Molecular phylogeny of the nematode genusLongidorus(Nematoda: Longidoridae) with description of three new species

Abstract

The phylum Nematoda includes the genus Longidorus, a remarkable group of invertebrates that are polyphagous root‐ectoparasites of many plants including various agricultural crops and trees. Damage is caused by direct feeding on root cells as well as by transmitting nepoviruses. Species discrimination in Longidorus is complicated by phenotypic plasticity (intraspecific variability and minor interspecific differences) leading to potential misidentification. We conducted nematode surveys in cultivated and natural environments in southern Spain that detected 11 species of Longidorus. We developed a comparative study amongst these related species by considering morphological and morphometric features together with molecular data from nuclear ribosomal RNA genes [D2‐D3 expansion segments of large ribosomal subunit (28S), internal transcribed spacer 1 (ITS1), and partial small ribosomal subunit (18S)]. The results of our molecular and phylogenetic analyses confirmed the morphological hypotheses and allowed the delimitation and discrimination of three new species of the genus, described herein as Longidorus baeticus sp. nov., Longidorus oleae sp. nov., and Longidorus andalusicus sp. nov., and eight known species (Longidorus alvegus, Longidorus crataegi, Longidorus fasciatus, Longidorus intermedius, Longidorus iuglandis, Longidorus magnus, Longidorus rubi, and Longidorus vineacola). Phylogenetic analyses of Longidorus spp. based on the three molecular markers resulted in a general consensus of these species grouping, as lineages were maintained for the majority of species (i.e. species with a conoid‐rounded lip region, amphidial fovea asymmetrically bilobed, female tail bluntly rounded), but not in some others (i.e. positions of L. crataegi, L. intermedius, and L. rubi were quite variable). To date, this is the most complete phylogenetic analysis for Longidorus and Paralongidorus species, with the highest number of species included. No correspondence between phylogenetic trees and morphological characters was found for ribosomal markers, with the exception of amphidial shape. Thus, polyphasic identification, based on integration of molecular analysis with morphology, is a tool beyond doubt in Longidorus identification. © 2013 The Linnean Society of London

Description and molecular phylogeny of one new and one known needle nematode of the genus Paralongidorus (Nematoda: Longidoridae) from grapevine in Portugal using integrative approach

“…D2-D3 expansion segments of 28S rRNA and ITS rRNA have proved to be more effective in species identification when compared to partial 18S rRNA, as both these markers display more molecular variability than partial 18S rRNA (He et al 2005, Palomares-Rius et al 2008, Pedram et al 2012, Kornobis et al 2015, Barsi & De Luca 2017. Additionally, the mitochondrial DNA (mtDNA) markers have been used for species identification, phylogeny and phylogeography in a large number of species inside Longidoridae (Lazarova et al 2006, Gutiérrez-Gutiérrez et al 2011, 2013a,b, Kumari 2014, Subbotin et al 2014, however there is a lack of the mitochondrial molecular data on Paralongidorus spp. Only a small fraction of Paralongidorus species (nine identified species) has so far sequences in the GenBank database.…”

An update on the genus Longidorus, Paralongidorus and Xiphinema (Family Longidoridae) in Portugal

“…Despite this, the taxonomy within the genus Longidorus, Paralongidorus and Xiphinema is controversial, with a large number of putative species continuously being the subject of debate (Decraemer & Chaves 2012;Archidona-Yuste et al 2016a, b;Esmaeili et al 2016). Currently, molecular techniques are used as supplementary tools to help in the differentiation at species level (Gutiérrez-Gutiérrez et al 2012, 2013aTzortzakakis et al 2014;Esmaeili et al 2016;Handoo et al 2016). An integrative approach based upon the combination of classical morphological taxonomy and molecular barcoding of ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) genes is a useful strategy for identification at species level within the family Longidoridae.…”

Characterisation of populations of Longidorus orientalis Loof, 1982 (Nematoda: Dorylaimida) from date palm (Phoenix dactylifera L.) in the USA and other countries and incongruence of phylogenies inferred from ITS1 rRNA and coxI genes

“…The new sequences of D2-D3 of 28S rRNA, ITS1 rRNA and coxl of mtDNA genes were aligned using ClustalX 1.83 with default parameters with their corre sponding published gene sequences (Kumari et al, 2009;Palomares-Rius et al, 2010;Gutierrez-Gutierrez et al, 2013;Tzortzakakis et al, 2014). Outgroup taxa for each data set were chosen according to the results of previously published data (Gutierrez-Gutierrez et a l, 2013; Subbotin et al, 2013).…”