Characterisation and phylogeny of repeated elements giving rise to exceptional length of ITS2 in several downy mildew genera (Peronosporaceae)

Thines, Marco

doi:10.1016/j.fgb.2006.08.002

Cited by 45 publications

(25 citation statements)

References 39 publications

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“…Both pathogens were rich in eicosapentaenoic acid (C20:5), a characteristic compound of P. halstedii (Spring and Haas 2002) underlining the relatedness of both taxa. However, Table 2 Fatty acid composition (ratio of total peak area) assayed by GC analysis of sporangia and sporangiophores of P. angustiterminalis propagated on sunflower lines and (Thines 2007). The total ITS length (3190 bp) exceeded the known size found so far within the Plasmopara genus by >20% (Spring et al 2006;Voglmayr et al 2006).…”

Section: Discussionmentioning

confidence: 97%

“…The more conserved 5.8S region (bases 219-374) shared 100% identity, and the next 76 bases (bases 375-450) of ITS-2 region showed 92.1% similarity between the two species. The extraordinary length of ITS2 with 2815 bases in total (bases 375-3190) was due to a large insertion containing 14 repeated elements (RE), which are homologous to the RE described for P. halstedii and other downy mildew species by Thines (2007). Phylogenetic trees estimated by Minimum Evolution (Rzhetsky and Nei 1993) using Jukes-Cantor distances on 610 bases of the conserved parts of ITS sequences of Plasmopara species (Fig.…”

Section: Molecular Characterisationmentioning

confidence: 99%

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Characteristics of a Plasmopara angustiterminalis isolate from Xanthium strumarium

Komjáti

Walcz²,

Virányi

et al. 2007

Eur J Plant Pathol

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Leaves of Xanthium strumarium infected with downy mildew were collected in the vicinity of a sunflower field in southern Hungary in 2003. Based on phenotypic characteristics of sporangiophores, sporangia and oospores as well as host preference the pathogen was classified as Plasmopara angustiterminalis. Additional phenotypic characters were investigated such as the size of sporangia, the number of zoospores per sporangium and the time-course of their release. Infection studies revealed infectivity of the P. angustiterminalis isolate to both X. strumarium and Helianthus annuus. Inoculation of the sunflower inbred line, HA-335 with resistance to all known P. halstedii pathotypes, resulted in profuse sporulation on cotyledons and formation of oospores in the bases of hypocotyls. Infections of sunflower differential lines often led to damping-off. Molecular genetic analysis using simple sequence repeat primers and nuclear rDNA sequences revealed clear differences to Plasmopara halstedii, the downy mildew pathogen of sunflower.

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Section: Discussionmentioning

confidence: 97%

Section: Molecular Characterisationmentioning

confidence: 99%

Characteristics of a Plasmopara angustiterminalis isolate from Xanthium strumarium

Komjáti

Walcz²,

Virányi

et al. 2007

Eur J Plant Pathol

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“…Whereas this primer has so far not found use in oomycete community studies, it has been used successfully to amplify the DNA of a wide range of oomycetes in phylogenetic research (Spring et al 2006, Thines 2007.…”

Section: Introductionmentioning

confidence: 99%

Oomycete-specific ITS primers for identification and metabarcoding

Riit¹,

Tedersoo²,

Drenkhan³

et al. 2016

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Microbial metabarcoding studies using high throughput sequencing technologies generate unprecedented amounts of DNA sequence data and make it possible to determine not only the composition of the communities but also the underlying factors powering the evolution of these communities. Despite the potential of community level studies in helping to better understand the ecology of pathogens and to manage the losses caused by them, very few oomycete addressing metabarcoding studies have been carried out and with highly variable results. The aim of this study was to develop new oomycete-specific ITS region PCR primers with improved specificity for metabarcoding and identification of oomycetes. The modified ITS1oo and the newly developed ITS3oo primers show improved in silico specificity for oomycetes and when paired with the universal ITS4 successfully amplified the DNA from all eleven tested oomycete species from six genera. High throughput sequencing of 20 soil samples from forest nurseries and bordering areas, using the primer pair ITS1oo/ITS4, recovered more than 400 oomycete OTUs, which is a significant increase over previous studies, and indicates the ability of the new method to detect various oomycete groups from complex substrates. The average fraction of oomycete reads per soil samples was 32-36%, with a maximum of 69%. The recovered oomycete OTUs represented the groups Lagenidiales, Peronosporales, Pythiales and Saprolegniales, with Pythiales dominating in all samples. In addition, the new primers were successfully used in identifying pathogens directly from infected plant tissues with Sanger sequencing. The pathogen was identified to the species or genus level in four samples out of six. In conclusion, the developed oomycete-specific primers provide a reliable method for the identification and metabarcoding of oomycetes.Copyright Taavi RESEARCH ARTICLETaavi Riit et al. / MycoKeys 14: 17-30 (2016) 18

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“…Thines (2007a) recorded similarities to the repetitive elements of the Plasmopara-Bremia clade and suggested that this may be indication of a closer relationship for these two lineages.…”

Section: Its Length Differences As Potential Markers For Speciesmentioning

confidence: 96%

“…This appears to be especially promising for the Plasmopara-Bremia clade, which was shown to have an ITS region of variable length up to about 3,200 bp (Choi et al 2007b;Komjáti et al 2007;Thines 2007a), which is remarkable compared to the usually about 800 bp in downy mildews (Voglmayr 2003;Göker et al 2004). Size increase mainly concerns the ITS2 region and originates from repetitive elements, the number and length of which appear to be taxon-specific (Choi et al 2007b;Thines 2007a, c).…”

Section: Its Length Differences As Potential Markers For Speciesmentioning

confidence: 99%

Progress and challenges in systematics of downy mildews and white blister rusts: new insights from genes and morphology

Voglmayr

2008

Eur J Plant Pathol

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Recent advances in the classification of downy mildews and white blister rusts are presented from ordinal to species level. Using molecular data (mainly LSU of nuclear ribosomal DNA and ITS rDNA data, but also cox2, beta-tubulin and NADH genes), ordinal, family and generic circumscriptions have been reconsidered and changed during the last years; species circumscription and concepts are also changing. These rearrangements also lead to a reevaluation of the traditional morphological characters used for classification. The recent changes have various implications for applied sciences (phytopathology, molecular biology) mainly at the species level; besides name changes for some taxa, revised species circumscriptions and improved species identification using genetic markers have important consequences on host ranges, source inocula and risk assessment of phytopathologically important taxa. However, there are also some substantial unresolved problems which need to be addressed in the future with new data and methods. These include the systematic position of some rarely sampled taxa, the phylogenetic relationships of the main downy mildew lineages to each other, more detailed molecular studies on speciation processes to develop appropriate sound species concepts and circumscriptions, and the development of a molecular bar coding system for downy mildews enabling reliable species identification. Applying molecular methods has the potential to greatly enhance our knowledge on the overall biodiversity of downy mildews.

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Characterisation and phylogeny of repeated elements giving rise to exceptional length of ITS2 in several downy mildew genera (Peronosporaceae)

Cited by 45 publications

References 39 publications

Characteristics of a Plasmopara angustiterminalis isolate from Xanthium strumarium

Characteristics of a Plasmopara angustiterminalis isolate from Xanthium strumarium

Oomycete-specific ITS primers for identification and metabarcoding

Progress and challenges in systematics of downy mildews and white blister rusts: new insights from genes and morphology

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