Genomics of the Parasitic Nematode Ascaris and Its Relatives

Wang, Jianbin

doi:10.3390/genes12040493

Cited by 22 publications

(22 citation statements)

References 137 publications

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“…About half of the eliminated genes are testis-specific in ascarids. 20,21,41 We used RNA-seq data from the male worms to determine if O. tipulae also eliminates male-specific genes. We identified 1,229 male-enriched genes (5x male over mature hermaphrodite, p-value < 0.05; Fig.…”

Section: Resultsmentioning

confidence: 99%

“…This is consistent with the observations in other nematodes where many eliminated genes are “novel” genes. 6,41…”

Section: Resultsmentioning

confidence: 99%

“…This is consistent with the observations in other nematodes where many eliminated genes are "novel" genes. 6,41 Surprisingly, eight genes from the eliminated regions are highly expressed in the 64-128 cell stage (Fig. 2D).…”

Section: Introductionmentioning

confidence: 98%

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The Nematode Oscheius tipulae as A Genetic Model for Programmed DNA Elimination

Dockendorff

Estrem

Reed

et al. 2022

Preprint

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Programmed DNA elimination (PDE) is a notable exception to the paradigm of genome integrity. In metazoa, PDE often occurs during early embryogenesis, coincident with germline to somatic cell differentiation. During PDE, portions of genomic DNA are lost, resulting in reduced somatic genomes. Recent studies have described the sequences lost and chromosome behavior in metazoa. However, a system for studying the mechanisms and consequences of PDE in metazoa is lacking. Here, we established a functional and genetic model for PDE in the free-living nematode Oscheius tipulae, a member of the Rhabditidae family, which includes Caenorhabditis elegans. O. tipulae was recently suggested to eliminate DNA. Using staged embryos, we show that O. tipulae PDE occurs during embryogenesis at the 2-16 cell stages, similar to the human/pig parasitic nematode Ascaris. We identified a conserved motif, named Sequence For Elimination (SFE), for all 12 break sites on the six chromosomes at the junction of retained and eliminated DNA. SFE mutants exhibit a "fail-to-eliminate" phenotype only at the modified sites. END-seq revealed that breaks can occur at multiple positions within the SFE, with extensive end resection followed by telomere addition to both retained and eliminated ends. We identified through END-seq in the wild-type embryos, genome sequencing of SFE mutants, and comparative genomics of 23 wild isolates a large number of functional SFEs at the chromosome ends. We suggest these alternative SFEs provide flexibility in the sequences eliminated and a fail-safe mechanism for PDE. These studies establish O. tipulae as a new, attractive model to study the mechanisms and consequences of PDE in a metazoan.

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Section: Resultsmentioning

confidence: 99%

“…This is consistent with the observations in other nematodes where many eliminated genes are “novel” genes. 6,41…”

Section: Resultsmentioning

confidence: 99%

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The Nematode Oscheius tipulae as A Genetic Model for Programmed DNA Elimination

Dockendorff

Estrem

Reed

et al. 2022

Preprint

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“…Якщо при цьому відомий вік ураженої тварини і дата забою, то нескладно визначити, звичайно приблизно, дату зараження. Використання цієї методики та експериментальних даних про вікові особливості трихінел у м'язах дозволило пізнати особливості сезонної і вікової динаміки поширення трихінельозної інвазії (Wang, 2021).…”

Section: результати та їх обговоренняunclassified

Trichinosis in Ukraine – epizootological situation, prevention and control (2015–2020)

et al. 2022

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The work is devoted to analyzing literary sources and the results of public research on epizootology, epidemiology, and approaches to the fight against trichinosis – one of the most unsafe helminthiasis in animals and people. In the statistics, the primary nutrition is comprehensive, the path and the sources of invasion, the dynamics of infection of pigs and other creatures, now look at the circulation of Trichinella in nature and the biocenosis associated with humans, as well as the main directions of preventive entry. We conducted a study on the monitoring of trichinosis infestation. We found that the territory of Ukraine has a stationary unfavorable incidence of trichinosis in pigs, and the most significant number of pig carcasses infected with larvae – 76.5 % were registered in Mykolaioblast. Z'yasovanie natural causes of trichinosis, as revealed in the Transcarpathian, Mykolaiv, and Kharkiv regions. The dominating significance of the circulation of the bug is given to the invasion of the environment of the wild fauna lies the red fox. At the same time, there is an important creature in the circulation of the census between the synanthropic and natural centers. With laboratory studies of carcasses of creatures infected with Trichinella larvae, it is possible to show a significant advantage to the method of over-etching of muscles in piece stomach juice is equal to compressor trichineloscopy. These methods objectively characterize the intensity of invasion in skin creatures and show their role in the circulation of trichinosis. Due to the support of the European legislation, the first leaders are to introduce into the practice of veterinary medicine in Ukraine new methods for post-life and prosperous diagnosis of trichinosis. The system for the complex of entry into the prevention and elimination of trichinosis of creatures is guilty of including preventive measures and the prevention of endemic middle infections.

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“…Briefly, adaptor sequences were trimmed and then the reads collapsed to non-redundant datasets. The reads were then mapped to the Ascaris genome and other various datasets [124] to determine targets and their expression levels. To define complementary regions in the genome corresponding to AsWAGO-1 and AsWAGO-2 small RNAs, we first mapped reads from each Argonaute IP-small RNA library to the genome using bowtie [125].…”

Section: Small Rna Data Analysismentioning

confidence: 99%

Nematode Small RNA Pathways in the Absence of piRNAs

Zagoskin

Wang

Neff

et al. 2021

Preprint

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Small RNA pathways play diverse regulatory roles in the nematode C. elegans. However, our understanding of small RNA pathways, their conservation, and their roles in other nematodes is limited. Here, we analyzed small RNA pathways in the parasitic nematode Ascaris. Ascaris has ten Argonautes with five worm-specific Argonautes (WAGOs) that are associated with secondary 5'-triphosphate small RNAs (22-24G-RNAs). These Ascaris WAGOs and their small RNAs target repetitive sequences (WAGO-1, WAGO-2, WAGO-3, and NRDE-3) or mature mRNAs (CSR-1, NRDE-3, and WAGO-3) and are similar to the C. elegans mutator, nuclear, and CSR-1 small RNA pathways. Ascaris CSR-1 likely functions to "license" gene expression in the absence of an Ascaris piRNA pathway. Ascaris ALG-4 and its associated 26G-RNAs target and appear to repress specific mRNAs during meiosis in the testes. Notably, Ascaris WAGOs (WAGO-3 and NRDE-3) small RNAs change their targets between repetitive sequences and mRNAs during spermatogenesis or in early embryos illustrating target plasticity of these WAGOs. We provide a unique and comprehensive view of mRNA and small RNA expression throughout nematode spermatogenesis that illustrates the dynamics and flexibility of small RNA pathways. Overall, our study provides key insights into the conservation and divergence of nematode small RNA pathways.

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Genomics of the Parasitic Nematode Ascaris and Its Relatives

Cited by 22 publications

References 137 publications

The Nematode Oscheius tipulae as A Genetic Model for Programmed DNA Elimination

The Nematode Oscheius tipulae as A Genetic Model for Programmed DNA Elimination

Trichinosis in Ukraine – epizootological situation, prevention and control (2015–2020)

Nematode Small RNA Pathways in the Absence of piRNAs

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