A Revision of the Phylogeny of Helicotylenchus Steiner, 1945 (Tylenchida: Hoplolaimidae) as Inferred from Ribosomal and Mitochondrial DNA

Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.

First report of Pratylenchus penetrans (Nematoda: Pratylenchidae) associated with artichokes in Vietnam

Pratylenchus penetrans is one of the world's most common and destructive root-lesion nematodes and can parasitize more than 400 plant species. P. penetrans has been reported to cause serious damage to artichokes in several countries, such as Greece, Brazil, and France. Until now, there have been no reports of P. penetrans associated with artichokes in Vietnam. In this study, we recorded this species in artichoke fields in Lam Dong province, Vietnam with an average density of 50 nematodes/100g of soil (frequency of appearance at 64.7%). This nematode was associated with symptoms such as yellowing leaves, stunt, and root necrosis of artichokes in Vietnam, indicating its high damaging potential and a need for suitable control strategies. The identification of this species in our study was confirmed by morphology, morphometric data, and molecular characterization of 18S and 28S rRNA regions. Our study also provides the first molecular data of P. penetrans in Vietnam. The inclusion of molecular data for P. penetrans in Vietnam represents a significant contribution to the scientific community and a pivotal advancement in addressing nematode-related challenges in agriculture. This dataset serves as an invaluable reference for various molecular-focused endeavors, including but not limited to molecular identification, pathogenicity studies, and the development of effective management strategies.

First Reports and Morphological and Molecular Characterization of Pratylenchus delattrei and Quinisulcius capitatus Associated with Chickpea in Ethiopia

Chickpea (Cicer arietinum L.) is classed among the most important leguminous crops of high economic value in Ethiopia. Two plant-parasitic nematode species, Pratylenchus delattrei and Quinisulcius capitatus, were recovered from chickpea-growing areas in Ethiopia and characterized using molecular and morphological data, including the first scanning electron microscopy data for P. delattrei. New sequences of D2-D3 of 28S, ITS rDNA and mtDNA COI genes have been obtained from these species, providing the first COI sequences for P. delattrei and Q. capitatus, with both species being found for the first time on chickpea in Ethiopia. Furthermore, Pratylenchus delattrei was recovered in Ethiopia for the first time. The information obtained about these nematodes will be crucial to developing effective nematode management plans for future chickpea production.

Remarks on phylogeny and molecular variations of criconematid species (Nematoda: Criconematidae) with case studies from Vietnam

The family Criconematidae is a remarkable group of nematodes, containing roughly 600 nominal root-ectoparasitic species, of which many species are known to be significant agricultural pests. Strikingly, our phylogenetic analyses based on 18S, D2-D3 of 28S rRNA, and COI mtDNA sequences of criconematid species, supported by tree topology tests (SH and AU tests), revealed that almost all studied genera, including Criconema, Ogma, Crossonema, Discocriconema, Hemicriconemoides, Criconemoides, Mesocriconema, and Lobocriconema, are not monophyletic groups, a finding that is partly contrary to those of previous studies on these groups. Our results suggest that key morphological characters used in the classification of Criconematidae are the consequence of convergent evolution. It is clear from our studies that the species status of at least 40 sequences of criconematid species from GenBank must be either revised or reconsidered, with analyses based on a polyphasic approach that includes different tree- and distance-based molecular species-delimitation methods (bPTP, GMYC, ABGD1, and ABGD2). Our studies found the ABGD2 output of the automatic barcode method to agree remarkably well with established species delimitations, while in general, the four species-delimitation results corresponding to three barcode regions forwarded significantly more putative species compared to those originally considered. This study also characterised for the first time the populations of Criconemoides myungsugae and Discocriconemella hensungica associated with Vietnamese ginseng, one of the most precious and rare ginseng varieties in the world. Although these populations are morphologically in agreement with the original descriptions of C. myungsugae and D. hengsungica, their molecular data display notable variations compared to the sequences deposited in GenBank. These species demonstrate clearly the immense molecular variations that can be observed in several species of the family Criconematidae.

