrum secundatum) grown on cleared bush land in Perth, Western Australia. The fungal strain was pathogenic on 12 plant species screened under the greenhouse conditions. The clamp connections and dolipore septa indicated that the isolate was a Basidiomycete. Mycelial features, growth rate at different temperatures, as well as pathogenicity patterns of this sterile white basidiomycete (SWB) were distinctly different from those of a strain with a similar morphology, ATCC 28344, previously described as a pathogen in Florida and Georgia (USA). All attempts to induce sporulation failed. The isolates were also compared using the nucleotide sequence analysis of the ribosomal DNA array. Approximately 1 kbp of the 5 end of the large subunit ribosomal RNA gene, complete sequences of the small subunit ribosomal RNA gene and the entire ITS region (including ITS1, ITS2 and 5.8S gene) were sequenced for the purpose. The obtained sequences were compared with the homologous regions of other genera of Agaricales available in GenBank. Relatively low sequence similarities between the American and Australian strains, as well as the phylogenetic analysis of the studied regions has suggested that these two fungi belong to different genera. Interesting results were achieved in the case of the large subunit ribosomal DNA since this region has been widely studied for taxonomy of Basidiomycetes. The Australian strain 3034 appeared to be closely related to the genus Campanella and the American SWB was identified as belonging to the genus Marasmius, possibly to M. graminum. Our data suggest that the Australian strain is a novel pathogen, and is different from the American SWB isolates described to date. 相似文献
12.
文中从古尔班通古特沙漠采集的沙样中,运用96孔板有限稀释法分离出两种形态各异的微藻物种GTD8A1和GTD9C2,形态学初步鉴定分别为绿藻门小球藻目和环藻目。利用GenBank中绿藻门不同科属种类序列的18S核糖体RNA基因保守区和28S核糖体RNA基因保守区分别设计18S rDNA特异性引物和5.8S rDNA-ITS区特异性引物。以自行设计的18S rDNA特异性引物与5.8S rDNA-ITS区特异性引物分别对以上两个物种进行PCR和测序后,经blastn比对,系统发育树及遗传距离分析,结果表明GTD8A1可能与Chlo-rella sp.MBIC10595为同一个物种,GTD9C2可能为Desmodesmus multivariabilis种内的一个变种。 相似文献
13.
Plants of corn (Zea mays L.) exhibiting symptoms of stunting and leaf reddening were assayed for the presence of phytoplasma gene sequences through the use of phytoplasma rRNA and ribosomal protein gene and maize bushy stunt (MBS) phytoplasma-specific oligonucleotide primers in polymerase chain reactions (PCR). Polymorphisms in 16S rDNA amplified from diseased plants were those characteristic of phytoplasmas classified in the16S rRNA gene group 16SrI, subgroup IB, of which MBS phytoplasma is a member. Amplification of ribosomal protein (rp) gene sequences in PCR primed by phytoplasma-specific primers confirmed presence of a phytoplasma in the diseased plants. Restriction fragment length polymorphism (RFLP) patterns of the amplified phytoplasma rp gene sequences were similar or identical to those observed for a known strain of MBS phytoplasma. In separate PCR, an MBS-specific oligonucleotide pair primed amplification of a MBS-characteristic DNA from templates derived from the diseased corn. Our data provide the first firm evidence for the presence of maize bushy stunt phytoplasma in corn in Brazil. 相似文献
14.
Sergei A. Subbotin Eugene A. Rogozhin Vladimir N. Chizhov 《European journal of plant pathology / European Foundation for Plant Pathology》2014,138(2):377-390
The needle nematodes of the genus Longidorus can cause diseases of various crops and trees, and are comprised of more than 150 valid species. Eleven valid and six unidentified species of the genus Longidorus collected in different regions of Russia, two states of USA, Germany, New Zealand and Ukraine were molecularly characterized using analysis of the partial 18S rRNA and the D2–D3 expansion segments of the 28S rRNA gene sequences. Fifty-four partial 28S rRNA and fifteen partial 18S rRNA gene sequences were obtained for the present study. Using molecular criteria, we confirmed the morphological identification and distinguished between the following species: L. aetnaeus, L. africanus, L. andalusicus, L. artemisiae, L. caespiticola, L. distinctus, L. elongatus, L. euonymus, L. intermedius, L. leptocephalus and L. lignosus. Two longidorid populations from Russia and four from California were not identified to a species level. We obtained the full length D2–D3 of 28S rRNA gene sequence from several freshly-collected L. artemisiae samples. We confirmed the identity of the D2 region of 28S rRNA gene sequence with a short D2 of 28S rRNA gene fragment sequence previously obtained from formalin-fixed nematodes embedded in the L. artemisiae paratype slides. Longidorus lignosus was molecularly characterized and L. aetnaeus was reported from Russia for the first time. PCR-D2-D3-RFLP diagnostic profiles generated by five restriction enzymes: AluI, HinfI, Bsp143I, Tru1I and RsaI are presented for sixteen Longidorus species. 相似文献
15.
