Molecular characterisation of some stubby root nematodes (Nematoda: Trichodoridae) from the USA and other countries

Nematology ◽  
2019 ◽  
Vol 22 (1) ◽  
pp. 39-52 ◽  
Author(s):  
Sergei A. Subbotin ◽  
Ignacio Cid Del Prado Vera ◽  
Renato N. Inserra ◽  
Vladimir N. Chizhov ◽  
Wilfrida Decraemer
Keyword(s):  
Nematode Species ◽  
Rrna Gene ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
28S Rrna Gene ◽  
Putative Species ◽  
Geographical Regions ◽  
Wide Range ◽  
The Usa ◽  
Stubby Root Nematode

Summary The stubby root nematodes are world-wide distributed polyphagous root ectoparasites and can cause damage to a wide range of crops and natural vegetation. In this study, 22 valid and putative species of stubby root nematodes were identified in 37 samples collected in Malaysia, Mexico, Russia, and the USA (California, Florida, Minnesota and Nevada). The analysis of 58 new sequences of the D2-D3 expansion fragments of 28S rRNA gene revealed the following species: Nanidorus minor from California, Florida and Mexico, N. renifer from Florida, two unidentified Nanidorus species from California and Malaysia, respectively, Paratrichodorus allius from Florida and Minnesota, P. pachydermus and Paratrichodorus sp. from Russia, Trichodorus californicus, T. intermedius, and T. obscurus from California, T. obtusus from Florida, eight unidentified Trichodorus species from California, one unidentified Trichodorus species from Nevada, and two unidentified species of stubby root nematodes, one of Trichodorus and another undetermined species from Mexico. Molecular characterisation of T. californicus, T. intermedius and T. obscurus is given for the first time. The phylogenetic tree reconstructed from the analysis of 108 D2-D3 of 28S rRNA gene sequences of 58 valid and putative species of the stubby root nematodes contained five major clades: i) Trichodorus from Europe, Asia and North America; ii) Nanidorus and Trichodorus from Asia; iii) Trichodorus from California; iv) Paratrichodorus from several distant geographical regions; and v) Monotrichodorus from Central and South America. It has been hypothesised that the California Floristic Province is one of the centres of origin and diversification of stubby root nematodes. There is no information on the economic importance of the stubby root nematode species found in California and Mexico. The confirmation of the occurrence of N. renifer and P. allius in Florida should be of concern for the blueberry and potato industries in the state.

Morphological and molecular characterisation of Tylencholaimellus zeinabadensis sp. n. (Dorylaimida: Tylencholaimellidae) from Iran, with additional data on five known species of the genus

Nematology ◽  
2019 ◽  
Vol 21 (6) ◽  
pp. 597-612
Author(s):  
Nasir Vazifeh ◽  
Gholamreza Niknam ◽  
Habibeh Jabbari ◽  
Arezoo Naghavi ◽  
Reyes Peña-Santiago
Keyword(s):  
New Species ◽  
Additional Data ◽  
Rrna Gene ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
Gene Sequences ◽  
Pharyngeal Bulb ◽  
Molecular Analyses ◽  
28S Rrna Gene ◽  
Region 10

Summary Six species of the genus Tylencholaimellus, one new and five known, collected in virgin and cultivated soils of East Azarbaijan province, Iran, are studied. Tylencholaimellus zeinabadensis sp. n. is morphologically characterised by its 1.2-1.7 mm long body, lip region 10-13 μm wide and offset by deep and broad constriction, odontostyle 16-20 μm long, stylet 22-30 μm long, neck 186-234 μm long, pharyngeal bulb 30-43 μm long, anterior uterine sac 55-103 μm long or 0.9-1.7 corresponding body diam. long, V = 34-41, tail short and rounded to conoid (20-30 μm, c = 45-83, c′ = 0.5-1.0), spicules 39-50 μm long, and one or two ventromedian supplements with hiatus. Molecular analyses using the D2-D3 expansion regions of the 28S rRNA gene sequences of the new species confirmed the monophyly of this genus based upon currently available data. A population of T. affinis is described and illustrated, and new data (morphometrics, pictures and distribution) are provided for T. loofi, T. paracinctus, T. polonicus and T. striatus.

