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ITS Sequences (its + sequence)
Selected AbstractsDifferentiation of Two Pathogens of Powdery Mildew Disease in Flowering Dogwood (Cornus florida) by PCR-mediated Method Based on ITS SequencesJOURNAL OF PHYTOPATHOLOGY, Issue 5 2009Ainong Shi Abstract Two fungi, Phyllactinia guttata and Erysiphe pulchra were identified as the pathogens of powdery mildew of flowering dogwood (Cornus florida). The objective of this research was to identify and distinguish the two fungi by developing species-specific primers. The internal transcribed spacer (ITS) universal primers and a series of species-specific primers designed from the ITS regions were used to evaluate and validate the two fungi causing powdery mildew in dogwood. Four primer pairs showed specificity to P. guttata and three to E. pulchra. These species-specific primer pairs can be used as molecular markers to provide diagnostic tools for detection and differentiation of the two powdery mildew pathogens in flowering dogwood. [source] Application of nr-DNA ITS sequence for identification of Fusarium culmorum isolates,EPPO BULLETIN, Issue 3-4 2000P. K. Mishra Variation within the internal transcribed spacers (ITS1 and ITS2) and 5.8S ribosomal DNA region of 60 Fusarium culmorum isolates (section Discolor), representing different hosts and diverse geographical origins was examined by polymerase chain reaction (PCR), coupled with sequencing. Phylogenetic relationships of these F. culmorum isolates were estimated in relation to Fusarium spp. from this and other sections of the form-genus, using sequences available from Genbank. The amplified ITS region was approximately 570 bp long in 56 isolates and approximately 585 bp in four other isolates. The inferred phylogeny distinguished clearly four isolates supplied as F. culmorum. These isolates differed in both morphology and sequence from the remaining F. culmorum material. Sequence analysis revealed that the remaining 56 isolates were divided into three ITS types, within which the divergence was extremely low. ITS sequence comparison among the Fusarium isolates showed two major clades, one comprising sections Discolor, Sporotrichiella and Gibbosum and the other comprising Elegans, Liseola, Martiella and Roseum. These results demonstrate the use of the ITS region to resolve the identification and taxonomic problems of Fusarium spp. especially at sectional level but demonstrate the need to develop some other molecular markers for identification at the level of species or race. [source] Biogeography of Plagiochila (Hepaticae): natural species groups span several floristic kingdomsJOURNAL OF BIOGEOGRAPHY, Issue 7 2003Henk Groth Abstract Aim This paper presents a synthesis of our recent results regarding the biogeography of Plagiochila using a molecular approach, and documents intercontinental ranges within this largest genus of the hepatics. Methods A maximum likelihood analysis of sixty-one nrITS sequences of Plagiochila was performed and the molecular topology obtained was compared with morphological, phytochemical and geographical data. Results Our molecular data set allowed the identification of eleven Plagiochila sections, the majority of which cover at least two floristic kingdoms. Seven sections have species in Europe (sect. Arrectae, Carringtoniae, Fuscoluteae, Glaucescentes, Plagiochila, Rutilantes, Vagae). Plagiochila species from Atlantic Europe are usually close to or conspecific with neotropical taxa, whereas species widespread in Europe are closely related to Asian ones and not to those in the Neotropics. Plagiochila sect. Arrectae represents a neotropical , Atlantic European clade. The section is not closely related , as has often been suggested , to the morphologically similar sect. Zonatae from Asia and western North America. Sequence data show that the African P. integerrima and the neotropical P. subplana are members of the Asian sect. Cucullatae (sect. Ciliatae, syn. nov.), which becomes pantropical in distribution. An ITS sequence of P. boryana from Uganda confirms the Afro-American range of the primarily neotropical sect. Hylacoetes. Similarities in sporophyte morphology between the sect. Cucullatae and sect. Hylacoetes are the result of parallel evolution. Main conclusions Our results indicate that intercontinental ranges at section and species level are common in Plagiochila. Carl's (1931) subdivision of Plagiochila into sections restricted to one floristic kingdom is outdated. Biogeographical patterns in Plagiochila are not dissimilar to those of other groups of bryophytes but elucidation of the geographical ranges of the taxa requires a molecular approach. Contrary to earlier belief, most Plagiochila species from Atlantic Europe do not have close relatives in Asia but are conspecific with or closely related to species from tropical America. [source] Hybridization among cryptic species of the cellar fungus Coniophora