Molecular and phylogenetic studies on Pratylenchidae from Iran with additional data on Pratylenchus delattrei, Pratylenchoides alkani and two unknown species of Hirschmanniella and Pratylenchus

Abstract

Thirteen species of Pratylenchidae: Pratylenchus coffeae, P. delattrei, P. loosi, P. neglectus, P. penetrans, P. pseudopratensis, P. thomei, P. vulnus, Pratylenchus sp., Pratylenchoides alkani, P. ritteri, Hirschmanniella sp. and Zygotylenchus guevarai were collected from different crops and plants throughout Iran. The specimens were identified using morphological and molecular methods. Morphometrics and morphology are given for Pratylenchus sp., P. delattrei, Pratylenchoides alkani and Hirschmanniella sp. The D2-D3 expansion segments of the 28S rRNA gene were amplified and sequenced for all 13 species studied. Diagnostic PCR-ITS-RFLP profiles are given for Pratylenchus delattrei, P. penetrans, P. pseudopratensis, Pratylenchus sp., Pratylenchoides alkani and P. ritteri. Pratylenchus neglectus and P. thomei, collected from cereal fields, P. loosi from tea plantations, P. coffeae from banana, P. penetrans from ornamental plants, P. vulnus from pines and Z. guevarai from almonds showed a high level of similarity in the D2-D3 sequences with corresponding GenBank sequences. Nucleotide differences between Iranian populations and reference species were in the intraspecific range. Pratylenchus delattrei, found in vegetable fields, and Pratylenchus sp. from palm rhizosphere, formed a highly supported clade with P. zeae, the two former species being morphologically very close to the latter except in tail shape. Pratylenchus pseudopratensis, from cereal fields, clustered with P. vulnus with low support. Phylogenetic relationships within Pratylenchus species were mainly congruent with those obtained in previous studies. Despite the morphological similarities between P. ritteri and P. alkani, the D2-D3 of 28S rRNA gene sequences differed by 5 bp. Hirschmanniella sp., from a rice field, formed a clade with H. loofi and H. kwazuna.

Phylogenetic relationships of Telotylenchidae Siddiqi, 1960 and Merliniidae Siddiqi, 1971 (Nematoda: Tylenchida) from Iran, as inferred from the analysis of the D2D3 expansion fragments of 28S rRNA gene sequences

“…The length of alignment had 704 positions. A new sequence of P. ritteri was identical to that already published for P. alkani (Majd Taheri et al, 2013) and sequence variation within P. ritteri/P. alkani varied from 0.0 to 1.2% (0-8 bp).…”

“…The newly obtained sequences of the D2D3 of 28S rRNA were aligned using ClustalX 1.83 (Thompson et al, 1997) with default parameters and corresponding pub lished gene sequences (Subbotin etal., 2006;Majd Taheri et al, 2013;Stirling et al, 2013). Outgroup taxa were chosen according to the result of a previous study (Sub botin et al, 2006).…”

Characterization of Pratylenchus crenatus and P. neglectus (Nematoda: Pratylenchidae) associated with wheat crop

“…Sequence analysis of D2/D3 expansion segments of P. neglectus (accession numbers KM580546-KM580550) differ by 0.17 -0.50 %. The sequences of D2/D3 differs from other accession numbers EU130854, EU130855 , HM469438 (unpublished), JQ303333 (Kumari, 2012), JX046968, JX046969 (Wang et al, 2012), JX261946, JX261947, JX261951 (Majd Taheri et al, 2013) by 0.17 -1.51 % and these 14 sequences (KM580546-KM580550, EU130854, EU130855, HM469438, JQ303333, JX046968, JX046969, JX261946, JX261947, JX261951) varied by 0.17 -2.01 %. The aim of this study was to identify two Pratylenchus species associated with wheat crop in the Czech Republic.…”

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

“…ZTM-2013 and Pratylenchus sp. DP-2010) were added to the clade VI based on the LSU D2D3 tree (Taheri et al 2013;Palomares-Rius et al 2014). The trees obtained from molecular analysis of different rDNA sequences placed P. parazeae n. sp.…”