Draft Genome Sequence of
            <i>Dermatophagoides pteronyssinus</i>
            , the European House Dust Mite

Waldron, R. M.; McGowan, Jamie; Gordon, Natasha; McCarthy, Charley G. P.; Mitchell, E. B.; Doyle, Seán; Fitzpatrick, David A.

doi:10.1128/genomea.00789-17

Cited by 20 publications

(30 citation statements)

References 14 publications

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“…These findings accord with the numbers of BUSCO orthologs for D . pteronyssinus (984; 92.3%) [ 25 ] and Tetranychus urticae (975; 91.5%) [ 26 ] ( Table 1 ). The statistics for the gene models of S .…”

Section: Resultsmentioning

confidence: 99%

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High-quality nuclear genome for Sarcoptes scabiei—A critical resource for a neglected parasite

Korhonen

Gasser

et al. 2020

PLoS Negl Trop Dis

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The parasitic mite Sarcoptes scabiei is an economically highly significant parasite of the skin of humans and animals worldwide. In humans, this mite causes a neglected tropical disease (NTD), called scabies. This disease results in major morbidity, disability, stigma and poverty globally and is often associated with secondary bacterial infections. Currently, anti-scabies treatments are not sufficiently effective, resistance to them is emerging and no vaccine is available. Here, we report the first high-quality genome and transcriptomic data for S . scabiei . The genome is 56.6 Mb in size, has a a repeat content of 10.6% and codes for 9,174 proteins. We explored key molecules involved in development, reproduction, host-parasite interactions, immunity and disease. The enhanced ‘omic data sets for S . scabiei represent comprehensive and critical resources for genetic, functional genomic, metabolomic, phylogenetic, ecological and/or epidemiological investigations, and will underpin the design and development of new treatments, vaccines and/or diagnostic tests.

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Section: Resultsmentioning

confidence: 99%

“…scabiei were similar to those of the well-assembled and annotated genome for D . pteronyssinus [ 25 ]: mean/median lengths of gene regions (2,735/1,601 bp), coding sequences (1,729/1,305 bp), exons (431/241 bp) and introns (334/71 bp)–excluding untranslated regions (UTRs)–were comparable with those of D . pteronyssinus (i.e.…”

Section: Resultsmentioning

confidence: 99%

High-quality nuclear genome for Sarcoptes scabiei—A critical resource for a neglected parasite

Korhonen

Gasser

et al. 2020

PLoS Negl Trop Dis

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“…The Benchmarking Universal Single-Copy Orthologs (BUSCO version 3.0.2) strategy was used according to [82] to assess the quality of the individual genome assemblies used in this study Table S1. [90], iFrom Waldron et al [91].…”

Section: Methodsmentioning

confidence: 99%

“…Asterick (*) indicates species with fully annotated genomes whereas no Asterick indicates species with a partial annotated genomes. aFrom Cornman et al [83], bFrom Techer et al [84], cFrom Hoy et al [85], dFrom Dong et al [86], eFrom Miller et al [87], fFrom Grbić et al [88], gFrom Rider et al [89], hFrom Rider et al [90], iFrom Waldron et al [91].…”

