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 ◽  
...  

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.

Nematology ◽  
2015 ◽  
Vol 17 (1) ◽  
pp. 27-52 ◽  
Author(s):  
Sergei A. Subbotin ◽  
Nicola Vovlas ◽  
Gregor W. Yeates ◽  
Johannes Hallmann ◽  
Sebastian Kiewnick ◽  
...  

Morphological identification of spiral nematodes of the genus Helicotylenchus is a difficult task because most characters used for their diagnosis vary within species. In this paper we provide morphological and molecular characterisations of several spiral nematodes, H. broadbalkiensis, H. digonicus, H. dihystera, H. microlobus, H. paxilli and H. pseudorobustus, collected in different geographical areas of USA, Switzerland, Italy, New Zealand, Spain, UK, South Korea and Russia. We suggest that H. microlobus and H. pseudorobustus are valid species separated from each other morphologically and molecularly. Seven species with distinct molecular characteristics are also distinguished, but are not ascribed morphologically to any specific taxon because of the low number of specimens available. Phylogenetic relationships of H. pseudorobustus with other Helicotylenchus species are given as inferred from the analyses of 154 sequences of the D2-D3 of 28S rRNA gene and 37 sequences of ITS rRNA gene.


Nematology ◽  
2017 ◽  
Vol 19 (2) ◽  
pp. 131-173 ◽  
Author(s):  
Esther Van den Berg ◽  
Louwrens R. Tiedt ◽  
Jason D. Stanley ◽  
Renato N. Inserra ◽  
Sergei A. Subbotin

The genusScutellonemacontains more than 40 species of spiral nematodes with enlarged phasmids called scutella. In this study, we provide morphological and molecular characterisation ofS. clavicaudatumsp. n.,S. brachyurus,S. bradys,S. cavenessi,S. transvaalense,S. truncatumandScutellonemasp. A. from North and Central America, and Africa. The new species,S. clavicaudatumsp. n., was found on sugarcane in South Africa and is characterised by a lack of lip annuli as inS. africanum,S. siamenseandS. truncatum. The lip region, in both males and females, is conical and marked by six large rectangular blocks separated or fused with the submedian and lateral lip sectors, which surround a round and distinct labial disc. Females of this new species also have large vaginal glands, a functional spermatheca, the lateral field posterior to the scutellum ending in a bluntly pointed shape and a clavate tail. Morphological descriptions, measurements, light and scanning electron microscopic photos and drawings are also given forS. bradys,S. cavenessi,S. transvaalenseandS. truncatum. The study of spiral nematode samples from Florida, USA, confirmed the presence of a morphologically and genetically atypical populations ofS. bradys. The morphology of theS. bradyspopulation from Bermuda grass in pasture land from central Florida fits that of type specimens of this species, but differs in having a truncate tail terminus rather than round and also a prominent spermatheca filled with flagellate spermatozoa. Other FloridaScutellonemasamples analysed in this study belonged toS. cavenessi, a species native to West Africa. This is the first report ofS. cavenessiin Florida, where it parasitises the ornamental plantSansevieria trifasciata. Our study showed a high level of intraspecific variation forScutellonemarRNA and mtDNA genes, which can reach 5.6% for the D2-D3 of 28S rRNA, 12.9% for the ITS rRNA genes and 14.4% for theCOIgene. Phylogenetic relationships withinScutellonemaare given as inferred from the analyses of the D2-D3 of 28S rRNA, ITS rRNA and theCOImtDNA gene sequences.


Nematology ◽  
2013 ◽  
Vol 15 (6) ◽  
pp. 719-745 ◽  
Author(s):  
Esther van den Berg ◽  
Esther van den Berg ◽  
Louwrens R. Tiedt ◽  
Esther van den Berg ◽  
Louwrens R. Tiedt ◽  
...  