Morphological and molecular characterisation of several Paratylenchus Micoletzky, 1922 (Tylenchida: Paratylenchidae) species from South Africa and USA, together with some taxonomic notes

Nematology ◽  
2014 ◽  
Vol 16 (3) ◽  
pp. 323-358 ◽  
Author(s):  
Esther Van den Berg ◽  
Esther Van den Berg ◽  
Louwrens R. Tiedt ◽  
Esther Van den Berg ◽  
Louwrens R. Tiedt ◽  
...  
Keyword(s):  
South Africa ◽  
Rrna Genes ◽  
Morphological Identification ◽  
Rrna Gene ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
Electron Microscopic ◽  
Wide Range ◽  
Its Rrna Gene ◽  
Its Rrna

Pin nematodes of the genus Paratylenchus are widely distributed across the world and associated with many plant species. Morphological identification of Paratylenchus species is a difficult task because it relies on many characters with a wide range of intraspecific variation. In this study we provide morphological and molecular characterisation of several pin nematodes: Paratylenchus aquaticus, P. dianthus, P. hamatus, P. nanus and P. straeleni, collected in different states of the USA and South Africa. Paratylenchus aquaticus is reported from South Africa and Hawaii and P. nanus is found from South Africa for the first time. Morphological descriptions, morphometrics, light and scanning electron microscopic photos and drawings are given for these species. Molecular characterisation of nematodes using the D2-D3 of 28S rRNA and ITS rRNA gene sequence revealed that samples morphologically identified as P. aquaticus, P. hamatus and P. nanus indeed represent species complexes containing several species. Sequences of the rRNA genes are also provided for several unidentified Paratylenchus. Phylogenetic relationships within the genus Paratylenchus are given as inferred from the analyses of the D2-D3 of 28S rRNA and ITS rRNA gene sequences. We present here the most complete phylogenetic analysis of the genus.

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

Nematology ◽  
2015 ◽  
Vol 17 (4) ◽  
pp. 459-477 ◽  
Author(s):  
Sergei A. Subbotin ◽  
Jason D. Stanley ◽  
Antoon T. Ploeg ◽  
Zahra Tanha Maafi ◽  
Emmanuel A. Tzortzakakis ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Date Palm ◽  
Nematode Species ◽  
Phoenix Dactylifera ◽  
28S Rrna ◽  
Gene Trees ◽  
Isolated Populations ◽  
Date Palms ◽  
Geographical Regions ◽  
The Usa

Needle nematode populations ofLongidorus orientalisassociated with date palm,Phoenix dactylifera, and detected during nematode surveys conducted in Arizona, California and Florida, USA, were characterised morphologically and molecularly. The nematode species most likely arrived in California a century ago with propagative date palms from the Middle East and eventually spread to Florida on ornamental date palms that were shipped from Arizona and California. This is the first validated continental record of this needle nematode species in the USA and the Americas. The USA populations ofL. orientaliscontained a small number of males that were not reported in the original description and are herein described.Longidorus orientaliswas able to survive for at least 4 years at very low numbers in the warm and humid environment of Florida on date palms imported from California and Arizona. Association ofL. orientaliswithL. africanuswas observed in all of the surveyed sites, indicating that date palm is a host of both nematodes. Phylogenetic relationships ofL. orientaliswith closely relatedLongidorusspecies, in addition to relationships between populations ofL. orientalisfrom the USA, Greece, Iran and Spain, were inferred from the analyses of D2-D3 of 28S rRNA, ITS1 rRNA and partialcoxIgene sequences. The PCR-D2-D3 expansion segments of 28S rDNA-RFLP diagnostic profile is provided.Longidorus orientalispopulations display a high level of intraspecific variation (up to 15.5%) incoxImtDNA sequences. Analysis of phylogenetic relationships of nematode populations revealed incongruence of the ITS1 rRNA andcoxImtDNA gene trees, which might be the result of selective introgression of mtDNA through gene flow between previously isolated populations introduced simultaneously into new geographical regions.