An evaluation of errors in the mitochondrial COI sequences of Hydrachnidia (Acari, Parasitengona) in public databases

Public molecular databases are fundamental tools for modern taxonomic studies whose usefulness rely on the soundness of the data within them. Here, we study potential errors that can arise along the data pipeline from sampling, specimen identification and molecular processing (digestion, amplification and sequencing) to the submission of sequences to these databases by using the DNA sequences of Hydrachnidia (Acari, Parasitengona) as a case study. Our results indicate that molecular information is available for only about 3% of the Hydrachnidia species known to date; yet, within this small percentage, errors are present in almost 5% of the species analyzed (0.5% of the sequences and almost 11% of the genera). This study underscores the scarcity of genetic data available for Hydrachnidia, but also that the proportion of errors in DNA sequences is relatively small. Even so, it highlights the danger associated with using DNA sequences from public databases, particularly for species identification, and reinforces the need for greater quality control measures and/or protocols to avoid an intensification of errors in the (post) genomics era. Finally, our study emphasizes that potential errors may also reveal cryptic diversity within a species.

Identification and pathogenicity of Pratylenchus scribneri on tomato in Sichuan Province of People's Republic of China

Root-lesion nematodes (Pratylenchus spp.) are a group of economically important pathogens that have caused serious economic losses in many crops. In 2019, root-lesion nematodes were recovered from tomato (Solanum lycopersicum) root samples collected from Sichuan Province, People's Republic of China (PRC). Extracted nematodes were disinfected, and one individual female was cultured on a carrot disc for propagation at 25 °C by parthenogenesis and designated the SC isolate. Afterwards, the isolate was identified on the basis of morphometric and molecular markers. Both morphometric characters and molecular analysis of the internal transcribed spacer region gene (ITS) of ribosomal DNA, the D2-D3 expansion region of the 28S rDNA gene and the mitochondrial cytochrome oxidase I (mtDNA-COI) gene revealed that the species of root-lesion nematode was Pratylenchus scribneri. The Bayesian tree inferred from the ITS rDNA, 28S rDNA and mtDNA-COI gene sequences also showed that this isolate formed a highly supported clade with other P. scribneri isolates. The pathogenicity of the root-lesion nematode SC isolate on tomato was assessed, showing that tomato was a suitable host for P. scribneri. To the best of our knowledge, this is the first report of P. scribneri on tomato in Sichuan Province, PRC. These are also the first molecular data obtained from P. scribneri on tomato in the PRC, and the pathogenicity of P. scribneri to tomato was studied for the first time. This study provides scientific data for the detection, identification and control of tomato root-lesion nematode disease.

Rotylenchus wimbii n. sp. (Nematoda: Hoplolaimidae) associated with finger millet in Kenya

Rotylenchus wimbii n. sp. was found associated with finger millet in Kenya and is described based on light microscopy, scanning electron microscopy, and molecular information. Sequence analysis was performed on ITS, 18S, and D2-D3 of 28S of ribosomal DNA and COI of mitochondrial DNA. This new species is characterized by a moderate female body size of 0.6 to 0.8 mm, a continuous hemispherical lip region with four annuli, 3 to 4 irregular blocks on the basal lip annule, absence of longitudinal cuticular striations in anterior region, four lateral lines forming three equal bands which are areolated mainly at pharynx level, a robust stylet of 23 to 27 µm of which 45 to 53% is cone part, and with rounded to sometimes indented knobs, a secretory-excretory pore around level of pharyngo-intestinal junction, didelphic-amphidelphic reproductive system, vulva without distinct epiptygma, indistinct to empty spermatheca, tail usually truncated with 5 to 9 annuli, phasmids located at 7 to 17 annuli anterior to anus, and absence of males. Molecular phylogenies, in combination with species delimitation, supported the distinctiveness of Rotylenchus wimbii n. sp. and revealed some mislabeled Rotylenchus brevicaudatus sequences in GenBank.