A new multivalvulid myxosporean species, Kudoa dianae sp. n., is described from bullseye puffer, Sphoeroides annulatus (Jenyns) (Tetraodontiformes: Tetraodontidae). Plasmodia develop in extramuscular sites, in the wall of oesophagus and less frequently on mesenteries. Mature spores can reach lumen of the digestive tract directly by disruption of plasmodial wall or via macrophage transport to the oesophageal epithelium. New species is characterised by morphology of spores and by the complete sequence of SSU rRNA gene that differs from all hitherto known sequences of Kudoa species. Spore morphology (moderate-sized, simple non-ornate spores, quadrate in apical view) clusters with that of Kudoa scienae, K. cerebralis, K. chilkaensis, K. leiostomi, K. finduli, K. cascasia and K. ovivora. Analysis of phylogenetic relationships (using SSU rRNA gene sequences) among five Kudoa species, the molecular data of which are available thus far, revealed that K. dianae is distinguishable from these five species and that its closest relation is with K. miniauiriculata. 相似文献
16.
Shiro KUNINAGA Donald E CARLING Toru TAKEUCHI Ryozo YOKOSAWA 《Journal of General Plant Pathology》2000,66(1):2-11
Genetic diversity among 51 isolates of Rhizoctonia solani AG-3, representing potato and tobacco populations, was inferred from the sequences of the internal transcribed spacer (ITS)
and 5.8S ribosomal RNA (rRNA) gene. The 5.8S rDNA sequence was completely conserved not only in AG-3, but across all the AG
isolates examined, whereas the rDNA-ITS sequence was found to be variable among the isolates. The nucleotide sequence similarity
in the ITS 1 region was high (96-100%) for isolates within each of the two populations, but was 91-92% for isolates from different
populations. The AG-3 isolates had 56 to 91% sequence similarities in the ITS 1 region with R. solani isolates of the other AGs. Phylogenetic analysis based on the ITS-5.8S rDNA sequence data indicated that the different populations
in AG-3 are distantly related to each other. Genetic divergence between the two populations was also supported by the results
of DNA-DNA hybridization studies. This study suggests that AG-3 consists of two genetically isolated groups corresponding
to separate subgroups: AG-3 PT (potato type) and AG-3 TB (tobacco type). Specific primer sets for the detection of the two
AG-3 subgroups were developed from the aligned rDNA-ITS sequences.
Received 22 April 1999/ Accepted in revised form 2 July 1999 相似文献
17.
Molecular analysis of the major Phytophthora species on cocoa 总被引：1，自引：0，他引：1
The internally transcribed spacer (ITS) regions of the ribosomal RNA (rRNA) gene cluster of 161 isolates of Phytophthora species involved in pod rot, stem canker and leaf blight of cocoa were analysed to determine inter- and intraspecific variation in this disease complex. The species P. palmivora , P. megakarya , P. capsici , P. citrophthora and P. nicotianae could all be clearly distinguished by PCR amplification of the ITS region followed by restriction analysis with Hae III, Hinf I, Pvu II and Alu I. This method provided a relatively rapid identification procedure for these species, and was able to distinguish isolates that had previously been misidentified by morphological methods. Sequence analysis showed that the four main cocoa-associated species formed two distinct groups, one comprising P. capsici and P. citrophthora , and the other P. palmivora and P. megakarya . Detailed sequence analysis and comparison with published literature suggested that P. capsici isolates from cocoa may be closely related to P. tropicalis , a species recently described from Cyclamen and Dianthus . 相似文献
18.
