Caenorhabditis monodelphis sp. n.: defining 1 the stem morphology 2 and genomics of the genus Caenorhabditis

Background: The genus Caenorhabditis has been central to our understanding of metazoan biology. The best-known species, Caenorhabditis elegans, is but one member of a genus with around 50 known species, and knowledge of these species will place the singular example of C. elegans in a rich phylogenetic context. How did the model come to be as it is today, and what are the dynamics of change in the genus? Results: As part of this effort to “put C. elegans in its place”, we here describe the morphology and genome of Caenorhabditis monodelphis sp. n., previously known as Caenorhabditis sp. 1. Like many other Caenorhabditis, C. monodelphis sp. n. has a phoretic association with a transport host, in this case with the fungivorous beetle Cis castaneus. Using genomic data, we place C. monodelphis sp. n. as sister to all other Caenorhabditis for which genome data are available. Using this genome phylogeny, we reconstruct the stemspecies morphological pattern of Caenorhabditis. Conclusions: With the morphological and genomic description of C. monodelphis sp. n., another key species for evolutionary and developmental studies within Caenorhabditis becomes available. The most important characters are its early diverging position, unique morphology for the genus and its similarities with the hypothetical ancestor of Caenorhabditis

18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences

Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant to nematology and updated for the most recent accepted nematode classifications. In addition, apparent erroneous sequences were removed. To test the efficacy and accuracy of 18S-NemaBase, we compared it to an older but also curated SILVA v111 and the newest SILVA v138 by assigning taxonomies and analyzing the diversity of a nematode dataset from the Western Nebraska Sandhills. We showed that 18S-NemaBase provided more accurate taxonomic assignments and diversity assessments than either version of SILVA, with a much easier workflow and no need for manual corrections. Additionally, observed diversity further improved when 18S-NemaBase was supplemented with reference sequences from nematodes present in the study site. Although the 18S-NemaBase is a step in the right direction, a concerted effort to increase the number of high-quality, accessible, full-length nematode reference sequences is more important now than ever

18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences

Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant to nematology and updated for the most recent accepted nematode classifications. In addition, apparent erroneous sequences were removed. To test the efficacy and accuracy of 18S-NemaBase, we compared it to an older but also curated SILVA v111 and the newest SILVA v138 by assigning taxonomies and analyzing the diversity of a nematode dataset from the Western Nebraska Sandhills. We showed that 18S-NemaBase provided more accurate taxonomic assignments and diversity assessments than either version of SILVA, with a much easier workflow and no need for manual corrections. Additionally, observed diversity further improved when 18S-NemaBase was supplemented with reference sequences from nematodes present in the study site. Although the 18S-NemaBase is a step in the right direction, a concerted effort to increase the number of high-quality, accessible, full-length nematode reference sequences is more important now than ever

Assessing the diversity and spatial distribution of nematodes in the Store Mosse National Park (Sweden) using metabarcoding

Nematode taxa of the Store Mosse National Park in the south of Sweden were surveyed using DNA metabarcoding. Samples were collected from a range of media across all the five vegetation types the park spans. A total of 50 samples consisting of soil, litter, lichens, sphagnum, roots, wood, moss, fungus and anthill materials were analysed. Nematodes were characterised using a ~350 bp region of their 18S ribosomal RNA gene that include V7 and V8 variable domains. The analysis identified 47 families, 76 genera (21 new to Swedish fauna) and 60 species (31 new to Swedish fauna). Some nematodes showed a strong association with certain medium types, especially at the species level. The results showed a strong justification for our strategy of sampling different medium types. Soil and litter communities, which were the most diverse, showed high levels of stability with good balance of all the various trophic and coloniser-persister groups

Description of Myolaimus mycophilus Slos & Bert sp. n. (Rhabditida: Myolaimidae)

Myolaimus mycophilus Slos & Bert sp. n. was isolated from mushrooms from different locations in Belgium and cultured on nutrient agar seeded with Escherichia coli OP50. Myolaimus mycophilus sp. n. is characterised by a unique combination of the following characters: adults with lateral fields not differentiated, buccal cavity triangular, cheilostom anisomorphic, female with a post-vulval uterine sac as long as the corresponding body diam., wrinkled eggshell, male with seven pairs of genital papillae, cloacal aperture covered by a trapezoidal cloacal flap and with a single ventral papilla at its base. The new species and M. goodeyorum Andrassy, 1984 were molecularly characterised by sequencing the 18S and D2-D3 28S expansion segments of rDNA. Phylogenetic relationships were reconstructed based on concatenated analyses and the phylogenetic placement of Myolaimus, an intriguing genus within the Rhabditida, is discussed

Assessing the diversity of nematodes in the Store Mosse National Park (Sweden) using metabarcoding

The Store Mosse National Park in the south of Sweden was surveyed for nematode diversity and distribution using DNA metabarcoding. Fifty samples were collected from five vegetation types in the park across a range of habitats (e.g. soil, litter, lichens, sphagnum and roots). The other habitats, aside from soil and litter, were sampled in order to capture the diversity of nematodes that may be uniquely associated with them. Nematodes were characterised using the V7-V8 variable domain (~ 350 bp) of the 18S ribosomal RNA gene. We identified 46 families, 76 genera (21 new to Swedish fauna) and 60 species (31 new to Swedish fauna). Some nematodes showed strong associations with their habitats, especially at the species level. Although soil and litter supported the most diverse nematode communities, our results support a strong justification for sampling across different media types to quantify nematode diversity accurately. Soil and litter communities showed high levels of stability with balanced distribution of all the various trophic and coloniser-persister groups

Supplementary material 1 from: Ahmed M, Slos D, Holovachov O (2024) Assessing the diversity of nematodes in the Store Mosse National Park (Sweden) using metabarcoding. Metabarcoding and Metagenomics 8: e111307. https://doi.org/10.3897/mbmg.8.111307

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Ultrastructural, phylogenetic and rRNA secondary structural analysis of a new nematode (Nematoda: Tylenchomorpha) from mushroom with recovery of intestinal crystals

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