Scutellonema spp. are widely distributed across tropical and subtropical regions of the world and are associated with numerous agricultural and horticultural crops. Identification of many Scutellonema species is not always reliable, in part because many species share very similar diagnostic characters. In this study, we provide morphological and molecular characterisation of S. brachyurus from the USA and South Africa, S. bradys from Nigeria and three unidentified species from California, USA, New Zealand and Burkina Faso. Morphological descriptions, measurements, light and scanning electron microscopic photos and drawings are given for S. brachyurus. Females of S. brachyurus from the USA (type A) and South Africa (type B) showed a significant variation in the number of sectors and blocks on the lip annuli, ranging from about 4-12 and from 8-20, respectively. Molecular analysis using the D2-D3 of 28S rRNA, ITS rRNA and the COI mtDNA gene sequences revealed two distinct genotypes within S. brachyurus samples: type A (samples from USA, Italy, Korea, Taiwan) and type B (South Africa). Multivariate analyses determined that S. brachyurus from the USA and Taiwan (type A) differed from that from South Africa (type B) mainly in body, tail and DGO lengths, and ratios b′, c′, c and V. Phylogenetic relationships within Scutellonema are given as inferred from the analyses of the D2-D3 of 28S rRNA, ITS rRNA and the COI mtDNA gene sequences. PCR-RFLP diagnostic profiles and PCR with species-specific primers are developed for the studied Scutellonema species.


Nematology ◽  
2012 ◽  
Vol 14 (8) ◽  
pp. 961-976 ◽  
Author(s):  
Esther van den Berg ◽  
Louwrens R. Tiedt ◽  
Sergei A. Subbotin

During recent collections in South Africa, two species of Criconemoides were found. Criconemoides brevistylus is described and illustrated from a golf course in KwaZulu-Natal Province. It is compared with several closely related species, and three previously described species (C. helicus, C. onostris and C. paronostris) are regarded as junior synonyms of C. brevistylus. Criconemoides obtusicaudatus is described and illustrated from a maize field in Limpopo Province. The male of the species is described for the first time. Molecular characterisation of C. brevistylus and C. obtusicaudatus using the D2-D3 expansions segments of 28S rRNA and ITS rRNA gene sequences are provided. Phylogenetic relationships of these species with other Criconemoides are discussed.


Nematology ◽  
2008 ◽  
Vol 10 (5) ◽  
pp. 611-632 ◽  
Author(s):  
Manuel Mundo-Ocampo ◽  
Alberto Troccoli ◽  
Sergei A. Subbotin ◽  
Julio Del Cid ◽  
James G. Baldwin ◽  
...  

Abstract Phylogenetic analysis of five gene fragments: ITS-rRNA, D2 and D3 of 28S rRNA, 18S rRNA, Hsp90 and actin, of Heterodera species and two representative Afenestrata species, A. koreana and A. orientalis, form a clade with H. cynodontis, H. bifenestra and an unidentified Heterodera sp. infecting grasses. Based on these results and the consideration that the key diagnostic characters of Afenestrata are convergent and do not define a clade, synonymisation of Afenestrata with Heterodera is proposed. The following new combinations are made: H. africana comb. n., H. axonopi comb. n., H. koreana comb. n., and H. orientalis comb. n. Furthermore, H. (= Afenestrata) sacchari is renamed as H. saccharophila nom. nov. to avoid homonymy. All these species, together with H. bamboosi, are regarded as members of a paraphyletic ‘Afenestrata group’ within Heterodera. Whilst recognised as artificial, the Afenestrata group is nevertheless an aid to discussion about these similar species. Morphological and molecular characterisation of populations of H. koreana comb. n. from Florida and H. orientalis comb. n. from Florida and Guatemala verify the identification of these populations as valid representatives for molecular studies of the species. Light and SEM observations also provide new detail and a broader understanding of the morphological range of both species. These include a longer stylet for females of H. koreana comb. n. and H. orientalis comb. n. than reported in the original descriptions. In addition, previously unreported tuberculate ridges are noted on the surface of vulval lips of H. orientalis comb. n. The lip region of second-stage juveniles of H. koreana comb. n. and H. orientalis comb. n. both include fused adjacent submedian lips that also fuse with the labial disc and the second lip annulus. The ITS-rRNA gene sequences of H. orientalis comb. n. populations from Florida and Guatemala were similar to those from the Russian type locality. Diagnostic PCR-RFLP of ITS-rRNA profiles with six enzymes for H. orientalis comb. n. and H. koreana comb. n. are given. A key for the morphological identification of species of the Afenestrata group is provided.


