Molecular Diagnostics, Taxonomy, and Phylogeny of the Stem Nematode Ditylenchus dipsaci Species Complex Based on the Sequences of the Internal Transcribed Spacer-rDNA

Evaluating the Influence of Water Scarcity on the Host Response of Garlic to the Stem and Bulb Nematode Ditylenchus dipsaci

Ditylenchus dipsaci is a plant-parasitic nematode with a great economic impact on bulbous crops, including garlic (Allium sativum L.), and is distributed worldwide, particularly in the Mediterranean region. Traditionally, garlic was a rainfed crop in Spain, but irrigated areas have increased during the last few decades. However, the expected climatic conditions, with longer and more intense droughts, will make it necessary to reduce the water supply to garlic crops. This poses the urgent need to select garlic cultivars more tolerant to water scarcity and that are also more resistant to plant pathogenic organisms. The aim of this work was to analyze the influence of water stress on the host response of garlic plants to D. dipsaci. The specific objectives were to evaluate the level of nematode infestation in plants from four garlic genotypes treated with a reduced irrigation regime and compare them with those of control plants not subjected to water stress. The observed results were correlated with changes in the bulb and root development, as well as in the physiological parameters (total chlorophyll concentration and proline accumulation). The effects were different depending on whether the plants were subjected to water stress before or after nematode inoculation, as well as whether the water stress was continuous or discontinuous. Garlic inter-cultivar variability also affected the obtained results.

Nematode-citrus plant interactions: host preference, damage rate and molecular characterization of Citrus root nematode Tylenchulus semipenetrans

Citrus plants are host to several plant parasitic nematodes (PPNs), which are microscopic organisms. Among PPNs, the citrus root nematode, T. semipenetrans (Cobb 1913) (Tylenchida: Tylenchulidae), causes significant damage to citrus plantations worldwide. Understanding citrus nematode populations, precise identification, host preference among citrus species, and damage threshold are crucial to control T. semipenetrans. The minutiae of citrus plant-nematode interactions, nematode density and molecular nematode identification are not well understood. In this study, nematode species and density in citrus orchards, host specialization, molecular and morphological characteristics of nematodes were assessed. Molecular and morphological methods, host-nematode interactions, host (citrus species) preference, damage economic threshold (ET), and economic injury level (EIL) were determined using laboratory methods and field sampling. Citrus plantations in different provinces in the Mediterranean region of Turkey were investigated. Nematode species were identified molecularly and morphologically. ITS sequences revealed that samples were infected by citrus root nematode T. semipenetrans. The lowest nematode density was in C. reticulata in Mersin (53 2nd stage juveniles (J2s) 100 g-1 soil), while the highest density was from Hatay in C. sinensis (12173 J2s 100 g-1 soil). Highest citrus nematode population density was on roots of C. reticulata, followed by C. sinensis, C. limon, and C. paradisi. The citrus nematode is more common than was thought and population fluctuations change according to specific citrus species. Environmental conditions, host and ecological factors, such as temperature, soil pH, and soil nutrients, might influence nematode populations in citrus orchards. Investigating nematode density in diverse soil ecologies and the responses of different resistant/tolerant citrus species and cultivars to nematode populations is essential in future studies.

Diagnosis and Characterization of Ditylenchus destructor Isolated from Mazus japonicus in China

The potato rot nematode (Ditylenchus destructor) is one of the most destructive pests in the production of tuber crops, resulting in severely decreased yields and inferior product quality. In 2021, a great number of nematodes were detected in the roots of Mazus japonicus, a weed that is harmful to crop growth, in Qingdao, Shandong Province, China. The present study was undertaken to characterize and identify the nematodes isolated from M. japonicus through morphological identification and molecular approaches. Their morphological characteristics were highly consistent with the descriptions of D. destructor Thorne, 1945. The nematodes collected from M. japonicus were identified as D. destructor haplotype B using D1/D2 and sequence characterized amplified region (SCAR) primers. PCR-ITS-RFLP analysis was conducted to monitor intraspecific variations. In addition, the phylogenetic analysis of the internal transcribed spacer (ITS) demonstrated that this D. destructor population was clustered in haplotype B, supported by a 100% bootstrap value. Another assay, in which M. japonicus was inoculated with a mixture of the life stages of D. destructor, was performed. This assay showed that M. japonicus exhibited a high susceptibility to D. destructor in pots. This is the first record of D. destructor parasitizing M. japonicus in China, and it is of great importance because M. japonicus could be a potential reservoir for D. destructor in the field.

New Records of Ditylenchus Species from Southern Alberta, Canada

The presence of plant-parasitic nematodes (PPNs) in cultivated areas is a limiting factor in achieving marketable crop yield. To control and alleviate the effects of these nematodes and determine appropriate management strategies, species-level identification is crucial. Therefore, we conducted a nematode diversity survey, which resulted in the detection of four Ditylenchus species in cultivated areas of southern Alberta, Canada. The recovered species had six lines in the lateral field, delicate stylets (>10 µm long), distinct postvulval uterine sacs, and pointed to rounded tail tips. The morphological and molecular characterization of these nematodes revealed their identity as D. anchilisposomus, D. clarus, D. tenuidens and D. valveus, all of which are members of the D. triformis group. All of the identified species were found to be new records in Canada except for D. valveus. Accurate Ditylenchus species identification is crucial because false-positive identification can result in the implementation of quarantine measures over the detected area. Our current study not only documented the presence of Ditylenchus species from southern Alberta, but also described their morpho-molecular characteristics and subsequent phylogenetic relationships with related species. The results of our study will aid in the decision on whether these species should become a part of nematode management programs since nontarget species can become pests due to changes in cropping patterns or climate.

