Synonymy of Afenestrata with Heterodera supported by phylogenetics with molecular and morphological characterisation of H. koreana comb. n. and H. orientalis comb. n. (Tylenchida: Heteroderidae)

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.

Download Full-text

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

Nematology ◽

10.1163/15685411-00002769 ◽

2014 ◽

Vol 16 (3) ◽

pp. 323-358 ◽

Cited By ~ 17

Author(s):

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.

Download Full-text

First Report of the Giant Stem Nematode, Ditylenchus gigas, from Broad Bean in Iran

Plant Disease ◽

10.1094/pdis-01-13-0069-pdn ◽

2013 ◽

Vol 97 (7) ◽

pp. 1005-1005 ◽

Cited By ~ 2

Author(s):

Z. Tanha Maafi ◽

Z. Majd Taheri ◽

S. A. Subbotin

Keyword(s):

Broad Bean ◽

Morphological Identification ◽

Rrna Gene ◽

28S Rrna ◽

African Countries ◽

First Report ◽

28S Rrna Gene ◽

The North ◽

Plant Samples ◽

Its Rrna

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.

Download Full-text

Description of Tylenchulus musicola sp. n. (Nematoda: Tylenchulidae) from banana in Iran with molecular phylogeny and characterisation of species of Tylenchulus Cobb, 1913

Nematology ◽

10.1163/156854111x596242 ◽

2012 ◽

Vol 14 (3) ◽

pp. 353-369 ◽

Cited By ~ 5

Author(s):

Zahra Tanha Maafi ◽

Majid Amani ◽

Jason D. Stanley ◽

Renato N. Inserra ◽

Esther Van den Berg ◽

...

Keyword(s):

New Species ◽

Rapid Identification ◽

Rrna Genes ◽

Rrna Gene ◽

28S Rrna ◽

Specific Primers ◽

Diagnostic Pcr ◽

Second Stage ◽

Species Specific ◽

A New Species

During a survey conducted on banana plantations in Sistan and Blouchestan province, south-east Iran, a new species of Tylenchulus was extracted from the soil and roots of banana plants. This species, named Tylenchulus musicola sp. n., is characterised by mature females having a swollen, hook-shaped body with a conical and elongate post-vulval portion ending in a round terminus, males having a weak stylet and a cylindrical and thick tail ending in a bluntly rounded and smooth terminus, and by second-stage juveniles having a slender body and a posterior body portion ending in a finely pointed or mucronate terminus. The results of glasshouse host tests indicated that the new species does not parasitise sugarcane ratoons or sour orange seedlings. Tylenchulus musicola sp. n. is distinguished from other known Tylenchulus species by the sequences of D2-D3 expansion segments of 28S rRNA and ITS rRNA genes. Phylogenetic relationships within Tylenchulus were reconstructed based on rRNA gene sequences using Bayesian inference. Diagnostic PCR-ITS-RFLP profiles are presented for T. musicola sp. n., T. furcus, T. graminis, T. palustris, T. semipenetrans and Trophotylenchulus floridensis. PCR with species-specific primers and genus-specific primer are tested and developed for rapid identification of five Tylenchulus species. An identification key to Tylenchulus species is provided.

Download Full-text

Characterization of South American Snails of the GenusBiomphalaria(Basommatophora: Planorbidae) andSchistosoma mansoni(Platyhelminthes: Trematoda) in Molluscs by PCR-RFLP

BioMed Research International ◽

10.1155/2016/1045391 ◽

2016 ◽

Vol 2016 ◽

pp. 1-5 ◽

Cited By ~ 7

Author(s):

Roberta Lima Caldeira ◽

Tatiana Maria Teodoro ◽

Liana Konovaloff Jannotti-Passos ◽

Pollanah M. Lira-Moreira ◽

Christiane De Oliveira Goveia ◽

...