K. Ntushelo N. A. Harrison M. L. Elliott 《European journal of plant pathology / European Foundation for Plant Pathology》2012,133(4):779-782
A comparison was made of the two palm yellows phytoplasmas affecting palms to determine if the entire ribosomal RNA operon portion of the phytoplasma genome, or portions thereof, could account for the observed palm host differences. Polymerase chain reaction (PCR) was used to amplify a 5.0?kb DNA fragment consisting of the entire ribosomal RNA operon from a subgroup 16SrIV-D phytoplasma that causes Texas Phoenix palm decline (TPD) in cabbage (Sabal palmetto) palm in west central Florida and from a subgroup 16SrIV-A phytoplasma that causes lethal yellowing (LY) in coconut (Cocos nucifera) palm in Jamaica. Before the PCR reaction, we sequenced by 454 sequencing a draft genome of the coconut LY phytoplasma, strain LYFL, that infects C. nucifera in Florida, and obtained from this draft sequence both copies of the entire ribosomal operon. Sequence analysis of the ribosomal RNA operons from both the LY and TPD phytoplasmas revealed the gene composition and orientation for the operons to be 5′16S rRNA-tRNAIle-23S rRNA-5S rRNA3′ and a tRNAVal3′ downstream of the 5S rRNA gene. Based on molecular comparisons using the sequences of the ribosomal RNA operon, the TPD (16SrIV-D) strain was 98?% similar to the LY (16SrIV-A) strains. 相似文献
19.
Design of Division Specific Primers of Ralstonia solanacearum and Application to the Identification of European Isolates 总被引：1，自引：0，他引：1
Geneviève Boudazin Anne Claire Le Roux Karine Josi Philippe Labarre Bernard Jouan 《European journal of plant pathology / European Foundation for Plant Pathology》1999,105(4):373-380
A PCR diagnostic test for detection of Ralstonia solanacearum at the infraspecific level was developed, based on polymorphisms within the 16S rRNA gene sequence. Partial sequences of this gene were determined for three French isolates which showed the characteristics of R. solanacearum subdivision 2a described by Taghavi et al. (1996). Oligonucleotide primers were designed to incorporate the nucleotide triplet (at positions 458–460 of the 16S rRNA gene) which differs between divisions 1 and 2 16S rRNA sequences of R. solanacearum isolates. A simple PCR test unambiguously revealed the division of each isolate. The PCR test was useful for identification of isolates of R. solanacearum from Europe. 相似文献
20.
Mohamed Hemida Abd-Alla Shymaa R. Bashandy Sylvia Schnell Stefan Ratering 《Phytoparasitica》2011,39(2):175-183
Bacterial contamination of fresh tomato fruits is of great concern. From naturally infected tomato fruits showing dark brown
irregularly shaped spots, 36 bacterial isolates were recovered and identified on phenotypic characteristics and sequences
of the gene encoding the 16S rRNA. Five isolates showing spots on tomato fruits in the pathogenicity test with healthy tomato
fruits belong to the genus Serratia on the basis of phenotypic characteristics. One representative isolate of these has been further identified as a Serratia rubidaea by sequencing of the 16S rRNA gene. This is the first evidence showing that a S. rubidaea strain can cause spots on tomato fruits. Virulence of the S. rubidaea was also confirmed by the production and secretion of a large variety of enzymes capable of degrading the complex polysaccharides
of the plant cell wall and membrane constituents. Nineteen bacterial isolates of the 36 did not induce any spot symptoms in
a pathogenicity test on artificially infected tomato fruits although these are known as phytopathogenic bacteria. Five of
these 19 bacterial isolates were identified as Ralstonia species on the basis of biochemical tests. Sequencing of the 16S ribosomal gene of one representative isolate revealed that
the isolate is closely related to Ralstonia solanacearum. Six isolates of the 19 were related to Xanthomonas vesicatoria on the basis of biochemical tests and eight were related to the Enterobacteriaceae. One representative isolate of the Enterobacteriaceae could be identified by the 16S rRNA gene as Enterobacter cloacae subsp. dissolvens. The 12 other strains were related to Proteus mirabilis based on the 16S RNA gene sequence of one representative isolate. The isolates related to P. mirabilis did not produce any symptoms on artificially infected tomato fruits. The nucleotide sequences of S. rubidaea strain E9, E. cloacae strain E23, P. mirabilis strain E11, and R. solanacearum strain E15 have been deposited in the GenBank nucleotide sequence database under accession numbers HM585373 to HM585376. 相似文献