The Highly Repetitive Genome of Myxobolus rasmusseni, an Emerging Myxozoan Parasite of Fathead Minnows.

Myxozoans are a monophyletic taxon of approximately 2,400 described species of parasites from the phylum Cnidaria. The recent focus on their negative impacts on fisheries, on their evolution from free-living ancestors, and on their emergence into new fish host populations has stressed the critical need for genomic resources for this parasitic group. Here, we describe the genome assembly and annotation of Myxobolus rasmusseni, an emerging parasite of fathead minnows in Alberta, Canada.

Corrigendum: Trickle infection with results in decreased worm burdens but increased intestinal inflammation and scarring.

[This corrects the article DOI: 10.3389/fimmu.2022.

The impact of FASTQ and alignment read order on structural variant calling from long-read sequencing data.

Background: Structural variant (SV) calling from DNA sequencing data has been challenging due to several factors, including the ambiguity of short-read alignments, multiple complex SVs in the same genomic region, and the lack of "truth" datasets for benchmarking. Additionally, caller choice, parameter settings, and alignment method are known to affect SV calling. However, the impact of FASTQ read order on SV calling has not been explored for long-read data.

IL-33-binding HpARI family homologues with divergent effects in suppressing or enhancing type 2 immune responses.

HpARI is an immunomodulatory protein secreted by the intestinal nematode , which binds and blocks IL-33. Here, we find that the genome contains three HpARI family members and that these have different effects on IL-33-dependent responses and , with HpARI1+2 suppressing and HpARI3 amplifying these responses. All HpARIs have sub-nanomolar affinity for mouse IL-33; however, HpARI3 does not block IL-33-ST2 interactions.

Proteome-wide comparison of tertiary protein structures reveals molecular mimicry in -human interactions.

Introduction: Molecular mimicry is a strategy used by parasites to evade the host's immune system and facilitate transmission to a new host. To date, high-throughput examples of molecular mimicry have been limited to comparing protein sequences. However, recent advances in the prediction of tertiary structural models, led by Deepmind's AlphaFold, enable the comparison of thousands of proteins from parasites and their hosts at the structural level, allowing for the identification of more mimics.

Transcriptional patterns of sexual dimorphism and in host developmental programs in the model parasitic nematode Heligmosomoides bakeri.

Background: Heligmosomoides bakeri (often mistaken for Heligmosomoides polygyrus) is a promising model for parasitic nematodes with the key advantage of being amenable to study and manipulation within a controlled laboratory environment. While draft genome sequences are available for this worm, which allow for comparative genomic analyses between nematodes, there is a notable lack of information on its gene expression.

Methods: We generated biologically replicated RNA-seq datasets from samples taken throughout the parasitic life of H.

Different structural variant prediction tools yield considerably different results in Caenorhabditis elegans.

The accurate characterization of structural variation is crucial for our understanding of how large chromosomal alterations affect phenotypic differences and contribute to genome evolution. Whole-genome sequencing is a popular approach for identifying structural variants, but the accuracy of popular tools remains unclear due to the limitations of existing benchmarks. Moreover, the performance of these tools for predicting variants in non-human genomes is less certain, as most tools were developed and benchmarked using data from the human genome.

Trickle infection with results in decreased worm burdens but increased intestinal inflammation and scarring.

Introduction: Intestinal roundworms cause chronic debilitating disease in animals, including humans. Traditional experimental models of these types of infection use a large single-dose infection. However, in natural settings, hosts are exposed to parasites on a regular basis and when mice are exposed to frequent, smaller doses of , the parasites are cleared more quickly.

Genomic signatures of selection associated with benzimidazole drug treatments in Haemonchus contortus field populations.

Genome-wide methods offer a powerful approach to detect signatures of drug selection. However, limited availability of suitable reference genomes and the difficulty of obtaining field populations with well-defined, distinct drug treatment histories mean there is little information on the signatures of selection in parasitic nematodes and on how best to detect them. This study addresses these knowledge gaps by using field populations of Haemonchus contortus with well-defined benzimidazole treatment histories, leveraging a recently completed chromosomal-scale reference genome assembly.

Genotyping Canadian Isolates to Supplement Cyclosporiasis Outbreak Investigations.

is an emerging foodborne parasite that causes cyclosporiasis, an enteric disease of humans. Domestically acquired outbreaks have been reported in Canada every spring or summer since 2013. To date, investigations into the potential sources of infection have relied solely on epidemiological data.

Draft Hybrid Genome Assembly of a Canadian Cyclospora cayetanensis Isolate.

The apicomplexan parasite Cyclospora cayetanensis causes foodborne gastrointestinal disease in humans. Here, we report the first hybrid assembly for C. cayetanensis, which uses both Illumina MiSeq and Oxford Nanopore Technologies MinION platforms to generate genomic sequence data.

Characterization of the β-tubulin gene family in Ascaris lumbricoides and Ascaris suum and its implication for the molecular detection of benzimidazole resistance.

Background: The treatment coverage of control programs providing benzimidazole (BZ) drugs to eliminate the morbidity caused by soil-transmitted helminths (STHs) is unprecedently high. This high drug pressure may result in the development of BZ resistance in STHs and so there is an urgent need for surveillance systems detecting molecular markers associated with BZ resistance. A critical prerequisite to develop such systems is an understanding of the gene family encoding β-tubulin proteins, the principal targets of BZ drugs.

