The complete mitochondrial genome of <i>Coronocyclus labratus</i> (Rhabditida: Cyathostominae)

Yang, Shuwen; Sun, Chenguang; Liu, Wei

doi:10.1080/23802359.2020.1721361

Cited by 3 publications

(3 citation statements)

References 8 publications

(10 reference statements)

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“…To overcome the described challenges owing to barcode properties, metagenomic shotgun sequencing on DNA extracted from faeces could resolve the horse gut biodiversity in a single-pot experiment. While gut microbial gene catalogues have been built recently ( Mach et al, 2022 ; Ang et al, 2022 ), the genomic resources for equine strongylids remain restricted to a few mitochondrial genomes that span the Coronocyclus ( Yang et al, 2020 ), Cyathostomum ( Wang et al, 2020 ), Cylicocyclus ( Gao et al, 2017b ), Cylicostephanus ( Gao et al, 2020 ), and Triodontophorus ( Gao et al, 2017a ) genera, and a single heavily fragmented genome assembly for C. goldi ( International Helminth Genomes, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing

Courtot

Boisseau

Dhorne–Pollet

et al. 2023

PeerJ

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Basic knowledge on the biology and epidemiology of equine strongylid species still needs to be improved to contribute to the design of better parasite control strategies. Nemabiome metabarcoding is a convenient tool to quantify and identify species in bulk samples that could overcome the hurdle that cyathostomin morphological identification represents. To date, this approach has relied on the internal transcribed spacer 2 (ITS-2) of the ribosomal RNA gene, with a limited investigation of its predictive performance for cyathostomin communities. Using DNA pools of single cyathostomin worms, this study aimed to provide the first elements to compare performances of the ITS-2 and a cytochrome c oxidase subunit I (COI) barcode newly developed in this study. Barcode predictive abilities were compared across various mock community compositions of two, five and 11 individuals from distinct species. The amplification bias of each barcode was estimated. Results were also compared between various types of biological samples, i.e., eggs, infective larvae or adults. Bioinformatic parameters were chosen to yield the closest representation of the cyathostomin community for each barcode, underscoring the need for communities of known composition for metabarcoding purposes. Overall, the proposed COI barcode was suboptimal relative to the ITS-2 rDNA region, because of PCR amplification biases, reduced sensitivity and higher divergence from the expected community composition. Metabarcoding yielded consistent community composition across the three sample types. However, imperfect correlations were found between relative abundances from infective larvae and other life-stages for Cylicostephanus species using the ITS-2 barcode. While the results remain limited by the considered biological material, they suggest that additional improvements are needed for both the ITS-2 and COI barcodes.

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Section: Discussionmentioning

confidence: 99%

Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing

Courtot

Boisseau

Dhorne–Pollet

et al. 2023

PeerJ

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show abstract

“…To overcome the described challenges owing to barcode properties, metagenomic shotgun sequencing on DNA extracted from faeces could resolve the horse gut biodiversity in a single-pot experiment. While gut microbial gene catalogs have been built recently (Ang et al, 2022; Mach et al, 2022), the genomic resources for cyathostomin remain restricted to a few mitochondrial genomes that span the Coronocyclus (Yang et al, 2020), Cyathostomum (Wang et al, 2020), Cylicocyclus (Y. Gao et al, 2017), Cylicostephanus (Gao et al, 2020), and Triodontophorus (J.-F. Gao et al, 2017) genera, and a single heavily fragmented genome assembly for C. goldi (International Helminth Genomes, 2019).…”

Section: Discussionmentioning

confidence: 99%

Evaluation of the nemabiome approach for the study of equine strongylid communities

Courtot

Boisseau

Dhorne–Pollet

et al. 2022

Preprint

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Basic knowledge on the biology and epidemiology of equine strongylid species remains insufficient although it would contribute to the design of better parasite control strategies. Nemabiome is a convenient tool to quantify and to identify species in bulk samples that could overcome the hurdle that cyathostomin morphological identification represents. To date, this approach has relied on the internal transcribed spacer 2 (ITS-2) of the ribosomal RNA cistron and its predictive performance and associated biases both remain unaddressed. This study aimed to bridge this knowledge gap using cyathostomin mock communities and comparing performances of the ITS-2 and a cytochrome c oxidase subunit I (COI) barcode newly developed in this study. The effects of bioinformatic parameters were investigated to determine the best analytical pipelines. Subsequently, barcode predictive abilities were compared across various mock community compositions. The replicability of the approach and the amplification biases of each barcode were estimated. Results were also compared between various types of biological samples, i.e. eggs, infective larvae or adults. Overall, the proposed COI barcode was suboptimal relative to the ITS-2 rDNA region, because of PCR amplification biases, a reduced sensitivity and higher divergence from the expected community composition. Metabarcoding yielded consistent community composition across the three sample types, although infective larvae may remain the most tractable in the field. Additional strategies to improve the COI barcode performances are discussed. These results underscore the critical need of mock communities for metabarcoding purposes.

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“…Nucleotide content and codon usage of V. eleguneniensis mtDNA were measured using Geneious and PhyloSuite [ 43 , 44 ]. The nucleotide skewness of V. eleguneniensis and their comparisons with 42 other nematodes in the order Strongylida ( Table 2 ) were performed using the formulas [ 26 , 34 , 35 , 36 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 ]: AT skew = (A − T)/(A + T) and GC skew = (G − C)/(G + C). Sequence lengths and nucleotide/amino acid identities of 12 PCGs among Strongylida species were determined using DNAstar [ 58 ].…”

Section: Methodsmentioning

confidence: 99%

Comprehensive Molecular Characterization of the Mitochondrial Genome of the Takin Lungworm Varestrongylus eleguneniensis (Strongylida: Protostrongylidae)

Xie

Chen

Wang

et al. 2022

IJMS

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The takin lungworm Varestrongylus eleguneniensis (Strongylida: Protostrongylidae) causes lethal bronchopneumonia and represents severe threats to captive and wild populations. However, until now there has been very limited information available concerning the molecular epidemiology and evolutionary biology of V. eleguneniensis. Mitochondrial genomes (mtDNAs) can provide resources for investigations in these areas and, therefore, can assist with the surveillance and control of this lungworm. Herein, the complete mtDNA of V. eleguneniensis was sequenced and characterized with Illumina pipeline analyses. This circular genome (13,625 bp) encoded twelve protein-coding genes (PCGs), two rRNAs, and twenty-two tRNAs, with notable levels of AT and GC skews. Comparative genomics revealed a purifying selection among PCGs, with cox1 and nad6 having the lowest and the highest evolutionary rate, respectively. Genome-wide phylogenies showed a close relationship between V. eleguneniensis and Protostrongylus rufescens in Strongylida. Single gene (PCGs or rRNAs)-based phylogenies indicated that cox1 and nad5 genes shared the same family-level topology with that inferred from genomic datasets, suggesting that both genes could be suitable genetic markers for evolutionary and phylogenetic studies of Strongylida species. This was the first mtDNA of any member of the genus Varestrongylus, and its comprehensive molecular characterization represents a new resource for systematic, population genetic and evolutionary biological studies of Varestrongylus lungworms in wildlife.

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The complete mitochondrial genome of Coronocyclus labratus (Rhabditida: Cyathostominae)

Cited by 3 publications

References 8 publications

Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing

Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing

Evaluation of the nemabiome approach for the study of equine strongylid communities

Comprehensive Molecular Characterization of the Mitochondrial Genome of the Takin Lungworm Varestrongylus eleguneniensis (Strongylida: Protostrongylidae)

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