Biology subjects

Dowle, E.

Publications and source records attributed to Dowle, E..

7 recordsLinked to original sources

bioRxiv2025

Revealing the genetic mechanisms underpinning the parasite-induced water-seeking behaviour of insects through RNA-seq

The water-seeking behaviour in arthropods infected by mermithid nematodes or nematomorphs is a classic example of host manipulation, yet how these parasites induce the behavioural change is poorly known. We investigated the molecular mechanisms at the basis of this aberrant behaviour in European earwigs (Forficula auricularia) infected with the nematode Mermis nigrescens. We performed comparative RNA-seq analysis at different stages of infection and behaviour manipulation in both the host and the parasite. We detected a total of 12,876 and 9,722 expressed genes in the earwig and nematode, respectively. Differential gene expression (DGE) analysis showed 673 genes upregulated and 593 downregulated in earwigs, and 2,672 genes upregulated and 2,293 downregulated in nematodes across all comparisons between stages of infection and parasite sizes. Clustering analysis produced six and four clusters of differentially expressed genes in earwigs and nematodes, respectively, based on temporal patterns of expression across stages of infection. With overrepresented analysis using gene ontology terms, we found that the earwig shows increased signalling and sensory pathways, while the nematode ramps up transport and secretory genes during manipulation. We found shared GATA transcription factor motif enriched in the differentially over expressed genes during manipulation in both host and the parasite. Our study provides valuable insights into candidate pathways and genes in the host and the parasite, improving our understanding of the molecular regulation of water-seeking behaviour.

ecology↗

bioRxiv2024

tombRaider - improved species and haplotype recovery from metabarcoding data through artefact and pseudogene exclusion.

Environmental DNA metabarcoding has revolutionized ecological surveys of natural systems. By amplifying and sequencing small gene fragments from environmental samples containing complex DNA mixtures, scientists are now capable of exploring biodiversity patterns across the tree of life in a time-efficient and cost-effective manner. However, the accuracy of species and haplotype identification can be compromised by sequence artefacts and pseudogenes. Despite various strategies developed over the years, effective removal of artefacts remains challenging and inconsistent data reporting standards hinder reproducibility in eDNA metabarcoding experiments. To address these issues, we introduce tombRaider, an open-source command line software program (https://github.com/gjeunen/tombRaider) and R package (https://github.com/gjeunen/tombRaider_R) to remove artefacts and pseudogenes from metabarcoding data post clustering and denoising. tombRaider features a modular algorithm capable of evaluating multiple criteria, including sequence similarity, co-occurrence patterns, taxonomic assignment, and the presence of stop codons. We validated tombRaider using various published data sets, including mock invertebrate communities, air eDNA from a zoo, and salmon haplotypes from aquatic eDNA. Our results demonstrate that tombRaider effectively removed a higher proportion of artefacts while retaining authentic sequences, thus enhancing the accuracy and reliability of eDNA-derived diversity metrics. This user-friendly software program not only improves data quality in eDNA metabarcoding studies, but also contributes to standardised reporting practices, an aspect currently lacking in this emerging research field.

bioinformatics↗

bioRxiv2024

Comparative genomics of parasitoid lifestyle as exemplified by Mermithidae and Nematomorpha

Mermithidae and Nematomorpha are parasitoids united by the commonalities in their lifestyle - immature stages infect arthropod hosts, species from both phyla can manipulate their host to induce a similar water-seeking behaviour, and both have a final free-living non-feeding adult reproductive stage, often killing their host upon emergence. Some of these species are of great economic importance, being evaluated as biological control agents against mosquito vectors responsible for diseases like malaria, and other insect pests, but with scarce genomic resources currently available. Nematomorpha, despite being closely related to Nematoda, received insufficient attention in genomic research, leading to gaps in our understanding of their diverse genetic makeup. This study aimed to investigate the genetic features encoded in the genomes of both parasitoid taxa to identify similarities and parallels linked to their ecological lifestyles. We performed a comparative analysis of 12 genomes, comprising parasitoid, parasitic and free-living worms. The investigation revealed genomic signatures unique to parasitoid species, including expanded gene families enriched in neural transmission modulation, likely linked to the known host manipulation that both mermithids and nematomorphs exert on their hosts. The analysis also uncovered a diverse array of conserved transposable element superfamilies across both lineages. The findings from this study provide valuable insights into the potential genomic adaptations associated with parasitoidism in nematode and nematomorph worms. The identification of expanded gene families and conserved transposable element superfamilies sheds light on the molecular underpinnings of their unique biological traits. Additionally, the core set of orthologs specific to parasitoid worms offers new avenues for understanding the evolution of parasitism within these groups of organisms.

genomics↗

bioRxiv2023

Whole genome assembly and annotation of the clover root weevil (Sitona obsoletus) using a combination of Illumina, 10X Genomics and MinION sequencing

