Molecular variability and phylogenetic relationships among different species and populations of Pratylenchus (Nematoda: Pratylenchidae) as inferred from the analysis of the ITS rDNA

Abstract

Sequence comparisons and molecular phylogenetic analyses were used to describe the nucleotide variability of the ITS containing regions of eighteen Pratylenchus species and several populations. Comparative analysis of nucleotide sequences of the rDNA internal transcribed spacers (ITS1 and ITS2) among Pratylenchus species used in the present study demonstrates that ITS sequences can widely vary in primary sequence and length. Alignment of eightyseven Pratylenchus sequences and one outgroup taxon reveals the presence of ambiguous regions that have the greatest effect on phylogeny reconstruction. Phylogenetic analyses using Bayesian Inference, Neighbour Joining-LogDet, Maximum Likelihood and Maximum Parsimony, distinguished twelve highly or moderately supported major clades within Pratylenchus. Our results support the taxonomic usefulness of the ITS region to identify root-lesion nematode species of the genus Pratylenchus but the high nucleotide variability, sometimes, can preclude its use to resolve relationships among all members of the genus. In addition, the phylogenetic groupings are not congruent with those defined by characters derived by lip patterns and numbers of lip annuli.

Morphological and molecular charaterisation of Pratylenchus parazeae n. sp. (Nematoda: Pratylenchidae) parasitizing sugarcane in China

“…The closest and published sequences were selected for phylogenetic analyses. Outgroup taxa for each dataset were chosen according to previous molecular phylogenetic analyses for rootlesion nematodes Palomares-Rius et al 2010;De Luca et al 2011). DNA sequences were aligned in MEGA4.0 (Tamura et al 2003) using default parameters.…”

Genetic diversity of ITS sequences of Bursaphelenchus xylophilus

“…Intraspecific diversity between virulent and avirulent B. xylophilus isolates has been detected using RFLP analysis with the enzyme HhaI (Aikawa et al, 2003(Aikawa et al, , 2006. ITS genetic diversity has been reported within species and individuals from a diverse range of eukaryotes, including insects (Fairley et al, 2005;Li and Wilkerson, 2007), marine sponges (Worheide et al, 2004;Vierna et al, 2010), fungi (Horton, 2002;Smith et al, 2007), and nematodes such as Meloidogyne (Hugall et al, 1999), Brugia (Areekit et al, 2009), Ascaris (Leles et al, 2010), and Pratylenchus (De Luca et al, 2011). However, to our knowledge, no data on ITS intra-isolate and intra-individual diversity in B. xylophilus or other Bursaphelenchus species have been published.…”

Genetic diversity of Bursaphelenchus cocophilus in South America

“…The present study focused on the molecular characterisation of B. cocophilus populations from Brazil and Colombia using the most informative ribosomal DNA genetic loci currently used for nematode phylogeny (Fouly et al, 1997;Kaplan et al, 2000;De Luca et al, 2011;Subbotin et al, 2011;Marek et al, 2014) and allowing the design of a species-specific primer pair for accurate identification of B. cocophilus. Here we characterised the genetic diversity of several B. cocophilus populations from Brazil and Colombia.…”

“…In recent years, much work has been done on the molecular characterisation of different Bursaphelenchus species (Burgermeister et al, 2005(Burgermeister et al, , 2009Mota et al, 2006;Ye et al, 2007;Zhang et al, 2008;Li et al, 2009;Cardoso et al, 2012;Valadas et al, 2012Valadas et al, , 2013Marek et al, 2014). Within this genus, the LSU (D2-D3) and the ITS-1/2 ribosomal regions have been targeted for diversity studies (Mota et al, 2006;De Luca et al, 2011;Subbotin et al, 2011;Cardoso et al, 2012;Sultana et al, 2013) and for diagnosis purposes (Burgermeister et al, 2005(Burgermeister et al, , 2009. Both regions are used since they provide a valuable tool in the identification of nematodes (PalomaresRius et al, 2010(PalomaresRius et al, , 2013 and reconstruction of phylogenetic relationships (Kaplan et al, 2000;Ye et al, 2007;Coomans et al, 2012).…”