A highly efficient electrophoretic method for discrimination between two Neoscytalidium species using a specific fungal internal transcribed spacer (ITS) fragment
Language English Country United States Media print-electronic
Document type Journal Article
PubMed
30109569
DOI
10.1007/s12223-018-0641-0
PII: 10.1007/s12223-018-0641-0
Knihovny.cz E-resources
- MeSH
- Ascomycota classification genetics isolation & purification MeSH
- DNA, Fungal genetics MeSH
- Species Specificity MeSH
- Electrophoresis, Agar Gel * MeSH
- Ficus microbiology MeSH
- Phylogeny MeSH
- Genetic Variation * MeSH
- DNA, Ribosomal Spacer chemistry genetics MeSH
- Plant Diseases microbiology MeSH
- Polymerase Chain Reaction MeSH
- RNA, Ribosomal, 5.8S chemistry genetics MeSH
- Sequence Analysis, DNA MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- DNA, Fungal MeSH
- DNA, Ribosomal Spacer MeSH
- RNA, Ribosomal, 5.8S MeSH
Neoscytalidium (or N.) dimidiatum and N. novaehollandiae are two aggressive plant pathogenic species that affect several agricultural crops. Early detection and identification of these fungi are of critical importance to bring about the effective minimization to the threat they pose to the infected plants. Herein, two species of Neoscytalidium were rapidly discriminated by utilizing the rRNA internal transcribed (ITS4-5.8S-ITS5) PCR primers. A total of 100 isolates of Neoscytalidium species, which were isolated from Iraqi canker-infected fig trees, were included in this study. Two discrete electrophoretic PCR bands were observed in Neoscytalidium isolates-A-variants were about 546 bp, while B-variants were about 993 bp in length. The comprehensive phylogenetic analysis of both DNA variants revealed that A-variants resided between N. novaehollandiae and N. hyalinum, while B-variants were closely related to N. dimidiatum. Furthermore, the highly specific re-constructed tree of both electrophoretic variants demonstrated that B-variants share a high similarity with N. novaehollandiae. Additionally, the secondary structures for both variants were predicted computationally to reveal the structural patterns that each variant follows. In conclusion, a small rRNA locus comprising 22 nucleotides that differs in the two variants is potentially responsible for this species-specific classification. The main divergence in the amplified loci led to the classification of these fungal variants into two main species, namely N. dimidiatum and N. novaehollandiae, demonstrating that the amplification by ITS4-ITS5 rRNA fragment is a beneficial strategy that can be employed for the assessment of Neoscytalidium diversity in the natural ecosystems.
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