Development of taxon-specific sequence characterized amplified region (SCAR) markers based on actin sequences and DNA amplification fingerprinting (DAF): a case study in the Phoma exigua species complex

M.M. Aveskamp, J.H.C. Woudenberg, J. de Gruyter, E. Turco, J.Z. Groenewald, P.W. Crous

    Research output: Contribution to journal/periodicalArticleScientificpeer-review

    49 Citations (Scopus)

    Abstract

    Phoma exigua is considered to be an assemblage of at least nine varieties that are mainly distinguished on the basis of host specificity and pathogenicity. However, these varieties are also reported to be weak pathogens and secondary invaders on non-host tissue. In practice, it is difficult to distinguish P. exigua from its close relatives and to correctly identify isolates up to the variety level, because of their low genetic variation and high morphological similarity. Because of quarantine issues and phytosanitary measures, a robust DNA-based tool is required for accurate and rapid identification of the separate taxa in this species complex. The present study therefore aims to develop such a tool based on unique nucleotide sequence identifiers. More than 60 strains of P. exigua and related species were compared in terms of partial actin gene sequences, or analysed using DNA amplification fingerprinting (DAF) with short, arbitrary, mini-hairpin primers. Fragments in the fingerprint unique to a single taxon were identified, purified and sequenced. Alignment of the sequence data and subsequent primer trials led to the identification of taxon-specific sequence characterized amplified regions (SCARs), and to a set of specific oligonucleotide combinations that can be used to identify these organisms in plant quarantine inspections.
    Original languageEnglish
    Pages (from-to)403-414
    Number of pages12
    JournalMolecular Plant Pathology
    Volume10
    Issue number3
    DOIs
    Publication statusPublished - 2009

    Keywords

    • Actins
    • Ascomycota
    • Base Sequence
    • DNA Fingerprinting
    • Genetic Markers
    • Genome, Fungal
    • Molecular Sequence Data
    • Nucleic Acid Amplification Techniques
    • Phylogeny
    • Polymerase Chain Reaction
    • Sequence Alignment
    • Sequence Analysis, DNA
    • Species Specificity

    Fingerprint

    Dive into the research topics of 'Development of taxon-specific sequence characterized amplified region (SCAR) markers based on actin sequences and DNA amplification fingerprinting (DAF): a case study in the Phoma exigua species complex'. Together they form a unique fingerprint.

    Cite this