Descriptions of Trichodorus lownsberyi sp. n., Nanidorus minor (Colbran, 1956) Siddiqi, 1974 (Nematoda: Trichodoridae) and Longidorus quercus sp. n. (Nematoda: Longidoridae) from Mexico

Nematology ◽  
2021 ◽  
pp. 1-15
Author(s):  
Ignacio Cid del Prado Vera ◽  
Sergei A. Subbotin ◽  
Wilfrida Decraemer
Keyword(s):  
New Species ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
The Body ◽  
Rrna Gene ◽  
28S Rrna ◽  
Gene Sequences ◽  
28S Rrna Gene ◽  
Buxus Sempervirens ◽  
Stubby Root Nematode

Summary A new species of stubby root nematode, Trichodorus lownsberyi sp. n., collected from soil around Buxus sempervirens at Montecillo Campus, Colegio de Postgraduados, Mexico, is described and illustrated. Trichodorus lownsberyi sp. n. is characterised by the abundant males with a characteristic spicule shape, the narrower part about mid-blade having visible bristles in most specimens, and the presence and position of the three ventromedian cervical papillae, which are all anterior to the secretory-excretory pore. Females possess a rhomboid-shaped vagina and oval to rounded triangular vaginal sclerotised pieces with a pore-like vulva. The phylogenetic relationships of T. lownsberyi sp. n. with related species were constructed using the ITS2 rRNA and the D2-D3 expansion segments of 28S rRNA gene sequences. Trichodorus lownsberyi sp. n. was a sister species to T. viruliferus in the phylogenetic trees. A Mexican population of Nanidorus minor from a peach orchard is also described and illustrated. The new needle nematode, Longidorus quercus sp. n., was recovered from soil around roots of oak, Quercus crassipes, from Cerro Jusda ‘El Diablo’ in Mexico State. Longidorus quercus sp. n. females are characterised by the C-shaped posterior end of the body after fixation, L = 4.9 (3.9-5.6) mm, a = 71 (60.8-93.2), lip region rounded, sometimes slightly flattened, marked by depression, odontostylet 170 (144-206) μm long, hemispherical to bluntly conoid tail and no males. The new species was characterised using the D2-D3 of 28S rRNA and COI gene sequences. The phylogenetic relationships of L. quercus sp. n. with other Longidorus species were reconstructed using the D2-D3 of 28S rRNA gene sequences.

Morphological and molecular characterisation of some Hemicriconemoides species (Nematoda: Criconematidae) together with a phylogeny of the genus

Nematology ◽  
2014 ◽  
Vol 16 (5) ◽  
pp. 519-553 ◽  
Author(s):  
Esther Van den Berg ◽  
Louwrens R. Tiedt ◽  
Renato N. Inserra ◽  
Jason D. Stanley ◽  
Nicola Vovlas ◽  
...  
Keyword(s):  
Fruit Trees ◽  
Valid Species ◽  
Rrna Gene ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
Electron Microscopic ◽  
Specific Primers ◽  
Scanning Electron Microscopic ◽  
The Usa ◽  
Species Specific

Sheathoid nematodes of the genusHemicriconemoidesare migratory root-ectoparasites of many plants including various agricultural crops and fruit trees. They are generally found inhabiting warm areas of the world and presently consist of 52 valid species. In this study we provide morphological and molecular characterisation of 12 species of this genusviz.:H. alexis,H. brachyurus,H. californianus,H. chitwoodi,H. macrodorus,H. minutus,H. ortonwilliamsi,H. promissus,H. silvaticus,H. strictathecatus,H. wessoniandHemicriconemoidessp. originating from China, Greece, Japan, Myanmar, Spain, South Africa and the USA. Morphological descriptions, measurements, light and scanning electron microscopic observations and drawings are given for several species. Phylogenetic relationships withinHemicriconemoides, as inferred from the analyses of the D2-D3 of 28S rRNA and ITS-rRNA gene sequences, resulted in trees with three major clades that corresponded with species groupings based on morphology of the lip pattern and vulval flap. PCR with species-specific primers were developed forH. californianus,H. chitwoodiandH. strictathecatus.

scholarly journals Intra-species sequence variability in 28s rRNA gene of Oesophagostomum venulosum isolated from goats of West Bengal, India

2010 ◽  
Vol 3 (7) ◽  
pp. 515-518 ◽  
Author(s):  
Subhasish Bandyopadhyay ◽  
Asit Kumar Bera ◽  
Sourav Sikdar ◽  
Sumanta De ◽  
Subhashree Ghosh ◽  
...  
Keyword(s):  
West Bengal ◽  
Rrna Gene ◽  
28S Rrna ◽  
Sequence Variability ◽  
28S Rrna Gene

scholarly journals Occurrence and molecular characterization of cyst nematode species (Globodera spp.) associated with potato crops in Colombia