Small Intestinal Levels of the Branched Short-Chain Fatty Acid Isovalerate Are Elevated during Infection with Heligmosomoides polygyrus and Can Promote Helminth Fecundity.

Heligmosomoides polygyrus is a helminth which naturally infects mice and is widely used as a laboratory model of chronic small intestinal helminth infection. While it is known that infection with alters the composition of the host's bacterial microbiota, the functional implications of this alteration are unclear. We investigated the impact of infection on short-chain fatty acid (SCFA) levels in the mouse intestine and sera.

Benchmarking hybrid assemblies of Giardia and prediction of widespread intra-isolate structural variation.

Background: Currently available short read genome assemblies of the tetraploid protozoan parasite Giardia intestinalis are highly fragmented, highlighting the need for improved genome assemblies at a reasonable cost. Long nanopore reads are well suited to resolve repetitive genomic regions resulting in better quality assemblies of eukaryotic genomes. Subsequent addition of highly accurate short reads to long-read assemblies further improves assembly quality.

Horizontal transfer of a retrotransposon between parasitic nematodes and the common shrew.

Background: As the genomes of more metazoan species are sequenced, reports of horizontal transposon transfers (HTT) have increased. Our understanding of the mechanisms of such events is at an early stage. The close physical relationship between a parasite and its host could facilitate horizontal transfer.

MIPhy: identify and quantify rapidly evolving members of large gene families.

After transitioning to a new environment, species often exhibit rapid phenotypic innovation. One of the fastest mechanisms for this is duplication followed by specialization of existing genes. When this happens to a member of a gene family, it tends to leave a detectable phylogenetic signature of lineage-specific expansions and contractions.

Improved enzyme annotation with EC-specific cutoffs using DETECT v2.

Summary: We present DETECT v2-an enzyme annotation tool which considers the effect of sequence diversity when assigning enzymatic function [as an Enzyme Commission (EC) number] to a protein sequence. In addition to capturing more enzyme classes than the previous version, we now provide EC-specific cutoffs that greatly increase precision and recall of assignments and show its performance in the context of pathways.

Availability And Implementation: https://github.

Expanding the view on the evolution of the nematode dauer signalling pathways: refinement through gene gain and pathway co-option.

Background: Signalling pathways underlie development, behaviour and pathology. To understand patterns in the evolution of signalling pathways, we undertook a comprehensive investigation of the pathways that control the switch between growth and developmentally quiescent dauer in 24 species of nematodes spanning the phylum.

Results: Our analysis of 47 genes across these species indicates that the pathways and their interactions are not conserved throughout the Nematoda.

Exploring the Gastrointestinal "Nemabiome": Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities.

Parasitic helminth infections have a considerable impact on global human health as well as animal welfare and production. Although co-infection with multiple parasite species within a host is common, there is a dearth of tools with which to study the composition of these complex parasite communities. Helminth species vary in their pathogenicity, epidemiology and drug sensitivity and the interactions that occur between co-infecting species and their hosts are poorly understood.

Does the arthropod microbiota impact the establishment of vector-borne diseases in mammalian hosts?

The impact of the microbiota on the immune status of its host is a source of intense research and publicity. In comparison, the effect of arthropod microbiota on vector-borne infectious diseases has received little attention. A better understanding of the vector microbiota in relation to mammalian host immune responses is vital, as it can lead to strategies that affect transmission and improve vaccine design in a field of research where few vaccines exist and effective treatment is rare.

Morphological variability and molecular identification of Uncinaria spp. (Nematoda: Ancylostomatidae) from grizzly and black bears: new species or phenotypic plasticity?

The hookworms Uncinaria rauschi Olsen, 1968 and Uncinaria yukonensis ( Wolfgang, 1956 ) were formally described from grizzly ( Ursus arctos horribilis) and black bears ( Ursus americanus ) of North America. We analyzed the intestinal tracts of 4 grizzly and 9 black bears from Alberta and British Columbia, Canada and isolated Uncinaria specimens with anatomical traits never previously documented. We applied morphological and molecular techniques to investigate the taxonomy and phylogeny of these Uncinaria parasites.

Kablammo: an interactive, web-based BLAST results visualizer.

Motivation: Kablammo is a web-based application that produces interactive, vector-based visualizations of sequence alignments generated by BLAST. These visualizations can illustrate many features, including shared protein domains, chromosome structural modifications and genome misassembly.

Availability And Implementation: Kablammo can be used at http://kablammo.

Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes.

Motivation: Gene models from draft genome assemblies of metazoan species are often incorrect, missing exons or entire genes, particularly for large gene families. Consequently, labour-intensive manual curation is often necessary. We present Figmop (Finding Genes using Motif Patterns) to help with the manual curation of gene families in draft genome assemblies.

Realizing the promise of parasite genomics.

Genomes and genomics are now part of the popular imagination and culture. Understanding what these massively long strings of As, Gs, Cs, and Ts actually mean is a challenge that has been taken up by many working on parasites. Our understanding of parasite biology and future treatment strategies has been significantly improved because of these genomes.