puteana (Basidiomycota)MOLECULAR ECOLOGY, Issue 2 2007HÅVARD KAUSERUD Abstract In this study we have analysed the genetic variation and phylogeography in a global sample of the cellar fungus Coniophora puteana, which is an important destroyer of wooden materials indoor. Multilocus genealogies of three DNA regions (beta tubulin, nrDNA ITS and translation elongation factor 1,) revealed the occurrence of three cryptic species (PS1,3) in the morphotaxon C. puteana. One of the lineages (PS3) is apparently restricted to North America while the other two (PS1,2) have wider distributions on multiple continents. Interspecific hybridization has happened between two of the lineages (PS1 and PS3) in North America. In three dikaryotic isolates, two highly divergent beta tubulin alleles coexisted, one derived from PS1 and one from PS3. Furthermore, one isolate included a recombinant ITS sequence, where ITS1 resembled the ITS1 version of PS3 while ITS2 was identical to a frequent PS1 ITS2 version. This pattern must be due to hybridization succeeded by intralocus recombination in ITS. The results further indicated that introgression has happened between subgroups appearing in PS1. We hypothesize that the observed reticulate evolution is due to previous allopatric separation followed by more recent reoccurrence in sympatry, where barriers to gene flow have not yet evolved. A complex phylogeographical structure is observed in the morphotaxon C. puteana caused by (i) cryptic speciation; (ii) the interplay between natural migration and distribution patterns and probably more recent human mediated dispersal events; and (iii) hybridization and introgression. [source] PCR-based identification of Pythium spp. causing cavity spot in carrots and sensitive detection in soil samplesPLANT PATHOLOGY, Issue 5 2008S. S. Klemsdal On the basis of ITS sequences PCR primers were designed for the identification of the five Pythium species found to be most important for the development of carrot cavity spot in Norway: P. intermedium, P. sulcatum, P. sylvaticum, P. violae and P. ,vipa'. The P. ,vipa' isolates had a unique ITS sequence, differed morphologically from all other Pythium isolates, and thus probably represent a new species. The PCR primers were species-specific with no cross-reaction to other Pythium species or to fungal isolates from carrot tested. The detection limits varied for the different primer pairs. The two most sensitive assays allowed detection of as little as 5 fg DNA. All five Pythium species could be detected in lesions from diseased carrots. Weak positive signals were obtained from some carrot samples without symptoms. PCR assays allowed detection of pathogens in soil. In samples of soil known to produce cavity spots on cropped carrots, strong signals were obtained. In several soil samples more than one of the five Pythium species could be detected. The utilization of this diagnostic PCR assay in analysis of field soil and carrot tissue might in the future be exploited to reduce the incidence of this serious carrot disease. [source] Analysis of the distribution of Phytophthora cinnamomi in soil at a disease site in Western Australia using nested PCRFOREST PATHOLOGY, Issue 2 2009N. Williams Summary The oomycete plant pathogen Phytophthora cinnamomi has infected a very large area of native vegetation in the south western corner of Australia. An important aspect of effective disease management depends on being able to accurately map areas of infestation. For this purpose, we have developed a nested polymerase chain reaction (PCR) protocol for the detection of P. cinnamomi in soil. The test uses two sets of primers developed from the rRNA ITS sequences of P. cinnamomi and can detect as little as 1 pg DNA. The degree of sensitivity was reduced with DNA extracted from soil although this depended on the type of soil. Soils with a high organic content, such as eucalypt forest soil and potting mix were more inhibitory than sandy soils. Inhibition by soil DNA could be reduced by the addition of bovine serum albumin and formamide to the reaction. Taq DNA polymerase was very sensitive to inhibitors compared with Tth+ or TaqF1*. In comparison with baiting (0,10% positive samples), nested PCR proved to be a very much more efficient (90,100% positive samples) method for the detection of P. cinnamomi in soil. [source] Elevated genetic heterogeneity and Pleistocene climatic instability: inferences from nrDNA in New Zealand Coprosma (Rubiaceae)JOURNAL OF BIOGEOGRAPHY, Issue 7 2002Stephen R. Wichman Aim To examine patterns of hybridization and genotype mixing within the genus Coprosma J.R.Forst. & G.Forst. (Rubiaceae). Location New Zealand Methods Nucleotide sequence was determined for the internal transcribed spacer (ITS) and external transcribed spacer (ETS) regions of nuclear ribosomal DNA for fifty individuals from thirty-six taxa within the New Zealand component of the genus Coprosma. Results Mixed