Integrative Taxonomy and Molecular Phylogeny of the Plant-Parasitic Nematode Genus Paratylenchus (Nematoda: Paratylenchinae): Linking Species with Molecular Barcodes

Pin nematodes of the genus Paratylenchus are obligate ectoparasites of a wide variety of plants that are distributed worldwide. In this study, individual morphologically vouchered nematode specimens of fourteen Paratylenchus species, including P. aculentus, P. elachistus, P. goodeyi, P. holdemani, P. idalimus, P. microdorus, P. nanus, P. neoamblycephalus, P. straeleni and P. veruculatus, are unequivocally linked to the D2-D3 of 28S, ITS, 18S rRNA and COI gene sequences. Combined with scanning electron microscopy and a molecular analysis of an additional nine known and thirteen unknown species originating from diverse geographic regions, a total of 92 D2-D3 of 28S, 41 ITS, 57 18S rRNA and 111 COI new gene sequences are presented. Paratylenchus elachistus, P. holdemani and P. neoamblycephalus are recorded for the first time in Belgium and P. idalimus for the first time in Europe. Paratylenchus is an excellent example of an incredibly diverse yet morphologically minimalistic plant-parasitic genus, and this study provides an integrated analysis of all available data, including coalescence-based molecular species delimitation, resulting in an updated Paratylenchus phylogeny and the corrective reassignment of 18 D2-D3 of 28S, 3 ITS, 3 18S rRNA and 25 COI gene sequences that were previously unidentified or incorrectly classified.

Barcoding a can of worms: testing cox1 performance as a DNA barcode of Nematoda

Accurate taxonomic identifications and species delimitations are a fundamental problem in biology. The complex taxonomy of Nematoda is primarily based on morphology, which is often dubious. DNA barcoding emerged as a handy tool to identify specimens and assess diversity, but its applications in Nematoda are incipient. We evaluated cytochrome c oxidase subunit I (cox1) efficiency as a DNA barcode for nematodes scrutinising 5241 sequences retrieved from BOLD and GenBank. The samples included genera with medical, agricultural, or ecological relevance: Anguillicola, Caenorhabditis, Heterodera, Meloidogyne, Onchocerca, Strongyloides, and Trichinella. We assessed cox1 performance through barcode gap and Probability of Correct Identification (PCI) analyses, and estimated species richness through Automatic Barcode Gap Discovery (ABGD). Each genus presented distinct gap ranges, mirroring the evolutionary diversity within Nematoda. Thus, to survey the diversity of the phylum, a careful definition of thresholds for lower taxonomic levels should be considered. PCIs were around 70% for both databases, highlighting operational biases and challenges in nematode taxonomy. ABGD inferred higher richness than the taxonomic labels informed by databases. The prevalence of specimen misidentifications and dubious species delimitations emphasise the value of integrative approaches to nematode taxonomy and systematics. Overall, cox1 is a relevant tool for integrative taxonomy of nematodes.

Plant-parasitic nematodes associated with sugarcane in Kilimanjaro, Tanzania

Morphological and molecular analyses of plant-parasitic nematodes (PPN) from 12 sugarcane plantation sites of Tanganyika Planting Company (TPC) Limited in Kilimanjaro region of Tanzania revealed the presence of six PPN genera, i.e. Helicotylenchus, Hemicycliophora, Pratylenchus, Rotylenchulus, Scutellonema, and Tylenchorhynchus. The genera with the highest densities and present in virtually all samples were Pratylenchus and Rotylenchulus, and the most important species appeared to be R. parvus, P. zeae, T. crassicaudatus, and T. ventrosignatus. A total sequences of 11 partial ITS, 15 D2-D3 of 28S, and 6 partial 18S of rRNA gene, and 7 partial COI gene of mtDNA of these species were obtained in this study. Morphology and molecular data comparisons between the Tanzanian R. parvus and the South African R. parvus indicated that R. parvus is a cryptic species complex. Based on the results of morphological and molecular analyses of T. crassicaudatus and T. agri from China, Haiti, Indonesia, Iran, Niger and the USA, T. agri syn. n. is proposed as a junior synonym of T. crassicaudatus.