Nematology ◽  
2016 ◽  
Vol 18 (1) ◽  
pp. 67-107 ◽  
Author(s):  
Esther Van Den Berg ◽  
Juan E. Palomares-Rius ◽  
Nicola Vovlas ◽  
Louwrens R. Tiedt ◽  
Pablo Castillo ◽  
...  

The reniform nematodes of the genusRotylenchulusare semi-endoparasites of numerous herbaceous and woody plant roots and are mainly distributed in tropical and subtropical regions. In this study, we provide morphological and molecular characterisation of six out of ten presently known valid species ofRotylenchulus:R. clavicaudatus,R. leptus,R. macrodoratus,R. macrosoma,R. reniformisandR. saccharifrom South Africa, USA, Italy and Spain.Rotylenchulus parvuswas only studied morphologically. A new species,R. macrosomoidessp. n., isolated from soil and roots of sugarcane in South Africa, is described. The phylogeny ofRotylenchulus, as inferred from the analyses of D2-D3 of 28S rRNA, ITS rRNA,coxImtDNA andhsp90gene sequences, is presented. The study revealed thatR. reniformisandR. macrosomahave a sister relationship, but that relationships between otherRotylenchulusspecies remain unresolved. The phylogenetic analysis also confirmed the hypothesis that this genus originated from the Afrotropical zoogeographical region. Our study revealed thatR. reniformisandR. macrosomoidessp. n. have two distinct rRNA gene types andR. macrosomahave three rRNA gene types in their genomes. PCR with species-specific primers was developed for rapid diagnostics ofR. reniformis.


Nematology ◽  
2010 ◽  
Vol 12 (2) ◽  
pp. 303-308 ◽  
Author(s):  
Esther van den Berg ◽  
Sergei A. Subbotin ◽  
Louwrens R. Tiedt

AbstractTwo Hemicycliophora species, H. lutosa and H. typica, found in samples from fallow soil and sugarcane soil in South Africa, were studied morphologically and, for the first time, molecularly. Diagnostic PCR-IT-rRNA-RFLP profiles generated by five restriction enzymes are provided. Study of phylogenetic relationships using D2-D3 expansion segment of 28S rRNA gene sequences revealed that H. lutosa was related to H. poranga. Hemicycliophora lutosa and H. poranga are compared morphologically. SEM photographs are given for H. typica and for H. lutosa for the first time. The male of H. typica represents a first report for South Africa.


Plant Disease ◽  
2013 ◽  
Vol 97 (7) ◽  
pp. 1005-1005 ◽  
Author(s):  
Z. Tanha Maafi ◽  
Z. Majd Taheri ◽  
S. A. Subbotin