sequences were found to be widespread in Coprosma. Direct sequencing of ITS polymerase chain reaction (PCR) products from seven polyploid taxa showed evidence of sequence mixtures. Cloning and sequencing of individual PCR products from two polyploids confirmed the presence of multiple templates, one of which corresponded to that of a diploid. Intra-individual heterogeneity was also seen in a hybrid diploid taxon, with the mixed nucleotides corresponding to those of the parental lineages. Finally the ITS sequences of twenty-two diploid taxa showed that eleven contained intra-individual heterogeneity. Conclusions We conclude that the widespread occurrence of sequence mixtures in Coprosma results from of frequent hybridization. We also conclude that concerted evolution of the ITS and ETS regions is depressed. We propose that these characteristics evolved as a mechanism to maintain high levels of heterogeneity and suggest that this is adaptive for Coprosma in climatically unstable and physically complex New Zealand landscapes. These landscapes have been subjected to repeated oscillations between stadial and interstadial environments during the Pleistocene. [source] A SYSTEMATIC STUDY OF GIGAR-TINACEAE FROM PACIFIC NORTH AMERICA BASED ON MOLECULAR AND MORPHOLOGICAL EVIDENCEJOURNAL OF PHYCOLOGY, Issue 2000J.R. Hughey Greater than 50 species of Gigartinaceae have been described from Pacific North America, about half of which are currently recognized. Although the family is treated extensively in the taxonomic literature, many of the species are still confused and a comprehensive revision is required. We sequenced the rbcL (RuBisCO) gene and ITS (Internal Transcribed Spacer) 1, 2, and 5.8S regions from a large number of recent collections and identified a discrete of number data sets. These were analysed in comparison with the morphological evidence for each of the taxa. Uncertain of the possibility that our operational taxonomic units may not correspond to the types, we developed a protocol for isolating PCR-friendly DNA from herbarium specimens, some reaching back as far as 1670. The DNA profiles of types and historically important specimens were compared to those for recently collected silica gel-dried and formalin-fixed material and assigned correct names. Species studied ranged from Alaska to Mexico and the Gulf of California and were compared to outgroup taxa from Pacific South America and the Southern Ocean. Particular attention was paid to variations in morphology as they relate to habitat with emphasis on the presence or absence of different morphological forms among sympatric and allopatric populations. We recognize 10 species in Chondracanthus (including one new combination and one new species) and 16 species in Mazzaella (including two new combinations and two new species). Finally, we tested a phylogenetic hypothesis inferred for the Gigartinaceae from rbcL sequences for congruence with one generated from ITS sequences. [source] THE PHYLOGENY OF CAULERPA BASED ON RDNA INTERNAL TRANSCRIBED SPACER SEQUENCESJOURNAL OF PHYCOLOGY, Issue 2000S. Nemeth Phylogenetic hypotheses for the pantropical marine green algal genus, Caulerpa, were inferred based on analyses of nuclear-encoded rDNA internal transcribed spacer (ITS) sequences. Results of these analyses were used to assess the correspondence between rDNA phylogeny and traditional sectional taxonomy, to identify synapomorphic morphological characters (including assimilator morphology and chloroplast ultrastructure), and to examine marine biogeographic hypotheses for the genus. Ribosomal DNA ITS sequences were aligned for thirty-three species and intraspecific taxa of Caulerpa. Results indicate limited correspondence between phylogeny and sectional taxonomy for the genus, (e.g., the sections Filicoideae and Sedoideae were not monophyletic). In contrast, chloroplast morphology could be mapped to the tree topology with limited homoplasy. Pantropical isolates of the filicoidean species, Caulerpa sertularioides and Caulerpa mexicana each formed monophyletic groups. Caulerpa reyesii was included as a derived taxon within the Caulerpa taxifolia clade, suggesting that these species were conspecific and affirmed the lack of correspondence between phylogeny and assimilator morphology. Isolates and various intraspecific taxa of Caulerpa racemosa did not form a monophyletic group. Instead, these taxa formed a heterogeneous assemblage with other sedoidean and filicoidean taxa. Within the C. sertularioides clade, Caribbean and Atlantic isolates formed a basal paraphyletic group, whereas eastern and western Pacific isolates formed a more derived monophyletic group. Therefore, these results are not consistent with an Indo-West Pacific origin of this species. [source] Molecular Identification of Phytophthora spp.JOURNAL OF PHYTOPATHOLOGY, Issue 11-12 2009Affecting some Economically Important Crops in Eastern India through ITS-RFLP, Sequencing of the