Description and molecular characterisation of Ditylenchus pedrami n. sp. (Rhabditida: Anguinidae) from Iran

Ditylenchus pedrami n. sp., recovered from the rhizospheric soil of date palm in Khuzestan province, southwest Iran, is described and illustrated based upon morphological and molecular data. The new species is characterised by having six lines in the lateral field, lip region smooth and continuous with body contour, stylet 9-11 μm long, median pharyngeal bulb oval with small valve, pharyngeal bulb offset from the intestine, V = 83.9 (80.2-88.1), conoid tail with a pointed, dull or rounded tip and males with 20.1 (17-24) μm long spicules. Morphologically, the new species comes close to D. africanus, D. anchilisposomus, D. australiae, D. clarus, D. clavicaudatus and D. parcevivens, mainly by having shared features like six lines in the lateral fields, stylet length and somewhat similar tail tip. The new species was also compared with D. stenurus and D. sarvarae, two species with close phylogenetic affinities to it. The phylogenetic relationships of the new species with representatives of the family Anguinidae were reconstructed and discussed using partial sequences of the small subunit, D2-D3 expansion segments of the large subunit, and internal transcribed spacer regions of ribosomal DNA (SSU, LSU D2-D3 and ITS rDNA) based on Bayesian inference (BI).

Molecular Phylogenetic Characterization of Anguina tritici (Steinbuch, 1799) Filipjev, 1936 (Rhabditida: Anguinidae) on Barley from Iraq

During a nematological survey in Iraq, in the Bashika area, Ninevah province, an anguinid nematode population was isolated from galls of infected barley plants. The morphological characteristics indicated that the recovered species is identical to Anguina tritici. The barley population of A. tritici was molecularly characterized by sequencing two ribosomal regions (ITS and 18S rRNA genes), and their phylogenetic analyses revealed the newly generated sequences are in sister relation to corresponding sequences of A. tritici from wheat in the Bayesian tree, providing further evidence that the host plant can contribute to the separation of new isolates of plant parasitic nematodes.

Characterisation of Ditylenchus paraoncogenus n. sp. (Nematoda: Anguinidae), a new stem nematode parasitising tumble thistle

During a survey, three populations of a new stem nematode were isolated from galls on the shoots of tumble thistle (Gundelia tournefortii) plants in Fars province, Iran, and identified. Ditylenchus paraoncogenus n. sp. is described based on morphometric and morphological characters. It is characterised by having long-sized females, 1252 (943-1628) μm long, narrow lateral fields with six incisures, rather developed stylet 9.9 (9.0-11.3) μm long with round knobs, usually elongate and offset from intestine basal pharyngeal bulb, oocytes in two rows in distal part of ovary, V = 83.3 (80.3-86.2), post-vulval uterine sac 68.1 (46.9-86.1)% of vulva to anus distance long, bursa covering 63.2 (33.3-74.4)% of tail length, spicules 24.7 (21.0-27.9) μm long with minute processes at the base of its manubrium and anteriorly pointed cuticle parts within the lamina, and thick conical tail, usually with a pointed terminus. In addition, the ITS and 18S rDNA sequences of 17 populations of D. destructor, D. dipsaci, D. medicaginis, D. myceliophagus, D. paraoncogenus n. sp., Ditylenchus sp. and Nothotylenchus geraerti plus one population of Anguinidae sp. were analysed. The results showed a close relationship between D. paraoncogenus n. sp. and the stem nematodes D. oncogenus, D. gigas, D. weischeri and D. dipsaci. Ditylenchus species were divided into two clades, one clade comprising stem nematodes and gall-forming nematodes of the family Anguinidae, and the other clade containing fungivorous species. Observations showed that the second-stage juvenile is the dormant stage of D. paraoncogenus n. sp. and can survive in anhydrobiotic condition for at least 4 years.

Observations on the Population Genetic Structure of the Leaf Galling Nematode, Ditylenchus gallaeformans

Ditylenchus gallaeformans is a plant parasitic nematode that induces galls on aboveground parts of Melastomataceae plants. It differs from most gall-inducing nematodes in that it is not an endoparasite and has been considered as a possible biological control agent against invasive species of Miconia. Little is known about D. gallaeformans biology, genetic differences among populations, and host preferences. This study examined the genetic differences among D. gallaeformans populations from different locations and host species and the phylogenetic relationships among them. Nematodes were collected from galls in plants from Costa Rica, Dominica, and Trinidad. The Cytochrome c oxidase 1 (cox1) region was sequenced from a total of 33 individual nematodes isolated from 33 different plant individuals, representing 21 species of Melastomataceae. Phylogenetic reconstructions, haplotype networks, and analysis of molecular variance showed that the species is monophyletic and has three major clades, which were mostly consistent with geographic location but not with host species. The first clade was composed by two subclades, one with individuals from Costa Rica and one with individuals from Dominica. The second and third clades comprised nematodes only from Trinidad. Overall, there is no evidence of host-species specialization in D. gallaeformans. Biocontrol efforts using the nematode against invasive Miconia could focus on geographical location matching but likely will not need to match host species.

Top Ten Most Important U.S.-Regulated and Emerging Plant-Parasitic Nematodes

Plant-parasitic nematodes (PPNs) are important pests that cause an estimated ten billion dollars of crop loss each year in the United States and over 100 billion dollars globally. The Animal and Plant Health Inspection Service (APHIS) within the U.S. Department of Agriculture maintains and updates the U.S. Regulated Plant Pest list. Currently, the number of PPNs regulated by APHIS includes more than 60 different species. This review focuses on the top ten most economically important regulated and emerging plant-parasitic nematodes and summarizes the diagnostics of morphological and some molecular features for distinguishing them. These ten major previously described nematode species are associated with various economically important crops from around the world. This review also includes their current distribution in the U.S. and a brief historical background and updated systematic position of these species. The species included in this review include three PPNs considered by the U.S. Department of Agriculture as invasive invertebrates Globodera pallida, Globodera rostochiensis, and Heterodera glycines; four regulated PPNs, namely Bursaphelenchus xylophilus, Meloidogyne fallax, Ditylenchus dipsaci, and Pratylenchus fallax; and the three emerging PPNs Meloidogyne chitwoodi, Meloidogyne enterolobii, and Litylenchus crenatae mccannii.