PPNID: a reference database and molecular identification pipeline for plant-parasitic nematodes

Motivation

The phylum Nematoda comprises the most cosmopolitan and abundant metazoans on Earth and plant-parasitic nematodes represent one of the most significant nematode groups, causing severe losses in agriculture. Practically, the demands for accurate nematode identification are high for ecological, agricultural, taxonomic and phylogenetic researches. Despite their importance, the morphological diagnosis is often a difficult task due to phenotypic plasticity and the absence of clear diagnostic characters while molecular identification is very difficult due to the problematic database and complex genetic background.

Results

The present study attempts to make up for currently available databases by creating a manually-curated database including all up-to-date authentic barcoding sequences. To facilitate the laborious process associated with the interpretation and identification of a given query sequence, we developed an automatic software pipeline for rapid species identification. The incorporated alignment function facilitates the examination of mutation distribution and therefore also reveals nucleotide autapomorphies, which are important in species delimitation. The implementation of genetic distance, plot and maximum likelihood phylogeny analysis provides more powerful optimality criteria than similarity searching and facilitates species delimitation using evolutionary or phylogeny species concepts. The pipeline streamlines several functions to facilitate more precise data analyses, and the subsequent interpretation is easy and straightforward.

Availability and implementation

The pipeline was written in vb.net, developed on Microsoft Visual Studio 2017 and designed to work in any Windows environment. The PPNID is distributed under the GNU General Public License (GPL). The executable file along with tutorials is available at https://github.com/xueqing4083/PPNID.

Supplementary information

Supplementary data are available at Bioinformatics online.

Morphological and molecular characterisation of Pratylenchus rwandae n. sp. (Tylenchida: Pratylenchidae) associated with maize in Rwanda

Pratylenchus rwandae n. sp., a root-lesion nematode associated with maize (Zea mays) from Rwanda, is described. This new species is characterised by females of medium to large size (469-600 μm) having an offset lip region with three annuli, stylet of 13-14.6 μm long with prominent rounded or anteriorly concave knobs, short to long pharyngeal gland overlap of 10.9-34.7 μm long, variable number of lateral lines (4-14) in different regions of the body, lateral field consisting of smooth bands, oval to slightly rounded spermatheca, vulva located at 75-80% of the total body length, post-vulval uterine sac (PUS) 20.3-26.5 μm long, tail subcylindrical to conoid with variation in tail tip shape from rounded to truncate or indented with generally smooth tip, and male unknown. The results of the phylogenetic analyses based on sequences of the D2-D3 expansion regions of 28S, partial 18S and ITS of rDNA and COI of mitochondrial DNA indicate that P. rwandae n. sp. is a species within the Penetrans group and appears as a sister species to a group comprising P. convallariae, P. dunensis, P. fallax, P. oleae, P. penetrans, P. pinguicaudatus, and three other unidentified species. A comparison of important morphological characters of the closely related Pratylenchus spp. is provided.

Molecular characterization and species delimiting of plant-parasitic nematodes of the genus Pratylenchus from the penetrans group (Nematoda: Pratylenchidae)

Root-lesion nematodes of the genus Pratylenchus are an important pest parasitizing a wide range of vascular plants including several economically important crops. However, morphological diagnosis of the more than 100 species is problematic due to the low number of diagnostic features, high morphological plasticity and incomplete taxonomic descriptions. In order to employ barcoding based diagnostics, a link between morphology and species specific sequences has to be established. In this study, we reconstructed a multi-gene phylogeny of the Penetrans group using nuclear ribosomal and mitochondrial gene sequences. A combination of this phylogenetic framework with molecular species delineation analysis, population genetics, morphometric information and sequences from type location material allowed us to establish the species boundaries within the Penetrans group and as such clarify long-standing controversies about the taxonomic status of P. penetrans, P. fallax and P. convallariae. Our study also reveals a remarkable amount of cryptic biodiversity within the genus Pratylenchus confirming that identification on morphology alone can be inconclusive in this taxonomically confusing genus.