ITS Region Abstract Molecular identification of the Phytophthora spp. affecting betelvine (Piper betel), brinjal (Solanum melongena), guava (Psidium guajava), roselle (Hibiscus subdariffa), black pepper (Piper nigrum), sesame (Sesamum indicum), taro (Colocasia esculenta), chilli (Capsicum annuum), pointed gourd (Trichosanthes dioica), papaya (Carica papaya) was performed through rDNA ITS-RFLP and also additionally by sequencing the Internal Transcriber spacer (ITS) ITS1 and ITS2 regions. Phytophthora nicotianae, Phytophthora capsici, Phytophthora colocasiae, Phytophthora melonis and Phytophthora palmivora isolates from these 10 different crops were accessioned and the ITS sequences were deposited in Genbank. ITS sequences for Phytophthora isolates from most of these crops are being reported here for the first time. In this study, a review of all earlier Indian reports based on morphology from the above crops and their molecular corroboration has been attempted. This study revealed that not only is P. nicotianae the most prevalent species but also there is the presence of both P. nicotianae and P. capsici, but not P. palmivora on betelvine; as well as possible first reports of P. nicotianae on pepper, P. capsici on chilli and P. palmivora on papaya from this vegetable growing Eastern region of the country. Mating type assays and RAPD markers were used to assess the genotypic diversity of the population. This detection of diversity is a first and critical step for helping to devise and adopt strategies for control and quarantine of these pathogens in this region. [source] Genetic diversity enhanced by ancient introgression and secondary contact in East Pacific black mangrovesMOLECULAR ECOLOGY, Issue 11 2008ALEJANDRO NETTEL Abstract Regional distribution of genetic diversity in widespread species may be influenced by hybridization with locally restricted, closely related species. Previous studies have shown that Central American East Pacific populations of the wide-ranged Avicennia germinans, the black mangrove, harbour higher genetic diversity than the rest of its range. Genetic diversity in this region might be enhanced by introgression with the locally restricted Avicennia bicolor. We tested the hypotheses of ancient hybridization using phylogenetic analysis of the internal transcribed spacer region (ITS) of the nuclear ribosomal DNA and intergenic chloroplast DNA; we also tested for current hybridization by population level analysis of nuclear microsatellites. Our results unveiled ancient ITS introgression between a northern Pacific Central American A. germinans lineage and A. bicolor. However, microsatellite data revealed contemporary isolation between the two species. Polymorphic ITS sequences from Costa Rica and Panama are consistent with a zone of admixture between the introgressant ITS A. germinans lineage and a southern Central American lineage of A. germinans. Interspecific introgression influenced lineage diversity and divergence at the nuclear ribosomal DNA; intraspecific population differentiation and secondary contact are more likely to have enhanced regional genetic diversity in Pacific Central American populations of the widespread A. germinans. [source] Measuring rDNA diversity in eukaryotic microbial systems: how intragenomic variation, pseudogenes, and PCR artifacts confound biodiversity estimatesMOLECULAR ECOLOGY, Issue 24 2007DANIEL J. THORNHILL Abstract Molecular approaches have revolutionized our ability to study the ecology and evolution of micro-organisms. Among the most widely used genetic markers for these studies are genes and spacers of the rDNA operon. However, the presence of intragenomic rDNA variation, especially among eukaryotes, can potentially confound estimates of microbial diversity. To test this hypothesis, bacterially cloned PCR products of the internal transcribed spacer (ITS) region from clonal isolates of Symbiodinium, a large genus of dinoflagellates that live in symbiosis with many marine protists and invertebrate metazoa, were sequenced and analysed. We found widely differing levels of intragenomic sequence variation and divergence in representatives of Symbiodinium clades A to E, with only a small number of variants attributed to Taq polymerase/bacterial cloning error or PCR chimeras. Analyses of 5.8S-rDNA and ITS2 secondary structure revealed that some variants possessed base substitutions and/or indels that destabilized the folded form of these molecules; given the vital nature of secondary structure to the function of these molecules, these likely represent pseudogenes. When similar controls were applied to bacterially cloned ITS sequences from a recent survey of Symbiodinium diversity in Hawaiian Porites spp., most variants (~87.5%) possessed unstable secondary structures, had unprecedented mutations, and/or were PCR chimeras. Thus, data obtained from sequencing of bacterially cloned rDNA genes can substantially exaggerate the level