Vladimir N. Chizhov

Phylogenetic analysis of Tylenchida Thorne, 1949 as inferred from D2 and D3 expansion fragments of the 28S rRNA gene sequences

The evolutionary relationships of 82 species of tylenchid and aphelenchid nematodes were evaluated by use of sequence data of the D2 and D3 expansion fragments of the 28S ribosomal RNA genes. Nine automatic and one culled sequence alignments were analysed using maximum parsimony and Bayesian inference approaches. The molecular data sets showed that the order Tylenchida comprises lineages that largely correspond to two suborders, Hoplolaimina and Criconematina, and other taxonomic divisions as proposed by Siddiqi (2000). Several significant results also derived from our study include: i) the basal position of groups that include entomoparasitic nematodes within tylenchid trees; ii) paraphyly of the superfamily Dolichodoroidea sensu Siddiqi (2000); iii) evidence for a Pratylenchus, Hirschmanniella and Meloidogyne clade; and iv) lack of support for widely held traditional placement of Radopholus within Pratylenchidae and placement of this genus within Hoplolaimidae or Heteroderidae. Congruence and incongruence of molecular phylogeny and traditional classifications and morphological-based hypotheses of phylogeny of tylenchids are discussed.

Evolution of the gall-forming plant parasitic nematodes (Tylenchida: Anguinidae) and their relationships with hosts as inferred from Internal Transcribed Spacer sequences of nuclear ribosomal DNA.

Phylogenetic relationships among gall-forming plant parasitic nematodes of the subfamily Anguininae are reconstructed by maximum parsimony and maximum likelihood analyses. Sequences of the ITS of rDNA from 53 populations and species of gall-forming nematodes and five populations of the Ditylenchus dipsaci species complex were analysed. The phylogenetic trees strongly support monophyly of the genus Anguina and show nonmonophyly for the genera Mesoanguina and Heteroanguina. Morphological and biological characters are generally congruent with the anguinid groups identified in the rDNA phylogeny. Analyses of evolution of different gall types among anguinids reveal that there are apparent evolutionary trends in gall evolution: from abnormal swelling and growth of infested plant organs toward small localised galls, and from infestation of vegetative toward generative organs. Our study demonstrates that the main anguinid groups are generally associated with host plants belonging to the same or related systematic groups. The comparison of the ITS phylogenies of anguinids parasitising Poaceae and their host grasses shows a high level of cospeciation events.

Molecular characterisation and diagnostics of some Longidorus species (Nematoda: Longidoridae) from Russia and other countries using rRNA genes

The needle nematodes of the genus Longidorus can cause diseases of various crops and trees, and are comprised of more than 150 valid species. Eleven valid and six unidentified species of the genus Longidorus collected in different regions of Russia, two states of USA, Germany, New Zealand and Ukraine were molecularly characterized using analysis of the partial 18S rRNA and the D2–D3 expansion segments of the 28S rRNA gene sequences. Fifty-four partial 28S rRNA and fifteen partial 18S rRNA gene sequences were obtained for the present study. Using molecular criteria, we confirmed the morphological identification and distinguished between the following species: L. aetnaeus, L. africanus, L. andalusicus, L. artemisiae, L. caespiticola, L. distinctus, L. elongatus, L. euonymus, L. intermedius, L. leptocephalus and L. lignosus. Two longidorid populations from Russia and four from California were not identified to a species level. We obtained the full length D2–D3 of 28S rRNA gene sequence from several freshly-collected L. artemisiae samples. We confirmed the identity of the D2 region of 28S rRNA gene sequence with a short D2 of 28S rRNA gene fragment sequence previously obtained from formalin-fixed nematodes embedded in the L. artemisiae paratype slides. Longidorus lignosus was molecularly characterized and L. aetnaeus was reported from Russia for the first time. PCR-D2-D3-RFLP diagnostic profiles generated by five restriction enzymes: AluI, HinfI, Bsp143I, Tru1I and RsaI are presented for sixteen Longidorus species.

