Biology subjects

Landeryou, T.

Publications and source records attributed to Landeryou, T..

2 recordsLinked to original sources

bioRxiv2025

Scalable Assembly of Ascaris Mitogenomes from Whole-Genome Data Reveals a Novel Clade

The genus Ascaris is an important group of giant parasitic roundworms, infecting over 700 million people globally, with substantial economic losses in domestic pigs. Whilst species of Ascaris are morphologically indistinguishable, analysis of mitochondrial and selected nuclear DNA loci has revealed three clades (A, B, C), which may inflate with the addition of genomic data. Here, we present a bioinformatic pipeline for de novo assembly of complete mitochondrial genomes (mtDNA) from low-coverage whole-genome data through host-read depletion or mtDNA read enrichment, followed by mtDNA-specific assembly. Our approach yielded 149 high-quality Ascaris mtDNA assemblies, enabling the study of population-level diversity, including the identification of a novel clade (Clade D, designated here) associated with human samples from Ethiopia. Our analysis further revealed Clade C to comprise of pig-derived samples from Europe based on characterisation of worms isolated in Germany. Furthermore, genetic diversity across all mitochondrial loci was high (concatenated dataset: S = 1261; h = 94; {pi} = 0.0224), indicating substantial intraspecies variation. Our methods described here provide a scalable framework for mtDNA genome reconstruction with insights into roundworm population-genomic and phylogenetic studies.

genomics↗

bioRxiv2024

Molecular epidemiology of Ascaris lumbricoides following multiple rounds of community-wide treatment: who infects whom?

Control and elimination of the parasite Ascaris lumbricoides relies on mass administration using a limited number of anti-helminthics. Whilst these programs have reduced the infection intensity and prevalence within many endemic regions transmission is poorly understood, with reinfection commonly occurring following cessation of treatment. Here, we utilise genomic data to understand parasite transmission within and between households in a community and the genomic impact of repeated MDA. We sequenced 54 whole-genomes from individuals in a longitudinal cohort epidemiological study of transmission and drug treatment extending over 6 years. We found that fine-scale population structure exists in spatially distinct clusters of infected individuals with reinfection occurring within or between geographically close households. This observation helps inform the policy of future control in low prevalence settings suggesting more targeted treatment of infection hotspots We found evidence of positive selection acting on members of gene families previously implicated in reduced drug efficacy but detect no high frequency of impactful variants. As efforts to eliminate A. lumbricoides intensify, our study provides a foundation for genomic surveillance to help identify both who infects whom and the impact of repeated drug treatment.

genomics↗