DNA barcoding, phylogeny and phylogeography of the cyst nematode species from the genus Globodera (Tylenchida: Heteroderidae)

Abstract

SummaryGlobodera presently contains 13 valid and three as yet undescribed species. Three species, G. rostochiensis, G. pallida and G. ellingtonae, the potato cyst nematodes (PCN), cause significant economic losses on potatoes around the world. In our study we provide comprehensive phylogenetic analyses of 455 ITS rRNA, 219 COI and 164 cytb gene sequences of 11 valid and two undescribed species of Globodera using Bayesian inference, maximum likelihood and statistical parsimony. New 205 COI, 116 cytb and 21 ITS rRNA gene sequences were obtained from 148 populations of these species collected from 23 countries. The phylogenetic analysis revealed that Globodera displayed two main clades in the trees: i) Globodera from South and North America parasitising plants from Solanaceae; and ii) Globodera from Africa, Europe, Asia and New Zealand parasitising plants from Asteraceae and other families. Based on the results of phylogeographical analysis and age estimation of clades with a molecular clock approach, it is hypothesised that Globodera species originated and diversified from several centres of speciation located in mountain regions and then dispersed across the world from these regions during the Pleistocene. High genetic diversity of Bolivian populations of G. rostochiensis was observed for both mtDNA genes. Analysis of phylogenetic relationships of G. pallida and G. rostochiensis populations revealed incongruence in topology between networks inferred from mtDNA genes, which might be an indication of possible recombination and selective introgression events through gene flow between previously isolated populations. This puts some limitations on the use of the mtDNA marker as universal DNA barcoding identifier for PCN. Globodera bravoae syn. n. is proposed as a junior synonym of G. mexicana.

Development and Validation of a Loop-Mediated Isothermal Amplification Diagnostic Method to Detect the Quarantine Potato Pale Cyst Nematode, Globodera pallida

“…However, we think that this species will not be a problem for PCN surveys in potato fields and for the specificity of the method because although G. mexicana is stimulated by potato root exudates, it is unable to establish and develop on potato crops [53,54]. This species seems to be present in a restricted area of Mexico (not widely spread) and only in wild Solanancearum species [55].…”

Occurrence and characterization of cyst nematode species (Globoderaspp.) associated with potato crops in Colombia

“…This finding suggests that G. pallida present in Colombia have a different origin than G. pallida present in countries such as Ukraine, England and Poland that cluster as a monophyletic clade with other Peruvian strains, and G. pallida present in Chile that cluster with a different Peruvian strain (Figs 2 and 3). Despite that P5A peruvian strain has been considered as a different species [12,17], a recent study based on ITS rRNA, COI and cytb mitochondrial regions concluded that all clades within G. pallida belong to a single species [2]. The 28S D2-D3 phylogeny, although with lower level of resolution, also clustered all but one PCN populations from Colombia with G. pallida around the globe as a monophyletic clade (Fig 2).…”

“…The cyst nematodes, Globodera Skarbilovich, 1959, are one of the most limiting plant parasitic nematodes around the world [1]. Within the genus, thirteen species have been identified, of which G. rostochiensis, G. pallida, G. ellingtonae , and G. tabacum are important for agriculture [2]. The potato cyst nematodes (PCN), Globodera rostochiensis (golden or yellow potato nematode) and Globodera pallida (pale potato nematode) cause major losses in potato ( Solanum tuberosum L.) crops [3], and are also considered as official control pests in many countries [4].…”

“…For plant-parasitic nematodes, molecular diagnostics not only improve speed and accuracy of nematode identification, but also have allowed a better understanding of the biology of nematodes as agricultural pests [10]. The genomic regions more often used to study phylogenetic relationships for plant-parasitic nematodes include DNA fragments from the 28S ribosomal DNA (rDNA), internal transcribed spacer (ITS), as well as mitochondrial DNA (mtDNA) [2,10–15]. Ribosomal genes exhibit enough conserved inter-specific neutral genetic variation as to inform species delimitation without being prone to marker saturation [15–18].…”

Taxonomy, Morphological and Molecular Identification of the Potato Cyst Nematodes, Globodera pallida and G. rostochiensis

“…There have been many phylogenetic analyses of species within the genus Globodera (e.g., [ 5 , 73 , 76 , 77 , 78 , 79 , 80 , 81 , 82 , 83 , 84 , 85 , 86 ]). A recent study, based on a phylogenetic analysis of gene sequences of three molecular markers (455 ITS rRNA, 219 COI , and 164 cytb ) of 11 valid and 2 undescribed species of Globodera [ 87 ], found that Globodera displayed two main clades in their phylogenetic trees: (i) Globodera from South and North America parasitizing plants from Solanaceae; and (ii) Globodera from Africa, Europe, Asia, and New Zealand parasitizing plants from Asteraceae and other families. They hypothesized that the split between solanaceous and non-solanaceous lineages occurred roughly 2.9 ± 0.5 Mya (million years ago), divergence dates of the solanaceous Globodera lineages started 2.7 ± 0.2 Mya and the nonsolanaceous Globodera lineages 1.6 ± 0.3 Mya, and dispersals of Globodera to Europe and New Zealand occurred 1.4 ± 0.3 and 0.9 ± 0.2 Mya, respectively.…”