The giant stem nematode, Ditylenchus gigas (Nematoda: Tylenchida) has been recorded from several European and African countries mainly bordering the Mediterranean Sea (2). This nematode causes considerable yield loss of broad bean, Vicia faba, and it may induce more severe damage than the typical faba bean race of D. dipsaci. Spread of infestation through seed limits export of broad bean and has made these nematodes quarantine pests in many countries (2). Broad bean is cultivated in the north, west, southwest, and central parts of Iran. Although D. dipsaci has been reported from different crops and regions in Iran, there is no record of broad bean infection by this nematode. A survey of broad bean fields was conducted in the north and west provinces in a continuation of a study on different populations of D. dipsaci in Iran in May to July of 2007 and 2008 and resampling from some farms in June 2012. The sampling was performed at flowering stage and after. The aboveground plant samples were collected and cut into pieces of 2 to 3 cm, then incubated for 5 to 6 h in Whitehead trays. Morphological and molecular analysis of isolated nematodes from Kermanshah and Lorestan provinces revealed the presence of D. gigas in the samples. Of the 23 plant samples of cv. Barekat collected from Mazandaran and Golestan provinces in the north, 47.8% were infected with stem nematode, mostly with high population density of over 20,000 nematodes per 5 plant stems. The percentage of infected samples of broad bean cv. Shakhbozy collected in Lorestan and Kermanshah provinces in the west was 76.5%. The symptoms of infection were observed as necrotic lesions on the stem surface and reduction of internode distances in severe infection. The giant stem nematode population from Kermanshah showed the following characters: females (n = 20), L = 1,650 ± 140 (1,270 to 1,875) μm; b′ = 8.6 ± 0.6 (7.7 to 10.0), c = 19.0 ± 1.3 (19.2 to 21.2), c′ = 4.7 ± 0.5 (1.1 to 5.3), stylet = 11.6 ± 0.5 (11 to 12) μm; post vulval sac = 96 ± 16 (58 to 140) μm; vulval-anus distance = 217.0 ± 21.0 (178 to 272) μm, tail = 86.4 ± 9.4 (66 to 102) μm; males (n = 10), L = 1,495 ± 148 (1,236 to 1,636) μm; b′ = 7.7 ± 0.3 (7.3 to 8.1), c = 17.3 ± 0.7 (16.3 to 18.6), stylet = 11.3 ± 0.5 (11 to 12) μm, tail = 86.5 ± 8.5 (71 to 95) μm, spicules = 24.8 ± 1.7 (23 to 28) μm. The morphological and morpohometric features were generally in agreement with those published for D. gigas (2). The morphological identification of D. gigas from Iran was supported by the analyses of the ITS rRNA and the D2-D3 expansion segments of the 28S rRNA gene sequences. The rRNA gene of D. gigas from broad bean and D. dipsaci from garlic were amplified and sequenced using two primer sets: (i) the TW81 and AB28 for the ITS-rRNA and (ii) D2A and D3B for partly 28S rRNA gene, as described by (2). New sequences were deposited in the GenBank under accession numbers KC310732 through KC310735. The Iranian D. gigas sequences showed 100% similarity with those of the Italian D. gigas isolates (ITS rRNA: HQ219231, HQ219232; D2-D3 of 28S rRNA: HQ219217 and HQ219216). The identification was further supported by PCR with species specific SCAR (sequence characterized amplified region) primers for this species (1). The specimens from broad bean generated a specific fragment ∼200 bp for D. gigas, whereas the samples with D. dipsaci from garlic and alfalfa produced one fragment ∼250 bp specific for this species. To our knowledge, this is the first report of D. gigas from broad bean in Iran. References: (1) M. Esquibet et al. Genome 46:1077, 2003. (2) N. Vovlas et al. Plant Pathol. 60:762, 2011.


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

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.


Nematology ◽  
2011 ◽  
Vol 13 (7) ◽  
pp. 773-785 ◽  
Author(s):  
Sergei A. Subbotin ◽  
Abbas Mohammad Deimi ◽  
Jingwu Zheng ◽  
Vladimir N. Chizhov

Abstract Seventy-eight ITS rRNA gene sequences obtained from the potato rot nematode, Ditylenchus destructor, collected across the world from different hosts were compared and analysed. The ITS rRNA gene sequences showed significant length variation between populations. The differences in this rRNA fragment length were due to the presence of repetitive elements in the ITS1, which were characterised by relatively higher rates of substitution changes. Reconstruction of secondary structure for the ITS1 revealed that these minisatellites formed a stem structure. Phylogenetic analyses of ITS rRNA and D2-D3 expansion segments of 28S rRNA gene sequences showed that all studied populations clustered in two major clades: a group of populations having the ITS sequences with the repetitive elements and a group of populations without the repetitive elements in the ITS. We propose to distinguish seven ITS rRNA haplotypes within potato rot nematode populations. PCR-ITS-RFLP diagnostic profiles are presented for these ITS haplotypes and usefulness of recently developed PCR methods with species-specific primers for D. destructor are analysed and discussed.


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