Open AccessSmall Subunit Ribosomal DNA-Based Phylogenetic Analysis of Foliar Nematodes (Aphelenchoidesspp.) and Their Quantitative Detection in Complex DNA Backgrounds
Author(s) -
Katarzyna Rybarczyk-Mydłowska,
Paul Mooyman,
Hanny van Megen,
Sven van den Elsen,
M.T.W. Vervoort,
Peter T. M. Veenhuizen,
J. van Doorn,
R.H.L. Dees,
Gerrit Karssen,
J. Bakker,
J. Helder
Publication year - 2012
Publication title -
phytopathology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.264
H-Index - 131
eISSN - 1943-7684
pISSN - 0031-949X
DOI - 10.1094/phyto-05-12-0114-r
Subject(s) - biology , ribosomal dna , monophyly , phylogenetic tree , dna barcoding , botany , ribosomal rna , internal transcribed spacer , molecular phylogenetics , phylogenetics , zoology , genetics , gene , clade
Foliar nematodes, plant-parasitic representatives of the genus Aphelenchoides, constitute a minority in a group dominated by fungivorous species. Distinction between (mostly harmless) fungal feeding Aphelenchoides species and high impact plant parasites such as A. besseyi, A. fragariae, A. ritzemabosi, and A. subtenuis is severely hampered by the scarcity of informative morphological characters, some of which are only observable in specific developmental stages. Poor description of a number of non-plant-parasitic Aphelenchoides species further complicates identification. Based on (nearly) full-length small subunit ribosomal DNA (SSU rDNA) sequences (≈1,700 bp), a phylogenetic tree was generated, and the four target species appeared as distinct, well-supported groups. Notably, this genus does not constitute a monophyletic group: A. besseyi and A. ritzemabosi cluster together and they are phylogenetically isolated from A. fragariae, A. subtenuis, and most other fungivorous species. A phylum-wide SSU rDNA framework was used to identify species-specific DNA motifs. For the molecular detection of four plant-parasitic Aphelenchoides species, polymerase chain reaction primers were developed with high, identical annealing temperatures (63°C). Within the molecular framework presented here, these primers can be used for the rapid screening of plant material and soil for the presence of one or multiple foliar nematode species.