of eukaryotic microbial diversity inferred from natural samples if appropriate controls are not applied. These considerations must be taken into account when interpreting sequence data generated by bacterial cloning of multicopy genes such as rDNA. [source] Phylogeny and ecological radiation of New World thistles (Cirsium, Cardueae , Compositae) based on ITS and ETS rDNA sequence dataMOLECULAR ECOLOGY, Issue 1 2003Dean G. Kelch Abstract Sequence data from a portion of the external transcribed spacer (ETS) and internal transcribed spacers (ITS-1 and ITS-2) of 18S-26S nuclear ribosomal DNA were used to resolve historical biogeography and ecology of true thistles (Cirsium, Cardueae, Compositae) in the New World. The 650 base-pair, 3, portion of the ETS examined here showed a level of variation across taxa similar to that of the ITS sequences included. A maximum-likelihood tree based on combined ETS and ITS sequences leads us to suggest that the New World species of true thistles constitute a major lineage, which in turn comprises several smaller lineages. A western North American lineage shows weak quartet-puzzling support, but includes a well-supported lineage of species endemic to the California Floristic Province. Comparisons of this Californian lineage with other neoendemic angiosperm groups of the region show that the Californian Cirsium lineage exhibits unusually high ecological diversity for a group displaying such low levels of rDNA sequence divergence across taxa. Similarly low levels of sequence divergence were found throughout the New World Cirsium lineage. These results indicate either that Cirsium underwent a rapid ecological radiation in North America, or that rDNA evolution in North American Cirsium has been highly conservative. [source] Spawning times, reproductive compatibilities and genetic structuring in the Acropora aspera group: evidence for natural hybridization and semi-permeable species boundaries in coralsMOLECULAR ECOLOGY, Issue 8 2002Madeleine J. H. Van Oppen Abstract Species boundaries among five sympatric coral species of the Indo-Pacific Acropora aspera group were examined by a combination of in vitro breeding trials, comparisons of spawning times and DNA sequence analysis of ribosomal DNA internal transcribed spacer (rDNA ITS) and 5.8S regions. The breeding trials showed that reproductive compatibility exists between at least some colonies of all the species pairs tested, suggesting a large potential for natural hybridization and introgression. The Acropora ITS regions exhibited extremely high levels of variability (up to ,62% for ITS1, ,11% for 5.8S and ,43% for ITS2), but most of the variation was shared among four of the five species, A. millepora, A. papillare, A. pulchra and A. spathulata, consistent with extensive introgression. Phylogenetic analyses did not resolve these four species as distinct clusters across a wide biogeographic region stretching from the southern Great Barrier Reef to Papua New Guinea. However, most colonies of the fifth species, A. aspera, constituted a distinct clade in phylogenetic analyses. This is consistent with our observations of a semi-permeable temporal barrier involving differences in spawning times between this and the other four species. Although the majority of colonies of all five species generally spawned within 90 min of each other, in two out of four years, gametes were absent prior to mass spawning episodes from at least some A. aspera colonies. Hence, our data suggest that transient reproductive barriers may be the result of year-to-year variation in the date of spawning and that this difference in spawning time contributes to the genetic structure detected among Acropora species in this group. Occasional leakage through the reproductive barrier was confirmed by the observation of A. aspera ×A. pulchra F1 hybrids, identified based on additivity of ITS sequences. [source] On the unreliability of published DNA sequencesNEW PHYTOLOGIST, Issue 1 2003Paul D. Bridge Summary ,,Here, the reliability of published fungal nucleic acid sequences is tested by the critical re-evaluation of 206 named sequences obtained from public-access databases. ,,Sequences from the ribosomal RNA (rRNA) gene cluster were examined as these are commonly used to establish fungal phylogeny and evolution, and are also increasingly employed in the identification of fungi from nonculture based studies. ,,Fifty-one rRNA internal transcribed spacer (ITS) sequences were obtained for species of Amanita, 55 ITS sequences were obtained for species of Phoma and 100 rRNA small subunit sequences were obtained from representative genera of the order Helotiales. In each case, the fungal group was selected partly on the basis of sequences deposited by three or more laboratories in order to avoid sample bias. The results suggest that up to 20% of the sequences available for each group may be unreliable, and this proportion is supported by additional