Genome Characterization and Development of Real-Time PCR Assays for Ditylenchus Dipsaci and D. Weischeri

The stem and bulb nematode Ditylenchus dipsaci is a destructive nematode pest on many crops and is internationally quarantined in many countries, whereas Ditylenchus weischeri, only known to infect a weed plant (Cirsium arvense), is an unregulated nematode species with no known economic importance. In this study, we used comparative genomics to identify multiple gene regions and developed novel real-time PCR assays for the detection of D. dipsaci and D. weischeri. We sequenced the genomes of two mixed-stage nematode populations of D. dipsaci and two mixed-stage nematode populations of D. weischeri. The assembled genomes of D. dipsaci were 228.2 Mb and 239.5 Mb, and the genomes of D. weischeri were 177.0 Mb and 196.3 Mb. Depending on the species, 21,403-27,365 gene models were predicted. Using orthologous group analysis, single-copy and species-specific genes were identified. Primers and probes were designed targeting two species-specific genes in each species. The assays detected as low as 12 pg of DNA from the target species, or as few as five nematodes, with a C_q of 31 cycles or less. Our study provides genome data for two additional D. dipsaci isolates and two D. weischeri isolates, and four new and validated molecular assays to be used for rapid detection and identification of the two species.

Development of Real-Time and Conventional PCR Assays for Identifying a Newly Named Species of Root-Lesion Nematode (Pratylenchus dakotaensis) on Soybean

A rapid and accurate PCR-based method was developed in this study for detecting and identifying a new species of root-lesion nematode (Pratylenchus dakotaensis) recently discovered in a soybean field in North Dakota, USA. Species-specific primers, targeting the internal transcribed spacer region of ribosomal DNA, were designed to be used in both conventional and quantitative real-time PCR assays for identification of P.dakotaensis. The specificity of the primers was evaluated in silico analysis and laboratory PCR experiments. Results showed that only P.dakotaensis DNA was exclusively amplified in conventional and real-time PCR assays but none of the DNA from other control species were amplified. Detection sensitivity analysis revealed that the conventional PCR was able to detect an equivalent to 1/8 of the DNA of a single nematode whereas real-time PCR detected an equivalent to 1/32 of the DNA of a single nematode. According to the generated standard curve the amplification efficiency of the primers in real-time PCR was 94% with a R2 value of 0.95 between quantification cycle number and log number of P.dakotaensis. To validate the assays to distinguish P.dakotaensis from other Pratylenchus spp. commonly detected in North Dakota soybean fields, 20 soil samples collected from seven counties were tested. The PCR assays amplified the DNA of P.dakotaensis and discriminated it from other Pratylenchus spp. present in North Dakota soybean fields. This is the first report of a species-specific and rapid PCR detection method suitable for use in diagnostic and research laboratories for the detection of P.dakotaensis.

A new primer set for amplification of ITS-rDNA in Ditylenchus destructor

A technique was developed for the identification of Ditylenchus destructor nematode belonging to the Ditylenchus genus, based on the use of different primers for polymerase chain reaction (PCR). Two universal ribosomal primers were amplified to the internal transcribed spacer region ITS-rDNA. The sequencing of PCR products confirmed the polymorphism between species. The primers were sensitive to generate a particular band of the correct size (300bp) from the DNA template of a single, separate D. destructor stage of development. Screening populations of D. destructor from Iran and the Russian Federation have tested the reliability of the primers, and the expected size of the band was produced for all test populations. Ditylenchus destructor closely related species have also been tested and no specific band was amplified. Such results showed that the primers currently developed are useful for quantifying the D. destructo r density in potato tuber.

Diagnosis of potato rot nematode Ditylenchus destructor using PCR-RFLP

During an investigation of nematodes in the Moscow region of Russia in 2019, a known species Ditylenchus destructor was recovered from tubers of potato plants. The genus Destructor is one of the most problematic genera of plant-parasitic nematodes. The numerous species reported for this genus have been cited from various sources. Due to the morphological similarity of many species and the lack of separation characteristics, the identification of D. destructor is difficult. Molecular taxonomy and phylogeny were used to confirm the identification. In the current study, PCR-RFLP illustrative models for the amplification of the ITS-rRNA gene were provided with two enzymes that could recognize D. destructor in potato tubers. Analysis of the rDNA sequences spanning both ITS1-ITS2 regions was carried out on the collected populations. The digestion of the PCR product of the ITS1-5.8S-ITS2 region with the enzyme TaqI produced three fragments; 100, 190, 550, and with Tru1I, two fragments were produced; 300 and 480 bp. The obtained DNA sequences were compared with those DNA sequences deposited in GenBank of populations isolated in other countries. The results showed no distinction between populations isolated from different host plant species, including populations found in the Russian Federation. New sequences from ITS-rRNA were deposited in the GenBank under accession number MN122076, MN658597, MN658599, MN658637, MN658638.

