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

Xue, Qiao; Slos, Dieter; Claeys, Myriam; Bert, Wim

doi:10.1016/j.jcz.2017.06.002

Cited by 5 publications

(2 citation statements)

References 39 publications

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“…(Neotylenchidae), and Abursanema quadrilineatum (Paurodontidae) also follow the "rhabditid" pattern (Qing et al, 2017;Yushin et al, 2006;Yushin, Kosaka, & Kusunoki, 2007), the insect parasitic females of Sphaerularioidea may be impregnated by numerous miniaturized spermatozoa with a highly simplified structure (Yushin & Kosaka, 2013;Yushin, Kosaka, & Kusunoki, 2007).…”

Section: Infraorder Rhigonematomorphamentioning

confidence: 99%

Structure, development, and evolutive patterns of spermatozoa in rhabditid nematodes (Nematoda: Rhabditida)

Slos

Yushin

Claeys

et al. 2020

Journal of Morphology

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Spermatogenesis of five rhabditid nematodes was studied using transmission electron microscopy and is described herein. Structure and development of nematode sperm in all available representatives of the extensive order Rhabditida have been analysed and the main characteristics of each infraorder are discussed. The ancestral sperm of the order Rhabditida was reconstructed using maximum likelihood and Bayesian methods based on 44 ultrastructural sperm characters. The hypothetical ancestral spermatogenesis of the order Rhabditida agrees with the previously suggested "rhabditid" pattern and appears to be conserved throughout the order Rhabditida. Despite the enormous variation of rhabditid nematodes, few groups deviate from the ancestral pattern. This conserved pattern can be informative within the phylum Nematoda at order level, but poses limitations when used in taxonomic and phylogenetic analysis within Rhabditida.

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Section: Infraorder Rhigonematomorphamentioning

confidence: 99%

Structure, development, and evolutive patterns of spermatozoa in rhabditid nematodes (Nematoda: Rhabditida)

Slos

Yushin

Claeys

et al. 2020

Journal of Morphology

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“…For instance, the V4 region in 18S shows significant sequence variability (Hadziavdic et al, 2014) and has been extensively used as a marker in DNA metabarcoding projects (Hadziavdic et al, 2014). D1, D2, and D3 of the 28S have similar properties and have been used to identify species where 18S has not provided the required taxonomic resolution (Douda et al, 2013; Qing et al, 2017; Rué et al, 2023; Sonnenberg et al, 2007). Knowing the level of variability and which taxonomic resolution the markers provide is crucial in DNA metabarcoding analyses.…”

Section: Introductionmentioning

confidence: 99%

The Ribosomal Operon Database (ROD): A full-length rDNA operon database derived from genome assemblies

Krabberød,

Stokke,

Thoen

et al. 2024

Preprint

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Current rDNA reference sequence databases are tailored towards shorter DNA markers, such as parts of the 16/18S marker or the ITS region. However, due to advances in long-read DNA sequencing technologies, longer stretches of the rDNA operon are increasingly used in environmental sequencing studies to increase the phylogenetic resolution. There is, therefore, a growing need for longer rDNA reference sequences. Here, we present the Ribosomal Operon Database (ROD), which includes eukaryotic full-length rDNA operons fished from publicly available genome assemblies. Full-length operons were detected in 34.1% of the 34,701 examined eukaryotic genome assemblies from NCBI. In most cases (53.1%), more than one operon variant was detected, which can be due to intragenomic operon copy variability, allelic variation in non-haploid genomes, or technical errors from the sequencing and assembly process. The highest copy number found was 5,947 in Zea mays. In total, 453,697 unique operons were detected, with 69,480 operon clusters remaining after intragenomic clustering at 99% sequence identity. The operon length varied extensively across eukaryotes, ranging from 4,136 to 16,463 bp, which will lead to considerable PCR bias during PCR amplification of the entire operon. Clustering the full-length operons revealed that the different parts (i.e., 18S, 28S, the hypervariable region V4 of 18S, and ITS) provide divergent taxonomic resolution, with 18S and the V4 region being the most conserved. The Ribosomal Operon Database (ROD) will be updated regularly to provide an increasing number of full-length rDNA operons to the scientific community.

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Widespread prevalence but contrasting patterns of intragenomic rRNA polymorphisms in nematodes: Implications for phylogeny, species delimitation and life history inference

Xue

Bik

Yergaliyev

et al. 2019

Molecular Ecology Resources

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Ribosomal RNA genes have long been a favoured locus in phylogenetic and metabarcoding studies. Within a genome, rRNA loci are organized as tandem repeated arrays and the copies are homogenized through the process of concerted evolution. However, some level of rRNA variation (intragenomic polymorphism) is known to persist and be maintained in the genomes of many species. In nematode worms, the extent of rRNA polymorphism (RP) across species and the evolutionary and life history factors that contribute to the maintenance of intragenomic RP is largely unknown. Here, we present an extensive analysis across 30 terrestrial nematode species representing a range of free‐living and parasitic taxa isolated worldwide. Our results indicate that RP is common and widespread, ribosome function appears to be maintained despite mutational changes, and intragenomic variants are stable in the genome and neutrally evolving. However, levels of variation were varied widely across rRNA locus and species, with some taxa observed to lack RP entirely. Higher levels of RP were significantly correlated with shorter generation time and high reproductive rates, and population‐level factors may play a role in the geographic and phylogenetic structuring of rRNA variants observed in genera such as Rotylenchulus and Pratylenchus. Although RP did not dramatically impact the clustering and recovery of taxa in mock metabarcoding analyses, the present study has significant implications for global biodiversity estimates of nematode species derived from environmental rRNA amplicon studies, as well as our understanding of the evolutionary and ecological factors shaping genetic diversity across the nematode Tree of Life.

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

Cited by 5 publications

References 39 publications

Structure, development, and evolutive patterns of spermatozoa in rhabditid nematodes (Nematoda: Rhabditida)

Structure, development, and evolutive patterns of spermatozoa in rhabditid nematodes (Nematoda: Rhabditida)

The Ribosomal Operon Database (ROD): A full-length rDNA operon database derived from genome assemblies

Widespread prevalence but contrasting patterns of intragenomic rRNA polymorphisms in nematodes: Implications for phylogeny, species delimitation and life history inference

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