informal observations. [source] Underground primary succession of ectomycorrhizal fungi in a volcanic desert on Mount FujiNEW PHYTOLOGIST, Issue 3 2003Kazuhide Nara Summary , , Ectomycorrhizal (ECM) fungi are indispensable symbionts for the normal growth of many tree species. Here, we report the underground primary succession of ECM fungi in a volcanic desert on Mt. Fuji, Japan. , , We identified all the underground fungal constituents by comparing the fragment lengths of the internal transcribed spacer (ITS) regions in nuclear r-DNA with those of sporocarps, considering intraspecific variation of each species at the research site. ITS sequences were also used for identification. , , In total, 21 ECM fungi associated with Salix reinii were identified. Species recorded as sporocarps dominated the underground ECM community. The sere of underground ECM fungi was initiated by one or two of three first-stage fungi, and additional species were recruited with host growth, especially in the soil that developed within a vegetation patch. The species richness of ECM fungi increased significantly with host growth. , , The underground ECM community associated with unhealthy hosts differed from that of normally growing hosts. The underground ECM communities and their successional patterns might influence plant growth and plant communities during early primary succession. [source] Phylogeny of Hystrix and related genera (Poaceae: Triticeae) based on nuclear rDNA ITS sequencesPLANT BIOLOGY, Issue 5 2008H.-Q. Zhang Abstract The taxonomic status of Hystrix and phylogenetic relationships among Hystrix and its related genera of Pseudoroegneria (St), Hordeum (H), Psathyrostachys (Ns), Elymus (StH), Leymus (NsXm), Thinopyrum bessarabicum (Eb) and Lophopyrum elongatum (Ee) were estimated from sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The type species of Hystrix, H. patula, clustered with species of Pseudoroegneria, Hordeum, Elymus, Th. bessarabicum and Lo. elongatum, while H. duthiei ssp. duthiei, H. duthiei ssp. longearistata, H. coreana and H. komarovii were grouped with Psathyrostachys and Leymus species. The results indicate that: (i) H. patula is distantly related to other species of Hystrix, but is closely related to Elymus species; (ii) H. duthiei ssp. duthiei, H. duthiei ssp. longearistata, H. coreana and H. komarovii have a close affinity with Psathyrostachys and Leymus species, and H. komarovii might contain the NsXm genome of Leymus; and (iii) the St, H and Ns genomes in Hystrix originate from Pseudoroegneria, Hordeum and Psathyrostachys, respectively, while the Xm in Hystrix and Leymus has a complex relationship with the E or St genomes. According to the genomic system of classification in Tiritceae, it is reasonable to treat Hystrix patula as Elymus hystrix L, and the other species of Hystrix as species of a section of Leymus, Leymus Sect. Hystrix. [source] Erysiphe trifolii, a newly recognized powdery mildew pathogen of peaPLANT PATHOLOGY, Issue 4 2010R. N. Attanayake Diversity of powdery mildew pathogens infecting pea (Pisum sativum) in the US Pacific Northwest was investigated using both molecular and morphological techniques. Phylogenetic analyses based on rDNA ITS sequences, in combination with assessment of morphological characters, defined two groups of powdery mildews infecting pea. Group I (five field samples and three glasshouse samples) had ITS sequences 99% similar to those of Erysiphe pisi in GenBank and exhibited simple, mycelioid type of chasmothecial appendages typical of E. pisi. Erysiphe pisi is normally considered as the powdery mildew pathogen of pea. Group II (four glasshouse samples and two field samples) had ITS sequences 99% similar to those of E. trifolii and produced chasmothecia with dichotomously branched appendages similar to those of E. trifolii. There are fourteen nucleotide differences in the ITS region between the two groups. The correlation of rDNA ITS sequences with teleomorphic features for each of the two groups confirms their identity. Repeated samplings and artificial inoculations indicate that both E. pisi and E. trifolii infect pea in the US Pacific Northwest. Erysiphe trifolii is not previously known as a pathogen of pea. The existence of two distinct powdery mildew species infecting pea in both glasshouse and field environments may interfere with the powdery mildew-resistance breeding programmes, and possibly explains putative instances of breakdown of resistance in previously resistant pea breeding lines. [source] Phylogenetic relationships and pathogenicity of Colletotrichum acutatum isolates from grape in subtropical AustraliaPLANT PATHOLOGY, Issue 3 2007M. A. Whitelaw-Weckert The identity of Colletotrichum acutatum as the causal pathogen of grape ripe-rot, which causes yield loss and a bitter taint that lowers wine quality in Australian subtropical wine-grape regions, was confirmed using species-specific primers. Cultural, morphological