[Quarantine nematode species and pathotypes potentially dangerous for domestic potato production: populations diversity and the genetics of potato resistance]

Обзор посвящен проблеме потенциально опасных для отечественного картофелеводства каран- тинных видов и патотипов нематод. Картофель поражают более 30 видов паразитических нематод, однако в статье основное внимание уделено самым вредоносным, приносящим большой ущерб картофелеводству пред- ставителям родов Globodera, Ditylenchus, Nacobbus и Meloidogyne. Проанализированы фитопатологические и молекулярные методы идентификации видов и патотипов и основные достижения в изучении изменчивости популяций паразитических нематод картофеля. Показано, что, благодаря особенностям жизненного цикла не- матод и лабильности их геномов, генетическая изменчивость этих организмов очень велика, что создает угрозу образования новых патогенных генотипов паразита. Сведения о внутри- и межпопуляционной изменчивости нематод важны для изучения путей интродукции и распространения отдельных видов, а также поиска корреля- ций молекулярных маркеров с определенным патотипом. Филогенетические исследования, основанные на со- временных данных по генетической изменчивости популяций, позволили выявить комплексы видов у Globodera pallida (Stone) Behrens и Nacobbus aberrans (Thorne) Thorne & Allen (sensu lato), включающие криптические виды. К основным составляющим успешной защиты, предотвращающей массовое распространение паразитических нематод, относятся карантинные мероприятия, агротехнические приемы, биологические способы защиты и возделывание устойчивых сортов. Особое внимание в обзоре уделено вопросам селекции сортов картофеля с длительной устойчивостью к различным видам нематод, поскольку возделывание таких сортов – экологически наиболее безопасный и экономически выгодный способ предотвращения эпифитотий. В настоящее время до- стигнуты значительные успехи в генетической защите сортов картофеля, особенно в отношении цистообразую- щих нематод. Приведены сведения об источниках устойчивости картофеля к паразитическим нематодам, выде- ленных в коллекциях диких и культурных видов. Проанализированы данные об идентифицированных R-генах и QTL устойчивости, которые были интрогрессированы в селекционный материал с помощью различных методов и подходов. Представлены результаты изучения структурной и функциональной организации генов устойчиво- сти к цистообразующим нематодам картофеля. Рассмотрены результаты исследований по использованию моле- кулярных маркеров определенных генов в маркер-опосредованной селекции для создания новых устойчивых сортов, в том числе с групповой устойчивостью.

A new rare nematode Nothocriconemoides hangzhouensis n. sp. (Nematoda: Criconematidae) from Hangzhou, China

The Family Criconematidae is commonly referred as ring nematodes that include some members with economic importance as plant parasites. During a recent nematode inventory survey at Zhejiang Province, China, a new species of genus Nothocriconemoides was detected in the rhizosphere of elm tree. Nothocriconemoides hangzhouensis n. sp. can be characterized by the female body having annuli with fine longitudinal striations and 2 to 3 anastomoses at the posterior half of the body. The first cephalic annulus is rounded and expanded enclosing the lip region, and the second annulus is narrow, offset, collar like. En face view shows a central elevated labial disk bearing four distinct equal-sized submedian lobes and "I" shaped oral aperture. Excretory pore is located 3-4 annuli posterior to esophageal bulb. Vagina is straight and vulva closed. The ventral side of postvulval annuli is inverted, in majority of individuals. Anus is indistinct and located on the next annuli posterior to vulva. Tail is short, conoid, with forked or branched terminus. Juveniles are devoid of collar-shaped annuli in the lip region. The cephalic region has two rounded annuli where the first annulus shows slight depression in the middle. Body annuli are finely crenated. Anus is indistinct and located 3 to 4 annuli from tail terminus. Tail is short ending in a single lobed terminus. Phylogenetic studies based on analysis of the D2-D3 expansion segments of the 28 S rRNA, ITS rRNA, partial 18 S rRNA, and coxI gene revealed that the new species formed a separate clade from other criconematid species, thereby supporting its status as a new species of the genus. The new species showed close relationships with Discocriconemella sinensis. Additionally, this is the first record of genus Nothocriconemoides from China.

The Family Criconematidae is commonly referred as ring nematodes that include some members with economic importance as plant parasites. During a recent nematode inventory survey at Zhejiang Province, China, a new species of genus Nothocriconemoides was detected in the rhizosphere of elm tree. Nothocriconemoides hangzhouensis n. sp. can be characterized by the female body having annuli with fine longitudinal striations and 2 to 3 anastomoses at the posterior half of the body. The first cephalic annulus is rounded and expanded enclosing the lip region, and the second annulus is narrow, offset, collar like. En face view shows a central elevated labial disk bearing four distinct equal-sized submedian lobes and “I” shaped oral aperture. Excretory pore is located 3–4 annuli posterior to esophageal bulb. Vagina is straight and vulva closed. The ventral side of postvulval annuli is inverted, in majority of individuals. Anus is indistinct and located on the next annuli posterior to vulva. Tail is short, conoid, with forked or branched terminus. Juveniles are devoid of collar-shaped annuli in the lip region. The cephalic region has two rounded annuli where the first annulus shows slight depression in the middle. Body annuli are finely crenated. Anus is indistinct and located 3 to 4 annuli from tail terminus. Tail is short ending in a single lobed terminus. Phylogenetic studies based on analysis of the D2–D3 expansion segments of the 28 S rRNA, ITS rRNA, partial 18 S rRNA, and coxI gene revealed that the new species formed a separate clade from other criconematid species, thereby supporting its status as a new species of the genus. The new species showed close relationships with Discocriconemella sinensis. Additionally, this is the first record of genus Nothocriconemoides from China.

