Restriction Fragment Length Polymorphisms in Nuclear and Mitochondrial DNA of<i>Sclerotinia</i>Species

Kohn, Linda M.; Petsche, Dawna M.; Bailey, Stuart; Novak, Lion; Anderson, James B.

doi:10.1094/phyto-78-1047

Cited by 68 publications

(39 citation statements)

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“…RFLP analysis allowed separation of species belonging to the genera Laccaria (Gardes et al, 1990), Armillaria (Smith & Anderson, 1989) and Sclerotinia The GenBank accession numbers for the sequences reported in this paper are given in Methods. (Khon et al, 1988). PCR investigations have mainly focused on nucleotide sequences of the internal transcribed spacer (ITS) located between the nuclear rDNA 18S and 28S subunit genes, and made it possible to determine the relationships between fungal species from the genus Ganoderma (Molcalvo et al, 1995).…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6 and V9 domains The GenBank accession numbers for the sequences reported in this paper are given in Methods.

Gonzalez

Labarère

2000

Microbiology

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A comparative study of the V4, V6 and V9 domains of the mitochondrial smallsubunit (SSU) rRNA was conducted to evaluate the use of these sequences to investigate phylogenetic relatedness within the genus Pleurotus. The PCR products encompassing these regions from 48 isolates belonging to 16 Pleurotus species were sequenced and compared. From this comparison, the length and sequence of the three domains were found to be constant within a species. Significant inter-species variations due to insertion/deletion events were found, in most cases occurring in regions not directly involved in the maintainance of the standard SSU rRNA secondary structure. Phylogenetic analysis based upon these mitochondrial sequences was in agreement with relationships previously established by morphological descriptions and with previous studies based upon the nuclear genome or isozymes ; moreover such analysis resolved some ambiguities in earlier analyses. It was confirmed that P. ostreatus and P. florida represent a single species, as well as P. pulmonarius and P. sajor-caju. The phylogenetic analysis also made it possible to assess the relative positions of P. rattenburyi, P. lampas, P. sapidus, P. colombinus and P. eryngii. The results clearly showed that sequences of the V4, V6 and V9 domains of the mitochondrial SSU rRNA could provide good markers for use in the taxonomy and phylogeny of species of Basidiomycota. Because of their nucleotide conservation, the major advantage of these species-specific markers was the possibility to study only one isolate from each species to determine phylogenetic relatedness.

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Section: Introductionmentioning

confidence: 99%

Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6 and V9 domains The GenBank accession numbers for the sequences reported in this paper are given in Methods.

Gonzalez

Labarère

2000

Microbiology

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“…Diverse isolates of both S. sclerotiorum and Sclerotinia trifoliorum differed in virulence on alfalfa cultivars, and experiment-cultivar and experiment-isolate interactions were observed, but no isolate-cultivar interaction was detected (Pratt and Rowe, 1995). However, comparisons of S. sclerotiorum population on cultivated oilseed rape and on wild perennial host Rannunculus ficaria indicated major differences between agricultural and wild populations (Kohn et al, 1988). DNA fingerprint diversity is high in agricultural populations but low in wild populations and there is no evidence of outcrossing in agricultural populations, even though recombination occurs in wild populations.…”

Section: Multiple Genetic Changes Associated With Gain Of Virulencementioning

confidence: 87%

Case Study: Sclerotinia sclerotiorum: Genetic Diversity and Disease Control

Petrofeza¹,

Nasser²

2012

The Molecular Basis of Plant Genetic Diversity

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“…It is morphologically indistinguishable from S. sclerotiorum, but it was shown to be a distinct species based on distinctive polymorphisms in sequences from internal transcribed spacer 2 (ITS2) of the nuclear ribosomal repeat (7). The other three species have been delimited using morphological, cytological, biochemical, and molecular characters (3,8,9,10,12,15). Interestingly, given that the ITS is sufficiently polymorphic in many fungal genera to resolve species, in Sclerotinia, only species 1 and S. trifoliorum are distinguished by characteristic ITS sequence polymorphisms; S. sclerotiorum and S. minor cannot be distinguished based on ITS sequence (2,7).…”

mentioning

confidence: 99%

“…In cultures freshly isolated from infected plants, investigators usually have mycelia and sclerotia but not apothecia. Restriction fragment length polymorphisms (RFLPs) in ribosomal DNA (rDNA) are diagnostic for Sclerotinia species (3,10), but the assay requires cloned probes (usually accessed from other laboratories) hybridized to Southern blots from vertical gels, an impractical procedure for large samples. We have analyzed sequence data from previous phylogenetic studies (2) and have identified diagnostic variation for the rapid identification of the four Sclerotinia species.…”

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confidence: 99%

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Single Nucleotide Polymorphism-Based Diagnostic System for Crop-Associated Sclerotinia Species

Andrew

Kohn

2009

Appl Environ Microbiol

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A molecular diagnostic system using single nucleotide polymorphisms (SNPs) was developed to identify four Sclerotinia species: S. sclerotiorum (Lib.) de Bary, S. minor Jagger, S. trifoliorum Erikss., and the undescribed species Sclerotinia species 1. DNAs of samples are hybridized with each of five 15-bp oligonucleotide probes containing an SNP site midsequence unique to each species. For additional verification, hybridizations were performed using diagnostic single nucleotide substitutions at a 17-bp sequence of the calmodulin locus. The accuracy of these procedures was compared to that of a restriction fragment length polymorphism (RFLP) method based on Southern hybridizations of EcoRI-digested genomic DNA probed with the ribosomal DNAcontaining plasmid probe pMF2, previously shown to differentiate S. sclerotiorum, S. minor, and S. trifoliorum. The efficiency of the SNP-based assay as a diagnostic test was evaluated in a blind screening of 48 Sclerotinia isolates from agricultural and wild hosts. One isolate of Botrytis cinerea was used as a negative control. The SNP-based assay accurately identified 96% of Sclerotinia isolates and could be performed faster than RFLP profiling using pMF2. This method shows promise for accurate, high-throughput species identification.

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Restriction Fragment Length Polymorphisms in Nuclear and Mitochondrial DNA ofSclerotiniaSpecies

Cited by 68 publications

References 0 publications

Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6 and V9 domains The GenBank accession numbers for the sequences reported in this paper are given in Methods.

Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6 and V9 domains The GenBank accession numbers for the sequences reported in this paper are given in Methods.

Case Study: Sclerotinia sclerotiorum: Genetic Diversity and Disease Control

Single Nucleotide Polymorphism-Based Diagnostic System for Crop-Associated Sclerotinia Species

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