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0241256
Author(s):  
Daniela Vallejo ◽  
Diego A. Rojas ◽  
John A. Martinez ◽  
Sergio Marchant ◽  
Claudia M. Holguin ◽  
...  
Keyword(s):  
Management Strategies ◽  
Nematode Species ◽  
Globodera Pallida ◽  
Rrna Gene ◽  
Potato Cyst Nematodes ◽  
28S Rrna ◽  
Cyst Nematodes ◽  
Nucleotide Substitutions ◽  
Internal Transcribed Spacer Region ◽  
The Status

Potato cyst nematodes (PCN) from the genus Globodera spp. cause major losses in the potato (Solanum tuberosum) industry worldwide. Despite their importance, at present little is known about the status of this plant pathogen in cultivated potatoes in Colombia. In this study, a total of 589 samples collected from 75 geographic localities in nine potato producing regions of Colombia (Cundinamarca, Boyacá, Antioquia, Nariño, Santander, Norte de Santander, Tolima, Caldas and Cauca) were assayed for the presence of potato cyst nematodes. Fifty-seven percent of samples tested positive for PCN. Based on phylogenetic analysis of the internal transcribed spacer region (ITS1-5.8S-ITS2) of the rRNA gene and D2-D3 expansion segments of the 28S rRNA gene, all populations but one were identified as Globodera pallida. Sequences of G. pallida from Colombia formed a monophyletic group closely related to Peruvian populations, with the lowest average number of nucleotide substitutions per site (Dxy = 0.002) and net nucleotide substitutions per site (Da = 0.001), when compared to G. pallida populations from Europe, South and North America. A single sample formed a well-supported subclade along with G. rostochiensis and G. tabacum from Japan, USA and Argentina. To our knowledge this is the first comprehensive survey of Globodera populations from Colombia that includes genetic data. Our findings on species diversity and phylogenetic relationships of Globodera populations from Colombia may help elucidate the status and distribution of Globodera species, and lead to the development of accurate management strategies for the potato cyst nematodes.

scholarly journals Phylogenetic Analysis of 28S rRNA Gene of Indigenous Xiphinema pachydermum

2019 ◽  
Vol 8 (07) ◽  
pp. 1960-1968
Author(s):  
Anju Sharma ◽  
Satish K. Sharma ◽  
Kiran Rana ◽  
Anil Kumar Verma
Keyword(s):  
Phylogenetic Analysis ◽  
Rrna Gene ◽  
28S Rrna ◽  
28S Rrna Gene

scholarly journals Detection and Discrimination of Pratylenchus neglectus and P. thornei in DNA Extracts from Soil

Plant Disease ◽  
2008 ◽  
Vol 92 (11) ◽  
pp. 1480-1487 ◽  
Author(s):  
Guiping Yan ◽  
Richard W. Smiley ◽  
Patricia A. Okubara ◽  
Andrea Skantar ◽  
Sandra A. Easley ◽  
...  
Keyword(s):  
Nematode Species ◽  
Wheat Root ◽  
Fungal Species ◽  
Parasitic Nematodes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Pratylenchus Neglectus ◽  
Pcr Products ◽  
Species Specific ◽  
Plant Parasitic

A species-specific polymerase chain reaction (PCR) method was developed to detect and identify the root-lesion nematodes Pratylenchus neglectus and P. thornei from soil. A primer set was designed from Pratylenchus 28S rRNA gene sequences of the D3 expansion domain. Primer specificity was confirmed with 23 isolates of 15 nematode species and other plant-parasitic and non-plant-parasitic nematodes typically present in the soil communities, and with six fungal species commonly associated with wheat root rot. DNA obtained using a commercially available kit and a method developed in our laboratory gave comparable amplification. PCR conditions were optimized and the two species were differentiated by PCR products of 144 bp for P. neglectus and 288 bp for P. thornei. With this assay, we detected a single juvenile in 1 g of sterile, inoculated soil. Examination of 30 field soil samples revealed that this method was applicable to a range of soils naturally infested with these two pathogens in Oregon. This PCR-based method is rapid, efficient, and reliable, does not require expertise in nematode taxonomy and morphology, and could be used as a rapid diagnostic tool for commercial and research applications for disease forecasting and management.

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