Updated description of Paratylenchus lepidus Raski 1975 and P. minor Sharma, Sharma and Khan, 1986 by integrating molecular and ultra-structural observations

Two populations of Paratylenchus lepidus and P. minor were detected in the rhizosphere of Elaeocarpus sp. and Chinese red pine from Taizhou and Hangzhou, Zhejiang Province, China. Previously, P. lepidus has been reported from China whereas P. minor was originally described from India decades ago in the rhizosphere of peach but was never reported thereafter. In this study, both species were characterized morphologically and molecularly coupled with SEM observations. Morphologically, both species have four incisures in the lateral field, vulval present (SEM observations), stylet less than 30 μm long and cephalic region without submedian lobes. Phylogenetically, both species grouped with paratylenchid species having short stylets. Both species can be differentiated from each other by the shape of lip region (rounded in P. lepidus and narrow truncated in P. minor) and tail terminus (pointed in P. lepidus and a broadly rounded in P. minor) and several morphomemtrical values.The study provided an updated description of P. lepidus and P. minor and a first record of P. minor from China. In addition, both species are the first paratylenchid species recorded from Elaeocarpus sp. and Pinus tabuliformis, respectively.

Litylenchus crenatae n. sp. (Tylenchomorpha: Anguinidae), a leaf gall nematode parasitising Fagus crenata Blume

Litylenchus crenatae n. sp., isolated from leaf galls of Fagus crenata from Japan, is described and figured. The new species is characterised by its dimorphism in adult females, six (or more) lateral lines, a more or less pointed tail tip in both sexes, male bursa arising posteriorly and reaching to near tail tip, presence of a quadricolumella and a post-uterine sac in females. Litylenchus crenatae n. sp. is distinguished from its only congener, L. coprosma, by the number of lateral lines, six or more vs four; the lip morphology, offset with very shallow constriction or dome-shaped without clear constriction vs clearly offset; tail tip morphology, more or less pointed vs blunt; and structure of the median bulb, weakly muscular with a clear valve vs not muscular with an obscure valve. The molecular phylogenetic analysis confirms that the new species is close to, but clearly different from, L. coprosma.

Molecular Characterization and Phylogeny of Ditylenchus weischeri from Cirsium arvense in the Prairie Provinces of Canada

Ditylenchus weischeri that parasitizes the weed Cirsium arvense (L.) Scop., 1772, (creeping thistle) was described in 2011 from Russia based on their morphology, ITS-RFLP analysis, and Hsp 90 gene sequence of a few individuals and one field collection of the plant. More recently, we found C. arvense parasitized by D. weischeri in the Prairie Provinces of Canada. Plant host preference for D. weischeri was also distinct from D. dipsaci (Kühn) Filipjev, 1936. In the current study, a comprehensive molecular analysis of many D. weischeri specimens from Canada is presented. Individuals from 41 C. arvense or yellow pea grain samples with seeds of C. arvense from the Prairie Provinces were sequenced for the internal transcribed spacer (ITS rDNA), large subunit (LSU) D2D3 28S rDNA, partial segment of small subunit (SSU) 18S rDNA, and the heat shock protein Hsp 90 gene. The analysis also included D. weischeri individuals from C. arvense from Russia and garlic with D. dipsaci from the Provinces of Ontario and Quebec in Canada. Available sequence data of Ditylenchus species retrieved from GenBank were used to phylogenetically position this species within the genus Ditylenchus . In all studied genes, several single-nucleotide polymorphisms between the Canadian D. weischeri and both Russian haplotype and individuals of D. weischeri from C. arvense from Russia were found. The sequences of ITS rDNA, LSU D2D3 28S rDNA, and Hsp 90 were used to construct separate dendrograms. For each of the three genes examined, D. weischeri was grouped separately from the other Ditylenchus . Ditylenchus samples from C. arvense was positioned to a single clade such as D. weischeri and distinct from D. dipsaci . With past reports of plant host preference and morphology, the results of this study provide further evidence for the fact that D. weischeri is distinct to be separated from D. dipsaci . Furthermore, minor differences in molecular divergence and morphology to the Russian haplotype and limited symptoms of disease on C. arvense in Prairie Canada suggest the Canadian and Russian populations of D. weischeri may be diverging.

The Ditylenchus destructor genome provides new insights into the evolution of plant parasitic nematodes

Plant-parasitic nematodes were found in 4 of the 12 clades of phylum Nematoda. These nematodes in different clades may have originated independently from their free-living fungivorous ancestors. However, the exact evolutionary process of these parasites is unclear. Here, we sequenced the genome sequence of a migratory plant nematode, Ditylenchus destructor We performed comparative genomics among the free-living nematode, Caenorhabditis elegans and all the plant nematodes with genome sequences available. We found that, compared with C. elegans, the core developmental control processes underwent heavy reduction, though most signal transduction pathways were conserved. We also found D. destructor contained more homologies of the key genes in the above processes than the other plant nematodes. We suggest that Ditylenchus spp. may be an intermediate evolutionary history stage from free-living nematodes that feed on fungi to obligate plant-parasitic nematodes. Based on the facts that D. destructor can feed on fungi and has a relatively short life cycle, and that it has similar features to both C. elegans and sedentary plant-parasitic nematodes from clade 12, we propose it as a new model to study the biology, biocontrol of plant nematodes and the interaction between nematodes and plants.