Keyword(s):

Latin American ◽

Morphological Characteristics ◽

Its Region ◽

Morphological Identification ◽

Correct Identification ◽

Lack Of Information ◽

Pcr Rflp ◽

Mollusc Species ◽

Identification Of Species ◽

Molecular Profiles

The identification of snails of the genusBiomphalariacan be done using morphological characteristics which depends on the size of the snails and skill and knowledge of researcher. These methods sometimes are not adequate for identification of species. The PCR-RFLP, using the ITS region of the rDNA, has been used to identify Brazilian species of the genusBiomphalaria. Nevertheless, there is a lack of information about snails from other Latin American countries. In addition, some snails may be infected bySchistosoma mansoniand when submitted to PCR-RFLP they show molecular profiles different from those previously standardized for the other mollusc species. In this work the molecular profiles of 15 species and the subspecies were established by PCR-RFLP of ITS-rDNA with the enzymeDdeI. Moreover, the molecular profiles of host species,B. glabrata,B. straminea,B. tenagophila, andB. prona, infected byS. mansoniwere also established. The molluscs were dissected to permit morphological identification. These results contribute to a correct identification of snails of the genusBiomphalariaand detection of these snails infected byS. mansoni.

Download Full-text

Morphological and molecular characterisation of Caloosia longicaudata (Loos, 1948) Siddiqi & Goodey, 1963 (Nematoda: Caloosiidae) from Maui, the Hawaiian Islands with notes on some species of the genus

Nematology ◽

10.1163/138855410x528947 ◽

2011 ◽

Vol 13 (4) ◽

pp. 381-393 ◽

Cited By ~ 2

Author(s):

Esther van den Berg ◽

Sergei Subbotin ◽

Louwrens Tiedt

Keyword(s):

18S Rrna ◽

Hawaiian Islands ◽

Rrna Gene ◽

28S Rrna ◽

Molecular Characterisation ◽

Diagnostic Pcr ◽

Rflp Profile ◽

First Time ◽

Partial 18S ◽

Scanning Electron

AbstractCaloosia longicaudata is described from Maui, the Hawaiian Islands, for the first time and both sexes are characterised morphologically using light and scanning electron microscopy. Molecular characterisation of C. longicaudata using the D2-D3 domain of 28S rRNA, partial 18S rRNA and ITS rRNA gene sequences is also provided. The phylogenetic relationships of this species with other representatives of the suborder Criconematina are presented and discussed. A diagnostic PCR-ITS-RFLP profile for C. longicaudata is given together with an identification table for eight species of Caloosia. Caloosia langola n. comb. is transferred to the genus and C. shorai is synonymised with H. psidii.

Download Full-text

Morphological and molecular characterisation of Hemicycliophora lutosa Loof & Heyns, 1969 and H. typica de Man, 1921 from South Africa (Nematoda: Hemicycliophoridae)

Nematology ◽

10.1163/138855409x12511010796671 ◽

2010 ◽

Vol 12 (2) ◽

pp. 303-308 ◽

Cited By ~ 7

Author(s):

Esther van den Berg ◽

Sergei A. Subbotin ◽

Louwrens R. Tiedt

Keyword(s):

South Africa ◽

Phylogenetic Relationships ◽

Restriction Enzymes ◽

Rrna Gene ◽

28S Rrna ◽

Molecular Characterisation ◽

Diagnostic Pcr ◽

Fallow Soil ◽

De Man ◽

First Time

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.

Download Full-text

Morphological and molecular characterisation of Helicotylenchus pseudorobustus (Steiner, 1914) Golden, 1956 and related species (Tylenchida: Hoplolaimidae) with a phylogeny of the genus

Nematology ◽

10.1163/15685411-00002850 ◽

2015 ◽

Vol 17 (1) ◽

pp. 27-52 ◽

Cited By ~ 11

Author(s):

Sergei A. Subbotin ◽

Nicola Vovlas ◽

Gregor W. Yeates ◽

Johannes Hallmann ◽

Sebastian Kiewnick ◽

...

Keyword(s):

New Zealand ◽

Related Species ◽

Phylogenetic Relationships ◽

Valid Species ◽

Molecular Characteristics ◽

Morphological Identification ◽

Rrna Gene ◽

28S Rrna ◽

Molecular Characterisation ◽

Its Rrna Gene

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.

Download Full-text

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

Nematology ◽

10.1163/15685411-00002707 ◽

2013 ◽

Vol 15 (6) ◽

pp. 633-651 ◽

Cited By ~ 14

Author(s):

Zahra Majd Taheri ◽

Zahra Tanha Maafi ◽

Zahra Majd Taheri ◽

Zahra Tanha Maafi ◽

...