and molecular methods (RAPD-PCR and sequencing of parts of the 5·8S-ITS regions and the ,-tubulin-2 gene) were used to determine the phylogenetic relationships of Australian C. acutatum isolates from wine grapes and other horticultural crops. A combination of RAPD-PCR and ,-tubulin-2 gene data showed that all wine-grape ripe-rot isolates from northern regions of New South Wales (NSW) and Queensland belong to a proposed new C. acutatum group (A9), together with isolates from Australian strawberry, mango, blueberry and olive. The 5·8S-ITS sequences for these grape pathogens were identical to published sequences for an isolate from Cyclamen (the Netherlands) and differed by 1 bp from isolates from Capsicum (Taiwan) and orange (Costa Rica). The grape ripe-rot isolates from the Shoalhaven Valley (southern NSW) were clustered within two other C. acutatum groups: A2 and A5. In vitro infection studies showed that Australian C. acutatum isolates from almond, blueberry, chilli, grape, mango, olive, strawberry and tomato were able to infect grape and could also infect blueberry and strawberry, indicating a lack of host specificity. This lack of host specificity, the genetic similarity with non-grape isolates, and the fact that many of the non-grape hosts were isolated from wine-growing regions, suggest the potential for cross-infection between grape and other horticultural crops. [source] There are High Levels of Functional and Genetic Diversity in Oxyrrhis marinaTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 3 2005CHRIS D. LOWE Abstract. Oxyrrhis marina, a widely distributed marine protist, is used to model heterotrophic flagellate responses in microbial food webs. Although clonal variability occurs in protists, assessments of intraspecific diversity are rare; such assessments are critical, particularly where species are used as models in ecological studies. To address the extent of intraspecific variation within O. marina, we assessed diversity among 11 strains using 5.8S rDNA and ITS sequences. The 5.8S rDNA and ITS regions revealed high divergence between strains: 63.1% between the most diverse. To compare O. marina diversity relative to other alveolates, 18S rDNA sequences for five strains were analysed with sequences from representatives of the major alveolate groups. 18S rDNA also revealed high divergence in O. marina. Additionally, consistent with phylogenies based on protein coding genes, maximum likelihood analysis indicated that O. marina was monophyletic and ancestral to the dinoflagellates. To assess ecophysiological differences, growth rates of seven O. marina strains were measured at 10 salinities (10,55,). Two salinity responses occurred: one group achieved highest growth rates at high salinities; the other grew best at low salinities. There was no clear correlation between molecular, ecophysiological, or geographical differences. However, salinity tolerance was associated with habitat type: intertidal strains grew best at high salinities; open-water strains grew best at low salinities. These data indicate the need to examine many strains of a species in both phylogenetic and ecological studies, especially where key-species are used to model ecological processes. [source] Large genetic divergence of new, morphologically similar species of sterile lichens from Europe (Lepraria, Stereocaulaceae, Ascomycota): concordance of DNA sequence data with secondary metabolitesCLADISTICS, Issue 4 2008Judith Fehrer Lichenized fungi of the genus Lepraria are known for their paucity of morphological characters. Species identification is therefore largely based on secondary chemistry. We investigated different chemotypes of the morphologically highly similar L. jackii species complex by internal transcribed spacer (ITS) sequencing. In phylogenetic analyses including all available Lepraria species, samples belonging to different chemotypes of the L. jackii agg. corresponded to four highly divergent clusters. While true L. jackii was genetically uniform, the other three clades represented previously unrecognized species. They originated from different major speciation events, and two of them were not closely related to any other species. Assessment of intraspecific genetic variability revealed four different patterns with respect to geographic scale. ITS sequences proved to be the most reliable and distinctive characters for species recognition in the Lepraria jackii complex and were in accordance with chemical and ecogeographic data. Frequent occurrence of long branches, relatively few resolved relationships despite high genetic variability, and the discovery and description of a considerable part of the Lepraria species within the last 10 years suggest that the genus is probably much larger than currently known. The diversification of this asexual group in the potential absence of recombination is discussed. © The Willi Hennig Society 2008. [source] | ||||||||||||||||||||||