Anatomical Alterations in Plant Tissues Induced by Plant-Parasitic Nematodes

Plant-parasitic nematodes (PPNs) interact with plants in different ways, for example, through subtle feeding behavior, migrating destructively through infected tissues, or acting as virus-vectors for nepoviruses. They are all obligate biotrophic parasites as they derive their nutrients from living cells which they modify using pharyngeal gland secretions prior to food ingestion. Some of them can also shield themselves against plant defenses to sustain a relatively long lasting interaction while feeding. This paper is centered on cell types or organs that are newly induced in plants during PPN parasitism, including recent approaches to their study based on molecular biology combined with cell biology-histopathology. This issue has already been reviewed extensively for major PPNs (i.e., root-knot or cyst nematodes), but not for other genera (viz. Nacobbus aberrans, Rotylenchulus spp.). PPNs have evolved with plants and this co-evolution process has allowed the induction of new types of plant cells necessary for their parasitism. There are four basic types of feeding cells: (i) non-hypertrophied nurse cells; (ii) single giant cells; (iii) syncytia; and (iv) coenocytes. Variations in the structure of these cells within each group are also present between some genera depending on the nematode species viz. Meloidogyne or Rotylenchulus. This variability of feeding sites may be related in some way to PPN life style (migratory ectoparasites, sedentary ectoparasites, migratory ecto-endoparasites, migratory endoparasites, or sedentary endoparasites). Apart from their co-evolution with plants, the response of plant cells and roots are closely related to feeding behavior, the anatomy of the nematode (mainly stylet size, which could reach different types of cells in the plant), and the secretory fluids produced in the pharyngeal glands. These secretory fluids are injected through the stylet into perforated cells where they modify plant cytoplasm prior to food removal. Some species do not produce specialized feeding sites (viz. Ditylenchus, Subanguina), but may develop a specialized modification of the root system (e.g., unspecialized root galls or a profusion of roots). This review introduces new data on cell types and plant organs stimulated by PPNs using sources varying from traditional histopathology to new holistic methodologies.

Quantification of Paratrichodorus allius in DNA extracted from soil using TaqMan Probe and SYBR Green real-time PCR assays

The ectoparasitic stubby root nematode,Paratrichodorus allius, transmits tobacco rattle virus, which causes corky ringspot disease resulting in significant economic losses in the potato industry. A diagnostic method for direct quantification ofP. alliusfrom soil DNA using TaqMan probe and SYBR Green real-time PCR assays was developed to assist the potato industry in management of this important vector. Specificity of primers/probe designed from the internal transcribed spacer of ribosomal DNA ofP. alliuswas demonstrated byin silicoanalysis and experimental PCR tests with no cross reactions using non-target nematode species and nematode communities. The SYBR Green method was more sensitive than the TaqMan probe method during detection using serial diluted DNA templates. Standard curves were generated from serial dilutions of DNA extracted from autoclaved soil with artificially inoculatedP. alliusindividuals and were validated by high correlations between the numbers of target nematodes quantified by the assays and added to the soil. Moreover, the numbers ofP. alliusdetermined by the real-time PCR assays and estimated by the microscopic method in 17 field soil samples presented positive correlation relationships (). Although the quantification using TaqMan probe overestimated the target nematodes compared to using SYBR Green in eight out of ten field soil samples, results of the two methods correlated well (). This is the first report ofP. alliusquantification from soil DNA extracts using real-time PCR, providing a rapid and sensitive diagnostic method obviating time-consuming manual nematode extraction from soil and microscopic identification and quantification.

Molecular and morphological characterisation of Ditylenchus persicus n. sp. (Nematoda: Anguinidae) from Kermanshah province, western Iran

A new species of the genusDitylenchus,D.persicusn. sp., was collected around the roots of grapevine and is described and illustrated herein based on morphological and molecular studies. The new species is characterised by a body length of 783 (635-928) μm and 689 (670-715)μm in female and male, respectively, delicate stylet 6.2 (5.0-7.0)μm long, six lines in the lateral field, median bulb of pharynx well developed, muscular with crescentic valve, basal pharyngeal bulb pyriform with 10 (8-13)μm long stem extending into intestine, post-vulval uterine sac relatively short, 16 (14-18)μm long, female and male tail elongate-conoid with finely rounded terminus, and bursa covering 65-80% of male tail length. Morphologically,D.persicusn. sp. appears closer to five known species of the genus, namely:D.arachis,D.caudatus,D.clarus,D.myceliophagusandD. nanus. The results of phylogenetic analyses based on sequences of D2-D3 expansion region of 28S rRNA, ITS and partial 18S rRNA genes confirmed the close molecular relationship betweenD.persicusn. sp. and otherDitylenchusspecies such asD. myceliophagus,D. africanus,D. arachis,D. destructorandD. halictus.

Ditylenchus laurae sp. n. (Tylenchida: Anguinidae) from Poland – a new species of the D. dipsaci complex associated with a water plant, Potamogeton perfoliatus L

The genus Ditylenchus consists of more than 60 species, some of which are plant parasites. In this paper we report on Ditylenchus laurae sp. n. from Poland, a new species associated with the aquatic plant, Potamogeton perfoliatus L. Ditylenchus laurae sp. n. is characterised by a long and slender body with L = 1881 (1523-2095) μm and 1875 (1690-2089) μm, a = 88.8 (72.5-102.5) and 89.7 (71.9-97.9), stylet length = 10.8 (9.6-12.1) μm and 8.3 (7.7-9.0) μm, tail length = 117.2 (103.5-126.7) μm and 102.4 (98.3-113.6) μm in females and males, respectively; four incisures, rounded stylet knobs, long basal bulb (about ten times as long as wide), post-vulval uterine sac from 4.3-5.6 vulval body diam. long, and mucronate tail. Characterisation using the ITS rRNA, COI and hsp90 gene sequences was conducted and a phylogenetic analyses revealed that D. laurae sp. n. belongs to the D. dipsaci complex.

Nothotylenchus persicus n. sp. (Nematoda: Anguinidae) from Kermanshah province, Iran

A new species of the genus Nothotylenchus, N. persicus n. sp. was collected around the roots of grapevine and is described and illustrated herein based on morphological and molecular studies. The new species is characterised by a body length of 776-900 μm, delicate stylet 5-6 μm long, six lines in the lateral field, post-vulval uterine sac short, 10-18 μm long, female tail elongate-conoid with pointed terminus, and bursa covering 40-45% of tail length. Morphologically, N. persicus n. sp. appears closer to four known species of the genus, namely: N. hexaglyphus, N. affinis, N. medians and N. taylori. The results of phylogenetic analyses based on sequences of D2-D3 expansion region of 28S rRNA gene confirmed the close molecular relationship between N. persicus n. sp. and other anguinids, but Nothotylenchus claded separately from Ditylenchus species.