Keyword(s):

Ornamental Plants ◽

Rrna Gene ◽

28S Rrna ◽

Diagnostic Pcr ◽

28S Rrna Gene ◽

Phylogenetic Studies ◽

Unknown Species ◽

Tea Plantations ◽

Cereal Fields ◽

High Level

Thirteen species of Pratylenchidae: Pratylenchus coffeae, P. delattrei, P. loosi, P. neglectus, P. penetrans, P. pseudopratensis, P. thornei, 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. thornei, 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.

Download Full-text

Additional data on Pratylenchoides riparius (Andrássy, 1985) Luc, 1986 (Nematoda: Merliniidae) from Iran

Nematology ◽

10.1163/15685411-00003257 ◽

2019 ◽

Vol 21 (8) ◽

pp. 827-836 ◽

Cited By ~ 1

Author(s):

Manouchehr Hosseinvand ◽

Ali Eskandari ◽

Reza Ghaderi

Keyword(s):

Taxonomic Status ◽

Molecular Data ◽

18S Rrna Gene ◽

Rrna Gene ◽

Similar Species ◽

28S Rrna ◽

Lateral Field ◽

Molecular Phylogenetic ◽

Type Population ◽

Stylet Length

Summary The second population of Pratylenchoides riparius, including females and males, is described and illustrated based upon morphological, morphometric and molecular data. The present population from Iran is characterised by some differences with the type population of the species from Hungary in stylet length (24-26 vs 21-22 μm), slightly longer body (1002-1230 vs 830-960 μm), pharynx (202-211 vs 182-190 μm) and tail (64-85 vs 48-57 μm), areolated outer bands of the lateral field (vs non-areolated), widening of the lateral field near tail terminus (vs lateral incisures connecting each other) and presence of males (vs absent). The taxonomic status of the species with regarding the data from the type and presently recovered population, as well as the closely similar species is discussed. The newly recovered population was studied based upon its molecular phylogenetic charactes using the D2-D3 of 28S rRNA and the partial 18S rRNA gene sequences and the results revealed that it forms a clade with P. magnicauda in 28S, but occupies a distant placement from it in 18S phylogeny.

Download Full-text

Molecular and morphological characterisation of Sphaeronema alni Turkina & Chizhov, 1986 (Nematoda: Sphaeronematidae) from Spain compared with a topotype population from Russia

Nematology ◽

10.1163/138855410x489338 ◽

2010 ◽

Vol 12 (4) ◽

pp. 649-659 ◽

Cited By ~ 6

Author(s):

Juan Palomares-Rius ◽

Nicola Vovlas ◽

Sergei A. Subbotin ◽

Alberto Troccoli ◽

Carolina Cantalapiedra-Navarrete ◽

...

Keyword(s):

Phylogenetic Trees ◽

18S Rrna ◽

Castanea Sativa ◽

Rrna Gene ◽

28S Rrna ◽

Rflp Profile ◽

Basal Clade ◽

Pcr Rflp ◽

First Time ◽

Partial 18S

Abstract The occurrence of a male-less population of Sphaeronema alni parasitising chestnut (Castanea sativa) roots and inducing a stelar syncytium is reported for the first time in Pola de Somiedo (Oviedo province), Spain. Morphometric and molecular characters of the Spanish population matched those of a topotype population from Russia. SEM observations showed swollen females having the first lip annulus wider than the second and appearing as a cap-like, circumoral elevation. The second-stage juveniles, having a single band in the lateral fields, were characterised by a non-annulated dome-shaped lip region derived from the fusion of the oral disc with all the lip sectors and lip annuli, and showing slit-like amphidial apertures and an oval prestoma. The sequences of the D2-D3 expansion segments of 28S rRNA, partial 18S rRNA and ITS rRNA gene for the Spanish and topotype populations of S. alni were congruent and matched those deposited in GenBank for another population from Germany, thereby confirming their conspecificity. A PCR-RFLP profile of D2-D3 of 28S rRNA for identification of this species was also provided. The phylogenetic relationships between S. alni populations and representatives of the suborder Criconematina, as inferred from analysis of partial 18S rRNA and D2-D3 of 28S gene sequences obtained in this and previous studies, indicated that S. alni formed a basal clade on the majority consensus Bayesian phylogenetic trees, standing together with Meloidoderita sp. or alone. These findings provide additional evidence of the need to clarify the position of Sphaeronema within Criconematina and its relationships with representatives of Tylenchulinae.

Download Full-text