Section: Figurementioning

confidence: 99%

A genome-wide screening for RNAi pathway proteins in Acari

Nganso

Sela

Soroker

2020

Preprint

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Background RNA interference (RNAi) is a highly conserved, sequence-specific gene silencing mechanism present in Eukaryotes. Three RNAi pathways critical for organismal development and survival are known, namely micro-RNA (miRNA), Piwi-interacting RNA (piRNA) and short interfering RNA (siRNA) pathways. Little knowledge exist about the genes involved in these pathways in Acari. Moreover, variable successes has been obtained in gene knockdown via siRNA pathway in functional genomics and management of Acari species. We hypothesized that the clue may be in the variability in the composition and the efficacy of siRNAi machinery among Acari. Results Both comparative genomic analyses and domain annotation suggest that all the analyzed species have orthologs of genes that mediate gene silencing via the three RNAi pathways though gene duplication and/or loss have occurred in the different species. We also identified orthologs of Caenorhabditis elegans RNA-dependent RNA polymerase (RdRP) gene in all Acari species though no secondary Argonaute homologs that operate with this gene in siRNA amplification mechanism were found. This finding suggests that the siRNA amplification mechanism present in Acari may be distinct from that described in C. elegans . Moreover, the genomes of these Acari species encode no ortholog of C. elegans systemic RNAi defective 1 (Sid-1) that mediate systemic RNAi, suggesting that the phenomena of systemic and parental RNAi that has been reported in some Acari species probably occur through a different mechanism. Orthologs of RNAi spreading defective-3 (Rsd-3) gene and scavenger receptors namely Eater and SR-CI that mediate endocytosis cellular update of dsRNA in C. elegans and Drosophila melanogaster were found in Acari genomes. This result suggests that cellular dsRNA uptake in Acari is endocytosis-dependent. Detailed phylogenetic analyses of core RNAi pathway genes in the studied Acari species revealed that their evolution is compatible with the proposed monophyletic evolution of this group. Conclusions Taken together, our in silico comparative analyses have revealed the potential activity of all three pathways in Acari. However, much experimental work remains to be done in elucidating the operating mechanisms behind these pathways in particular those that govern systemic/parental RNAi and siRNA amplification in Acari.

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“…The recent generation of the P. ovis genome, which included the prediction and annotation of the P. ovis transcriptome [18] has substantially improved the resources available and enables more detailed genomic and transcriptomic analyses of P. ovis. At 63.2Mb, the draft genome assembly demonstrated that P. ovis has one of the smallest arthropod genomes sequenced to date, smaller than the genome of the two-spotted spider mite (Tetranychus urticae (90Mb)) but comparable in size with the closely related house dust mite (HDM) genomes (Dermatophagoides farinae (53.5Mb) and D. pteronyssinus (70.76Mb)) and the ectoparasitic scabies mite (Sarcoptes scabiei (56.2Mb)) [18][19][20][21][22]. Herein, using the recently described P. ovis genome [18], we described the detailed annotation of the genome to Gene Ontology (GO) level along with a quantitative transcriptomic analysis of P. ovis gene expression across multiple life-cycle stages, providing for the first time a complete transcriptomic atlas of stage-specific and feeding-related gene expression in this economically-important ectoparasite of livestock.…”

Section: Introductionmentioning

confidence: 99%

A genomic analysis and transcriptomic atlas of gene expression inPsoroptes ovisreveals feeding- and stage-specific patterns of allergen expression

Burgess

Marr

Bartley

et al. 2019

Preprint

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Psoroptic mange, caused by infestation with the ectoparasitic mite, Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock industry Worldwide. Control relies on injectable endectocides and organophosphate dips, but concerns over residues, environmental contamination, and the development of resistance threaten the sustainability of this approach, highlighting interest in alternative control methods. However, development of vaccines and identification of chemotherapeutic targets is hampered by the lack of P. ovis transcriptomic and genomic resources. Building on the recent publication of the P. ovis draft genome, here we present a genomic analysis and transcriptomic atlas of gene expression in P. ovis revealing feeding-and stage-specific patterns of gene expression, including novel multigene families and allergens. Network-based clustering revealed 14 gene clusters demonstrating either single-or multi-stage specific gene expression patterns, with 3,075 female-specific, 890 male-specific and 112, 217 and 526 transcripts showing larval, protonymph and tritonymph specific-expression, respectively. Detailed analysis of P. ovis allergens revealed stage-specific patterns of allergen gene expression, many of which were also enriched in "fed" mites and tritonymphs, highlighting an important feeding-related allergenicity in this developmental stage. Pair-wise analysis of differential expression between life-cycle stages identified patterns of sex-biased gene expression and also identified novel P. ovis multigene families including known allergens and novel genes with high levels of stage-specific expression. The genomic and transcriptomic atlas described here represents a unique resource for the acarid-research community, whilst the OrcAE platform makes this freely available, facilitating further community-led curation of the draft P. ovis genome.3

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Draft Genome Sequence of Dermatophagoides pteronyssinus , the European House Dust Mite

Cited by 20 publications

References 14 publications

High-quality nuclear genome for Sarcoptes scabiei—A critical resource for a neglected parasite

High-quality nuclear genome for Sarcoptes scabiei—A critical resource for a neglected parasite

A genome-wide screening for RNAi pathway proteins in Acari

A genomic analysis and transcriptomic atlas of gene expression inPsoroptes ovisreveals feeding- and stage-specific patterns of allergen expression

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