Resistance to Ditylenchus destructor Infection in Sweet Potato by the Expression of Small Interfering RNAs Targeting unc-15, a Movement-Related Gene

Stem nematode (Ditylenchus destructor) is one of most serious diseases that limit the productivity and quality of sweet potato (Ipomoea batatas), a root crop with worldwide importance for food security and nutrition improvement. Hence, there is a global demand for developing sweet potato varieties that are resistant to the disease. In this study, we have investigated the interference of stem nematode infectivity by the expression of small interfering RNAs (siRNAs) in transgenic sweet potato that are homologous to the unc-15 gene, which affects the muscle protein paramyosin of the pathogen. The production of double-stranded RNAs and siRNAs in transgenic lines with a single transgene integration event was verified by Northern blot analysis. The expression of unc-15 was reduced dramatically in stem nematodes collected from the inoculated storage roots of transgenic plants, and the infection areas of their storage roots were dramatically smaller than that of wild-type (WT). Compared with the WT, the transgenic plants showed increased yield in the stem nematode-infested field. Our results demonstrate that the expression of siRNAs targeting the unc-15 gene of D. destructor is an effective approach in improving stem nematode resistance in sweet potato, in adjunct with the global integrated pest management programs.

A new stem nematode, Ditylenchus oncogenus n. sp. (Nematoda: Tylenchida), parasitizing sowthistle from Adriatic coast dunes in southern Italy

Morphological and molecular analyses of a stem nematode causing a severe disease on infected sowthistle (Sonchus bulbosus) plants, involving the formation of gall-like structures on infected leaves and stems, have led to the description of a new species named Ditylenchus oncogenus n. sp. Morphologically, the new species is characterized by a medium to large body size (all adults more than 1 mm in length); a delicate stylet (9.0-11.0 μm long) with minute, rounded knobs; a long post-vulval uterine sac (c. 65% of the vulva-anus distance); six incisures at the lateral fields and characteristic D. destructor-pattern of spicules (with pronounced ventral tumulus and anteriorly pointed, less sclerotized, cuticle parts present within the lamina). The results of molecular analysis of rRNA gene sequences, including the D2-D3 expansion regions of 28S rRNA, internal transcribed spacer (ITS) rRNA, partial 18S rRNA gene, the protein-coding mitochondrial gene, cytochrome oxidase c subunit I (COI), and the heat-shock protein 90 (hsp90) gene, support the new species status. The results of a host-suitability test indicated that the new species does not parasitize potato (Solanum tuberosum) tubers and broad bean (Vicia faba) seedlings. Histopathological observations on naturally infected sowthistle tissues revealed that D. oncogenus n. sp. causes floral stem neoplasia and midrib leaf gall formation on the type, and to date only known, host. The galls were characterized by extensive hyperplasia, where several necrotic cells in the neoplasic area were directly damaged by feeding of the nematode, whereas a number of adjacent cells showed typical cytological changes, such as granulated cytoplasm with hypertrophied nuclei and nucleoli.

A fast and sensitive method for the simultaneous identification of three important nematode species of the genus Ditylenchus

BACKGROUND

Nematodes of the genus Ditylenchus are parasites of a wide range of hosts, including higher plants. The most destructive of these species are D. dipsaci and D. destructor, two frequently quarantined pests. No rapid molecular method is available for unambiguous detection and distinguishing of these species from each other or from D. gigas, a pest of Vicia faba, either by multiplex PCR or real-time PCR.

RESULTS

By aligning all D. dipsaci, D. destructor and D. gigas rDNA sequences, the authors found a constant-sequence region that could be used as a universal 5' primer and constant regions in the ITS1 regions of the rDNAs that could be used as species-specific 3' primers for PCR detection of these nematodes. A standardised protocol was developed for both singleplex- and triplex-mode PCR that yields a single product of distinct length for each of the species. The PCR protocol has also been adapted for real-time PCR.

CONCLUSION

The present diagnostic PCR protocol is the only method that can identify all three species with the use of a triplex and/or a singleplex PCR assay. Importantly, the 3' primer for D. destructor ITS1 rDNA was designed so that it would hybridise all haplotypes.

Utilizing ribosomal DNA gene marker regions to characterize the metacercariae (Trematoda: Digenea) parasitizing piscine intermediate hosts in Manipur, Northeast India

Freshwater fishes in Manipur, Northeast India frequently harbour several types of metacercariae, which based on morphological criteria were identified as Clinostomoides brieni, Euclinostomum heterostomum (Clinostomidae) and Polylekithum sp. (Allocreadiidae). Molecular techniques utilizing PCR amplification of rDNA regions of larger subunit (LSU or 28S), smaller subunit (SSU or 18S) and inter transcribed spacers (ITS1, 2) were used for molecular characterization of these types. Sequences generated from the metacercariae were compared with their related sequences available in public databases; an analysis of the identity matrices and phylogenetic trees constructed was also carried out, which confirmed their identification. Similarly, the sequences generated from Polylekithum sp. were found to be highly similar to the species of the same genus. The rDNA ITS2 secondary structure provided additional confirmation of the robustness of the molecular marker as a tool for taxon-specific characterization.

Banning of methyl bromide for seed treatment: could Ditylenchus dipsaci again become a major threat to alfalfa production in Europe?

