Biology subjects

Eyck, H. J. F.

Publications and source records attributed to Eyck, H. J. F..

4 recordsLinked to original sources

bioRxiv2024

Repeat-rich regions cause false positive detection of NUMTs - a case study in amphibians using an improved cane toad reference genome

Mitochondrial DNA (mtDNA) has been widely used in genetics research for decades. Contamination from nuclear DNA of mitochondrial origin (NUMT) can confound studies of phylogenetic relationships and mtDNA heteroplasmy. Homology searches with mtDNA are widely used to detect NUMTs in the nuclear genome. Nevertheless, false positive detection of NUMTs is common when handling repeat-rich sequences, whilst fragmented genomes might result in missing true NUMTs. In this study, we investigated different NUMT detection methods and how the quality of the genome assembly affects them. We presented an improved nuclear genome assembly (aRhiMar1.3) of the invasive cane toad (Rhinella marina) with additional long-read Nanopore and 10x linked-read sequencing. The final assembly was 3.47 Gb in length with 91.3% of tetrapod universal single-copy orthologs (n=5,310), indicating the gene-containing regions were well assembled. We used three complementary methods (NUMTFinder, dinumt and PALMER) to study the NUMT landscape of the cane toad genome. All three methods yielded consistent results, showing very few NUMTs in the cane toad genome. Furthermore, we expanded NUMT detection analyses to other amphibians and confirmed a weak relationship between genome size and the number of NUMTs present in the nuclear genome. Amphibians are repeat-rich, and we show that the number of NUMTs found in highly repetitive genomes is prone to inflation when using homology-based detection without filters. Together, this study provides an exemplar of how to robustly identify NUMTs in complex genomes when confounding effects on mtDNA analyses are a concern. SignificanceThis study uses an updated cane toad nuclear genome assembly and multiple NUMT detection methods to confirm a lack of NUMTs that might confound the use of mtDNA as a population genetic marker in the cane toad. We provide an exemplar study for NUMT detection accounting for genome assembly quality and composition, and highlight the risks of using BLASTN-based approaches in highly repetitive nuclear genomes.

genomics↗

bioRxiv2023

Infection by the lungworm Rhabdias pseudosphaerocephala affects the expression of immune-related microRNAs by its co-evolved host, the cane toad Rhinella marina.

Parasites may suppress the immune function of an infected host using microRNAs (miRNAs) to prevent protein production. Nonetheless, little is known about the diversity of miRNAs and their mode(s) of action. In this study, we investigated the effects of infection by a parasitic lungworm (Rhabdias pseudosphaerocephala) on miRNA and mRNA expression of its host, the invasive cane toad (Rhinella marina). We compared miRNA and mRNA expression in naive toads that had never been infected by lungworms to toads that were infected with lungworms for the first time in their lives, and to toads that were infected the second time in their lives (i.e., had two consecutive infections). In total, we identified 434 known miRNAs and 106 potential novel miRNAs. Compared to uninfected toads, infected animals upregulated five (single-infection treatment) or four (multiple-infection treatment) miRNAs. Seven of these differentially expressed miRNAs were associated with gene pathways related to the immune response, potentially reflecting immunosuppression of cane toads by their parasites. Infected hosts did not respond with substantial mRNA transcription, with only one differentially expressed gene between control and single-infection hosts. Our study suggests that miRNA-mediated interactions may play a role in mediating the interaction between the parasite and its host. Our findings clarify the role of miRNAs in host-parasite interactions, in a system in which an ongoing range expansion by the host has generated substantial divergence in host-parasite interactions.

genetics↗

bioRxiv2023

First in family Rhabdiasidae: the reference-guided genome assembly of an invasive parasite, the cane toad lungworm (Rhabdias pseudosphaerocephala)

Rhabdias pseudosphaerocephala is a well-studied invasive nematode parasite of amphibians. However, there are several outstanding questions about R. pseudosphaerocephala that are best answered using genomic data. This species differs phenotypically across its invasive range. These differences are challenging to interpret because this species is part of a complex that is diverse and cryptic in its home-range, and we do not know how many species from this complex originally colonised Australia. For this reason, it is unknown whether the phenotypic differences across the introduced range are due to intraspecific differentiation between populations or due to the presence of multiple species. In addition, there is little consensus in the placement of Rhabdiasidae family within the phylum Nematoda, making it difficult to perform comparative analyses with other nematodes. Within this paper, we assemble a reference genome for R. pseudosphaerocephala, the first assembly of any Rhabdiasidae species. We then use resequencing data to address outstanding questions about this species. Specifically, we combine population genetic and phylogenetic analyses to determine that there is likely only a single R. pseudosphaerocephala lineage within Australia, and identify that the invasive range population is closely related to home rage isolates that infect similar host species. We present compelling evidence for a genetic bottleneck following introduction to Australia and genetic differentiation occurring between invasive range populations. We then use genome-scale phylogenomic analysis to place the Rhabdiasidae family in the suborder Rhabditina. Ultimately, this paper brings the study of Rhabdiasidae into the genomic era, and sheds light on its ancient and modern evolutionary history.

genomics↗

bioRxiv2021

In an arms race between host and parasite, a lungworm's ability to infect a toad is determined by host susceptibility, not parasite preference

Evolutionary arms races can alter both parasite infectivity and host resistance, and it is difficult to separate the effects of these twin determinants of infection outcomes. Using a co-introduced, invasive host-parasite system (the lungworm Rhabdias pseudosphaerocephala and the cane toad Rhinella marina), we quantified behavioural responses of parasite larvae to skin-chemical cues of toads from different invasive populations, and rates at which hosts became infected following standardised exposure to lungworms. Chemical cues from toad skin altered host-seeking behaviour by parasites, similarly among populations. The number of infection attempts (parasite larvae entering the hosts body) also did not differ between populations, but rates of successful infection (establishment of adult worm in host lungs) was higher for range-edge toads than for range-core conspecifics. Thus, lower resistance to parasite infection in range-edge toads appears to be due to less effective immune defences of the host rather than differential behavioural responses of the parasite. In this ongoing host-parasite arms-race, changing outcomes appear to be driven by shifts in host immunocompetence.

evolutionary biology↗