Weevils are a highly diversified taxon, comprising about 70,000 described species that include many agricultural pests, biological control agents, and nutrient recyclers. Despite their importance and vast diversity, the number of sequenced genomes for the weevil family is still low (n=15). Here, we present a high-quality and contiguous genome assembly of Sitona obsoletus (Coleoptera: Curculionidae: Entiminae), a widespread invasive forage pest that infests clover species (Trifolium spp.) worldwide. We sequenced, assembled, and annotated the S. obsoletus genome using a hybrid approach that employed Nanopore long reads, 10X Chromium linked reads, Illumina short reads for assembly, and mRNA short read sequencing of various developmental stages for annotation. Our final annotated genome has a size of 1.2 Gb, with an N50 length of 313.85 kb. Benchmarking analyses against conserved single-copy Orthologs (BUSCO) found that over 94% of the genes were complete from each of the three BUSCO databases (Eukaryota, Insecta, and Arthropoda). A total of 9,777 protein-coding genes were annotated using the MAKER2 pipeline, of which 65% were functionally annotated. The annotated repeat elements make up 84.26% of the genome. The high-quality annotated genome of the weevil will facilitate a wide range of genetic, genomic, and phylogenetic studies on invasive weevils, as well as other weevil species in the subfamily Entiminae.

genomics↗

bioRxiv2022

Genome assembly and annotation of the mermithid nematode Mermis nigrescens

Genetic studies of nematodes have been dominated by Caenorhabditis elegans as a model species. Lack of genomic resources has been a limiting factor for expansion of genetic research to other groups of nematodes. Here, we report a draft genome assembly of a mermithid nematode, Mermis nigrescens. Mermithidae are insect parasitic nematodes with hosts including a wide range of terrestrial arthropods. We sequenced, assembled, and annotated the whole genome of M. nigrescens using nanopore long-reads and 10X chromium link-reads. The assembly is 524 Mb in size consisting of 867 scaffolds. The N50 value is 2.42 Mb, and half of the assembly is in the 30 longest scaffolds. The assembly BUSCO score from the eukaryotic database (eukaryota_odb10) indicates that the genome is 86.7% complete and 5.1% partial. The genome has a high level of heterozygosity (6.6%) with a repeat content of 78.7%. mRNA-seq reads from different sized nematodes ([≤]2 cm, 3.5-7 cm, and >7 cm body length) representing different developmental stages were also generated and used for the genome annotation. Using ab initio and evidence-based gene model predictions, 12,313 protein-coding genes and 24,186 mRNAs were annotated. These genomic resources will help researchers investigate the various aspects of the biology and host-parasite interactions of mermithid nematodes.

genomics↗

bioRxiv2022

Whole genome assembly and annotation of the lucerne weevil Sitona discoideus

Weevils are a diverse insect group that includes many economically important invasive pest species. Despite their importance and diversity, only nine weevil genomes have been sequenced, representing a tiny fraction of this heterogeneous taxon. The genus Sitona consists of over 100 species, including Sitona discoideus (Coleoptera: Curculionidae: Entiminae), commonly known as lucerne (or alfalfa root) weevil. Sitona discoideus is an important pest of forage crops, particularly Medicago species. Using a dual sequencing approach with Oxford Nanopore MinION long-reads and 10x Genomics linked-read sequencing, we generated a high-quality hybrid genome assembly of S. discoideus. Benchmarks derived from evolutionarily informed expectations of gene content for near-universal single-copy orthologs comparison (BUSCO) scores are above 96% for single-copy orthologs derived from eukaryotes, arthropods, and insects. With a de novo repeat library, Repeatmasker annotated 81.45% of the genome as various repeat elements, of which 22.1% were unclassified. Using the MAKER2 pipeline, we annotated 10,008 protein-coding genes and 13,611 mRNAs. Furthermore, 68.84% of total predicted mRNAs and 67.90% of predicted proteins were functionally annotated to one or more of InterPro, gene ontology, and Pfam databases. This high-quality genome assembly and annotation will enable the development of critical novel genetic pest control technologies and act as an essential reference genome for broader population genetics and weevil comparative genetic studies.

genomics↗

bioRxiv2022

A high-quality genome assembly and annotation of the European earwig Forficula auricularia.

The European earwig Forficula auricularia is an important model for studies of maternal care, sexual selection, sociality and host-parasite interactions. However, detailed genetic investigations of this species are hindered by a lack of genomic resources. Here we present a high-quality hybrid genome assembly for F. auricularia. The genome was assembled using nanopore long-reads and 10x chromium link-reads. The final assembly is 1.06Gb in length with 31.03% GC content. It consists of 919 scaffolds with an N50 of 12.55Mb. Half of the genome is present in only 20 scaffolds. Benchmarking Universal Single-Copy Orthologs scores are ~90% from three sets of single-copy orthologs (eukaryotic, insect, and arthropod). The total repeat elements in the genome are 64.62%. The MAKER2 pipeline annotated 12,876 protein-coding genes and 21,031 mRNAs. A phylogenetic analysis revealed the isolate used in our genomic analysis belongs to Subspecies B, one of the two known genetic subspecies of F. auricularia. The genome assembly, annotation, and associated resources will be of high value to a large and diverse group of researchers working on Dermapterans.

genomics↗