In Europe, the stem and bulb nematode Ditylenchus dipsaci has been listed as a quarantine pest by EPPO: without any control, it may cause complete failure of alfalfa crops. Movement of nematodes associated with seeds is considered to be the highest-risk pathway for the spread of this pest. Since the 2010 official withdrawal of methyl bromide in Europe, and in the absence of any alternative chemical, fumigation of contaminated seed batches is no longer possible, which makes the production of nematode-free alfalfa seeds difficult to achieve and leads to unmarketable seed batches. Thermotherapy is being considered as a realistic alternative strategy, but its efficiency still remains to be validated. The combination of the currently available methods (i.e. use of resistant cultivars, seed production according to a certification scheme, mechanical sieving, seed batch inspection) could significantly reduce the likelihood of seed contamination. However, it does not guarantee a total eradication of the nematode. Although it is already widely distributed all over Europe, reclassification of D. dipsaci as a regulated non-quarantine pest to reduce the possibility of further introductions and the rate of spread of this pest appears to be a risky strategy because of the lack of up-to-date documented data to evaluate damage thresholds and determine acceptable tolerance levels.

Genetic structure of Xiphinema pachtaicum and X. index populations based on mitochondrial DNA variation

The dagger nematodes Xiphinema pachtaicum and X. index are two of the most widespread and frequently occurring Xiphinema spp. co-infesting vineyards and other crops and natural habitats worldwide. Sexual reproduction is rare in these species. The primary objective of this study was to determine the genetic structure of X. pachtaicum and X. index populations using eight and seven populations, respectively, from different "wine of denomination of origin (D.O.) zones" in Spain and Sardinia (Italy), by studying mitochondrial (cytochrome oxidase c subunit 1 or COI) and nuclear (D2-D3 expansion segments of 28S rDNA) markers. Both Xiphinema spp. showed low intraspecific divergence among COI sequences, ranging from 0.2% (1 base substitution) to 2.3% (10 substitutions) in X. pachtaicum and from 0.2% (1 base substitution) to 0.4% (2 substitutions) in X. index. Population genetic structure was strong for both species. Nevertheless, molecular differences among grapevine-growing areas were not significant, and intrapopulation diversity was very low. It is hypothesized that this genetic homogeneity in the nematode populations reflects their predominant parthenogenetic reproduction mode and low dispersal abilities. Our results also show that X. pachtaicum populations in Spain have possibly been established from two different populations of origin. Results also demonstrated that the two DNA regions studied are suitable diagnostic markers for X. index and X. pachtaicum.

Detection and quantification of root-knot nematode (Meloidogyne javanica), lesion nematode (Pratylenchus zeae) and dagger nematode (Xiphinema elongatum) parasites of sugarcane using real-time PCR

A number of different plant parasitic nematode species are found associated with sugarcane in South Africa. Of these, the root-knot nematode (Meloidogyne javanica), the lesion nematode (Pratylenchus zeae) and the dagger nematode (Xiphinema elongatum) are potentially the most damaging pests. Identification and enumeration of the number of these nematodes are necessary for providing advice to farmers as well as studying the effects of various treatments in field and glasshouse trials. We report on the development, use, and extent of specificity of three sets of primers, for M. javanica, P. zeae and X. elongatum, and on tests to detect and quantify the number of these nematodes in soil samples using SYBR Green I dye and real-time PCR technology. Amplicons from the three target species (obtained with their respective primer sets) are discernible in size by gel electrophoresis (380bp for M. javanica, 250bp for P. zeae and 500bp for X. elongatum). Also, these amplicons have characteristic melting temperatures of 83.8 degrees C (M. javanica), 86.6 degrees C (P. zeae) and 86.1 degrees C (X. elongatum). Investigations into multiplex reactions found competition between species with M. javanica competing with P. zeae and X. elongatum. Subsequent single tube (simplex) assays, enabled the construction of calibration curves for each of the three species. These were then used for quantification of the numbers of each of these species in nematode samples extracted from the field, with a high (R2=0.83) and significant positive correlation between real-time PCR and counts performed with microscopy.

Cold tolerance of an Antarctic nematode that survives intracellular freezing: comparisons with other nematode species

Panagrolaimus davidi is an Antarctic nematode with very high levels of cold tolerance. Its survival was compared with that of some other nematodes (P. rigidus, Rhabditophanes sp., Steinernema carpocapsae, Panagrellus redivivus and Ditylenchus dipsaci) in both unacclimated samples and those acclimated at 5 degrees C. Levels of recrystallization inhibition in homogenates were also compared, using the splat-cooling assay. The survival of P. davidi after the freezing of samples was notably higher than that of the other species tested, suggesting that its survival ability is atypical compared to other nematodes. In general, acclimation improved survival. Levels of recrystallization inhibition were not associated with survival but such a relationship may exist for those species that are freezing tolerant.

Host-Parasite Relationships in Fall-Sown Sugar Beets Infected by the Stem and Bulb Nematode, Ditylenchus dipsaci

Stunted growth of fall-sown sugar beets (Beta vulgaris) associated with high incidence of crownroot infections and large soil infestations by Ditylenchus dipsaci were observed at the end of the crop growing season in southern Spain by early June 2005. The largest proportion (75%) of the nematode life-stages in plant and soil was the fourth-stage juvenile. The large number (up to 3,750 nematodes per gram of fresh tissue) of D. dipsaci individuals and severe anatomical alterations observed in storage sugar beet roots suggest that the stem and bulb nematode is the causal agent of the impaired growth of sugar beets observed in commercial fields. Observed morphological traits of nematode specimens and results of specific polymerase chain reaction (PCR) and phylogenetic analyses confirmed that the population of D. dipsaci infecting sugar beet belongs to the normal (nongiant) biological type of the nematode. Results of host-range bioassays indicated that the population of D. dipsaci infecting sugar beet in southern Spain reproduces on pea (including seeds and pods), onion, potato, spinach, and tomato, but not on bean, cotton, maize, and tobacco. These results indicate that D. dipsaci may be an important constraint for sugar beet crops in the affected area, but also for other important crops commonly used in rotation with them.