Morpho-Molecular and Ultrastructural Characterization of Discocriconemella parasinensis n. sp. from Zhejiang Province, China

During a recent inventory survey of the nematofauna of tea plantation at Zhejiang Province, China, Discocriconemella parasinensis n. sp. was detected in the rhizosphere of Camellia sinensis. The new species can be characterized by having the uninterrupted rounded labial disc, en face view showing rectangular-rounded labial plate without submedian lobes, R = 82.6 (80–86), Rex = 22 (21–23), stylet length of 68.3 (59–76) μm, excretory pore located 1–2 annuli posterior to the esophageal bulb, vulva open, postvulval body elongated conoid, and tail conoid with bilobed terminus. Morphologically, the species shares the same lip-type with D. discolabia, D. mauritiensis, D. mineira, D. perseae, and D. sinensis. Phylogenetic relationships of the new species based on D2–D3 expansion segments of 28S, ITS, and 18S rRNA genes revealed that D. parasinensis n. sp. formed a separated clade from other criconematid species, thereby supporting its status as a new species of the genus. The new species showed close phylogenetic relationships with Criconemoides geraerti.

First Report of Three Tylenchidae Taxa from Southern Alberta, Canada

Members of the family Tylenchidae are highly abundant in soil habitats, including agricultural settings, where they play key ecological roles. In the present study, we identified three Tylenchidae species, namely Basiria bhabi, Coslenchus acceptus, and Filenchus vulgaris, using integrative taxonomy. The detailed morphological and morphometric characteristics, distribution, and host associations of each species were also discussed. Phylogenetic analyses of these populations with other Tylenchidae nematodes indicated the presence of divergent lineages in Filenchus and Basiria, whereas Coslenchus appeared to be a monophyletic genus. Herein, we aim to grow awareness about this common but least studied group of nematodes. The species reported in this study are new records for Canada, revealing that the identified nematode diversity in our cultivated areas is relatively underrepresented. Our analyses also provided greater taxonomic resolution and captured rare taxa that might have been missed or misidentified in prior nematode inventory surveys. These findings will add to our understanding of the nematofauna of southern Alberta, thereby providing a more complete picture of existing nematode diversity present in the fields of this highly cultivated region.

Discopersicus hexagrammatus n. sp. (Rhabditida: Tylenchidae), the second species of the genus

Discopersicus hexagrammatus n. sp., is described and illustrated from a population associated with the rhizosphere of carrot (Daucus carota L.) in Dezful, Khuzestan province, south-western Iran. Based on morphological and morphometric data, the new species is characterized by a 601-734 µm long body, a prominent perioral labial disc and oblique amphidial slits, 10-11 µm long stylet, vulva at 65-67% of body length, 15.5-17 µm long spicules, and an elongate conoid tail with a pointed terminus. It is the second species of the genus Discopersicus and differs from its counterpart D. iranicus, by its anterior position of vulva, shorter stylet, lower M.B. ratio, different shape of tail tip, and shorter spicules in male specimens. A molecular phylogenetic analysis using the D2-D3 expansion segments of 28S rDNA sequences, placed the new species in close relationship with five sequences of the genus Boleodorus.

Overview of the Genus Boleodorus and First Reports of Boleodorus thylactus and B. volutus from Southern Alberta, Canada

Simple Summary

Two Boleodorus species were detected in cultivated areas of southern Alberta. The aim of the present work was to characterize the discovered populations of Boleodorus using morphological and molecular methods. Boleodorus is the least studied genus in family Tylenchidae, with very few species reported after formal descriptions and outside their type locality. To date, Boleodorus species are not considered nematode pest species, rather they can serve as environmental indicators. Therefore, it is important to quantify and monitor the population densities of these species for soil health management studies. The current study encompasses the distribution and host association of all described Boleodorus species. In addition, morphometrical characters of all valid species are listed for their prompt identification.

Abstract

The present study provides the morphological and molecular characterization of Boleodorus thylactus and B. volutus populations, recovered from agricultural fields of southern Alberta. Despite a significant abundance of this group of nematodes, none of the Boleodorus species were previously reported in Canada. Therefore, representative adult specimens of each population were photographed and examined morphometrically. Phylogenetic trees were reconstructed using partial D2–D3 expansion segments of the 28S and 18S rDNA sequences to understand the relationships of Boleodorus species with Tylenchidae-related genera. Boleodorus species are relevant to soil ecological studies and therefore we summarized the important morphological and morphometric characters in tabular form for easy and efficient species identification. Moreover, we discuss the associated hosts and the distribution of all described Boleodorus species. This study will serve as a guide and basic framework for species diagnostics in the genus Boleodorus and will aid in filling the gaps in our knowledge of the species present in our cultivated lands.

Mitochondrial COI gene is valid to delimitate Tylenchidae (Nematoda: Tylenchomorpha) species

Tylenchidae is a widely distributed soil-inhabiting nematode family. Regardless their abundance, molecular phylogeny based on rRNA genes is problematic, and the delimitation of taxa in this group remains poorly documented and highly uncertain. Mitochondrial Cytochrome Oxidase I (COI) gene is an important barcoding gene that has been widely used species identifications and phylogenetic analyses. However, currently COI data are only available for one species in Tylenchidae. In present study, we newly obtained 27 COI sequences from 12 species and 26 sequences from rRNA genes. The results suggest that the COI gene is valid to delimitate Tylenchidae species but fails to resolve phylogenetic relationships.

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.