Biology subjects

Challis, R. J.

Publications and source records attributed to Challis, R. J..

4 recordsLinked to original sources

bioRxiv2025

Snail plots are badges of genome assembly quality

Assembly quality is frequently assessed using independent measures of assembly span, contiguity, sequence composition and completeness. Among contiguity metrics, contig and scaffold N50 have perhaps gained the most traction, despite well known limitations. Several authors have suggested considering the complete Nx curve rather than just the N50 value, but while using N90 values or considering the area under the Nx curve with auN statistics provide more complete measures of contiguity, they share the limitation of being unsuited to direct comparison across a range of genome sizes. We introduced snail plots to provide a genome-size independent way to summarise a range of commonly used assembly metrics. Here we demonstrate that easily-learnt visual differences between snail plots allow simultaneous consideration of metrics across several key areas of assembly quality to rapidly identify high- and low-quality assemblies. We show that prominent features in snail plots of high-quality assemblies effectively highlight N50, N90 and auN contiguity statistics, but since the presentation is scaled to the longest scaffold, plots can be compared effectively across a wide range of taxa and assembly sizes. We use the core features of a snail plot to derive a proportional measure of assembly quality based on auN, adjusted for ambiguous, N, bases and scaled to the length of the longest scaffold. We show that this "snail score" value corresponds closely to a qualitative assessment of overall assembly quality from visual interpretation of a snail plot.

bioinformatics↗

bioRxiv2019

BlobToolKit Interactive quality assessment of genome assemblies

Reconstruction of target genomes from sequence data produced by instruments that are agnostic as to the species-of-origin may be confounded by contaminant DNA. Whether introduced during sample processing or through co-extraction alongside the target DNA, if insufficient care is taken during the assembly process, the final assembled genome may be a mixture of data from several species. Such assemblies can confound sequence-based biological inference and, when deposited in public databases, may be included in downstream analyses by users unaware of underlying problems. We present BlobToolKit, a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. BlobToolKit can be used to process assembly, read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility. We have been running an automated BlobToolKit pipeline on eukaryotic assemblies publicly available in the International Nucleotide Sequence Data Collaboration and are making the results available through a public instance of the Viewer at https://blobtoolkit.genomehubs.org/view. We aim to complete analysis of all publicly available genomes and then maintain currency with the flow of new genomes. We have worked to embed these views into the presentation of genome assemblies at the European Nucleotide Archive, providing an indication of assembly quality alongside the public record with links out to allow full exploration in the Viewer.

bioinformatics↗

bioRxiv2018

Silent crickets reveal the genomic footprint of recent adaptive trait loss

Secondary trait loss is widespread and has profound consequences, from generating diversity to driving adaptation. Sexual trait loss is particularly common1. Its genomic impact is challenging to reconstruct because most reversals occurred in the distant evolutionary past and must be inferred indirectly2, and questions remain about the extent of disruption caused by pleiotropy, altered gene expression and loss of homeostasis3. We tested the genomic signature of recent sexual signal loss in Hawaiian field crickets, Teleogryllus oceanicus. Song loss is controlled by a sex-linked Mendelian locus, flatwing, which feminises male wings by erasing sound-producing veins. This variant spread rapidly under pressure from an eavesdropping parasitoid fly. We sequenced, assembled and annotated the T. oceanicus genome, produced a high-density linkage map, and localised flatwing on the X chromosome. We characterised pleiotropic effects of flatwing, including changes in embryonic gene expression and alteration of another sexual signal, chemical pheromones. Song loss is associated with pleiotropy, hitchhiking and genome-wide regulatory disruption which feminises flatwing male pheromones. The footprint of recent adaptive trait loss illustrates R. A. Fishers influential prediction that variants with large mutational effect sizes can invade genomes during the earliest stages of adaptation to extreme pressures, despite having severely disruptive genomic consequences.

evolutionary biology↗

bioRxiv2018

Genomic architecture and introgression shape a butterfly radiation

We here pioneer a low-cost assembly strategy for 20 Heliconiini genomes to characterize the evolutionary history of the rapidly radiating genus Heliconius. A bifurcating tree provides a poor fit to the data, and we therefore explore a reticulate phylogeny for Heliconius. We probe the genomic architecture of gene flow, and develop a new method to distinguish incomplete lineage sorting from introgression. We find that most loci with non-canonical histories arose through introgression, and are strongly underrepresented in regions of low recombination and high gene density. This is expected if introgressed alleles are more likely to be purged in such regions due to tighter linkage with incompatibility loci. Finally, we identify a hitherto unrecognized inversion, and show it is a convergent structural rearrangement that captures a known color pattern switch locus within the genus. Our multi-genome assembly approach enables an improved understanding of adaptive radiation.

evolutionary biology↗