Length variation and repetitive sequences of Internal Transcribed Spacer of ribosomal RNA gene, diagnostics and relationships of populations of potato rot nematode, Ditylenchus destructor Thorne, 1945 (Tylenchida: Anguinidae)

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.

Molecular and morphological characterisation of Xiphinema americanum-group species (Nematoda: Dorylaimida) from California, USA, and other regions, and co-evolution of bacteria from the genus Candidatus Xiphinematobacter with nematodes

The Xiphinema americanum -group is a large species complex containing more than 50 nematode species. They are economically important because they are vectors of nepoviruses. The species differentiation of X. americanum -group is problematic because the species share similar morphological characters. In the present study we collected nematode samples from different locations in the USA, Italy and Russia. Six valid species, X. americanum s. str. , X. brevicolle , X. californicum , X. pachtaicum , X. rivesi and X. simile , and four unidentified putative Xiphinema species were characterised by morphology and sequencing of D2-D3 of 28S rRNA, ITS1 rRNA and mitochondrial COI genes. New nematode sequences generated totalled 147. Phylogenetic relationships of the X. americanum -group species reconstructed by Bayesian inference for D2-D3 of 28S rRNA gene sequences did not provide clear species delimitation of the samples studied, although the mtDNA presented interspecific variations useful for demarcation among species. Xiphinema americanum s. str. , X. californicum , X. pachtaicum , X. rivesi , and two unidentified Xiphinema species were found in 72 soil samples from California. We also reconstructed the phylogenetic relationships using partial 16S rRNA gene sequences within endosymbiotic bacteria of the genus Candidatus Xiphinematobacter and provided solid evidence for distinguishing 17 species of this genus based on the analysis of new and previously published sequences. Fifty-five new bacterial sequences were obtained in the present study and comparison of the bacterial 16S rRNA and nematode COI phylogenies revealed a high level of co-speciation events between host and symbiont.

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

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.

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

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.

Diagnostics of stem and bulb nematodes, Ditylenchus weischeri and D. dipsaci (Nematoda: Anguinidae), using PCR with species-specific primers

Abstract The stem and bulb nematodes of the Ditylenchus dipsaci (Kühn) Filipjev species complex are obligate endoparasites of various agricultural plants, causing stunting and swelling and resulting in significant economic losses. Recently, a new closely related Ditylenchus species, D. weischeri Chizhov, Borisov and Subbotin, a parasite of the cosmopolitan herbaceous perennial weed, Cirsium arvense (L.) Scop., was described. Many countries impose quarantine restrictions for the presence of D. dipsaci in imported plant and soil materials. In the current study, we developed PCR with species-specific primers for the rapid and reliable separation of D. weischeri and D. dipsaci using gel electrophoresis and melting curve analysis. Species-specific primer sets were designed based on the nucleotide sequence of the heat shock protein (hsp90) gene for both nematode species. The PCR protocol was verified using samples of D. weischeri, D. dipsaci and the closely related species, D. gigas, which parasitizes broadbean (Vicia faba L.). The species-specific primer sets were able to detect D. weischeri and D. dipsaci from samples containing mixtures of Ditylenchus species. The PCR species-specific protocol should allow for more rapid identification of Ditylenchus species recovered from plant materials than previously possible.

An implementation of the matrix multiplication algorithm SUMMA in mpf

In this paper, we present a new parallel Fortran extension called mpF. The language based on both data and task parallelism allows explicit specification of data and computations distribution. We discuss some reasons for the language design and demonstrate the basic mpF features on an example of the parallel matrix multiplication algorithm SUMMA. The mpF implementation is compared with its MPI counterpart.

A fortran evolution of mpc parallel programming language

mpF is a new parallel extension of Fortran 90. It was developed on base of experience of development and use of the mpC parallel programming language. The paper compares programming models of mpC and mpF.