Biology subjects

Whitehead, M. A.

Publications and source records attributed to Whitehead, M. A..

6 recordsLinked to original sources

bioRxiv2026

An improved Trypanosoma vivax genome assembly confirms the distinct organisation of its variant antigen repertoire

Trypanosoma vivax is a unicellular parasite spread by biting flies and an important livestock pathogen across sub-Saharan Africa and South America. Alongside its better known relative, T. brucei, it causes animal trypanosomosis. An accurate genome sequence is essential to functional genetics as well as the design of novel diagnostics, drugs and vaccines. However, the existing T. vivax genome sequence is fragmentary, making it difficult to examine genomic features such as the Variant Surface Glycoprotein (VSG) genes that are the basis for antigenic variation, a key phenotype that underpins immune evasion by African trypanosomes. Our aim was to produce a T. vivax genome sequence with improved contiguity to properly characterise the VSG genes. We present a new core genome assembly in 23 scaffolds, forming approximately 10 chromosomes. Many scaffolds are articulated with extensive sub-telomeric domains that, like T. brucei, contain VSG gene arrays but in T. vivax these are near-perfect repeats of intact genes. Using transcriptomic and proteomic analysis of VSG expression during bloodstream infection we show that the active VSG is expressed from a sub-telomeric array while other arrays are silent. We find no evidence for a VSG expression site at the telomeres or elsewhere. Therefore, although monoallelic expression and antigenic switching occur in T. vivax, the familiar regulatory mechanism of T. brucei does not exist in T. vivax. This improved T. vivax genome assembly demonstrates that T. brucei is a poor guide for T. vivax genetics generally and for regulation of antigenic variation specifically.

genomics↗

bioRxiv2026

A near-complete chromosome from a bacterial pathogen integrated into the genome of its arthropod vector

Lateral gene transfer (LGT) from organellar to eukaryotic genomes is ubiquitous, resulting in the presence of widespread nuclear mitochondrial DNA segments (NUMTs) and/or plastid gene transfers. While LGT from bacterial associates of eukaryotes is generally less common, many arthropod genomes are littered with LGT originating from Wolbachia (order Rickettsiales) - a vertically transmitted, obligate intracellular symbiont of invertebrates. This contrasts with Rickettsia, a related genus including many important human pathogens, which has not been shown to promulgate LGT within its arthropod vectors. Here, we present the 8.6 Gb genome of a cell line derived from A. variegatum (the tropical bont tick), which is the primary vector of Rickettsia africae (agent of African tick-bite fever). In addition to numerous NUMTs and diverse families of transposable elements, an almost-complete chromosome of R. africae origin was identified in the cell line genome, localised to the putative sex chromosome. Sequencing of field-collected A. variegatum confirmed the presence of this large LGT in wild ticks, although the absence of transferred genes from the R. africae plasmid provided a means to differentiate LGT from genuine rickettsial infections. These findings highlight the imperative to consider the possibility of LGT when screening vectors for pathogens by PCR.

genomics↗

bioRxiv2026

Chromosome assembly for the Black bean aphid Aphis fabae

The black bean aphid, Aphis fabae is a crop pest and vector of insect-transmitted pathogens, comprising closely related sub-species with overlapping host ranges. In other Aphis species, over-expression of specific detoxification genes has been linked to insecticide tolerance. We present two chromosome-scale assemblies for a clonal A. fabae line, representing two phased haplotypes, generated using HiFi and Hi-C sequencing technologies. A comprehensive genome annotation, built with PacBio Iso-Seq data, was used to investigate genes underlying insecticide tolerance. Both genomes are comprised of four chromosomal blocks (haplotype 1: 427 Mb; haplotype 2: 396 Mb) with high BUSCO completeness (98.7%). Comparative genomics revealed an expansion of UDP-glycosyltransferases, whose expression is linked to insecticide detoxification in other Aphis species. These high-quality references provide a foundation for studying A. fabae sub-species and a genomic resource for investigating insecticide tolerance across the Aphis genus. Author summaryHere we have provided a comprehensive assembly and annotation for further study into the Black bean aphid, Aphis fabae, using up to date long-range sequencing technologies. The final assemblies for both haplotypes are chromosome length and consist of 4 main chromosome blocks, consistent with the literature. The A. fabae genome was found to contain an increase in copy number of UDP-glycosyltransferases, which have previously been linked to insecticide resistance. The work here will be a resource to those studying insecticide tolerance in crop pests, as well as the differences between A. fabae sub-species.

genomics↗

bioRxiv2024

Genetic diversity in vector populations influences the transmission efficiency of an important plant virus

The transmission efficiency of aphid-vectored plant viruses can differ between aphid populations. Intra-species diversity (genetic variation, endosymbionts) is a key determinant of aphid phenotype; however, the extent of which intra-species diversity contributes towards variation in virus transmission efficiency is unclear. Here, we use multiple populations of two key aphid species that vector barley yellow dwarf virus (BYDV) strain PAV (BYDV-PAV), the grain aphid (Sitobion avenae) and the bird cherry-oat aphid (Rhopalosiphum padi), and examine how diversity in vector populations influences virus transmission efficiency. We use Illumina sequencing to characterise genetic and endosymbiont variation in multiple S. avenae and R. padi populations and conduct BYDV-PAV transmission experiments to identify links between intra-species diversity in the vector and virus transmission efficiency. We observe limited variation in the transmission efficiency of S. avenae, with transmission efficiency consistently low for this species. However, for R. padi we observe a range of transmission efficiency and show that BYDV transmission efficiency is influenced by genetic diversity within the vector, identifying 542 SNPs that potentially contribute towards variable transmission efficiency in R. padi. Our results represent an important advancement in our understanding of the relationship between genetic diversity, vector-virus interactions, and virus transmission efficiency.

pathology↗

bioRxiv2023

Genomic insights into clonal diversity in UK populations of the Potato aphid, Macrosiphum euphorbiae

The potato aphid Macrosiphum euphorbiae is one of many polyphagous crop pests involved in the transmission of insect-vectored pathogens. While their North American counterparts reproduce via cyclical parthenogenesis, UK populations of M. euphorbiae appear to persist asexually, resulting in the maintenance of several genotypes, with some demonstrating genotype-specific traits; this includes innate resistance to parasitism from the hymenopterous parasitoid wasp Aphidius ervi. The genetic and molecular basis for genotype-specific traits is often unknown. Here we present a chromosome scale assembly for a parasitoid-resistant clonal line of M. euphorbiae and provide insights into the genotypic composition and distribution of UK potato aphid populations using microsatellite and whole-genome sequencing (WGS) techniques, focusing on geographically separated potato crops within two distinct areas of the UK (Merseyside and Tayside). We show that the genome consists of five chromosomal blocks, has a total size of 560 Mbp and is highly complete based on BUSCO (C: 95.6%). The sampled potato aphid populations were dominated by two genotypes, one of which is absent from commercial farm settings, suggesting either an intolerance to farming practices, such as insecticide use, or a broader host range. We suggest some putative gene functions using WGS data to explain the observed frequency of aphid genotypes. WGS data highlighted the asexual clonal lifestyle of M. euphorbiae genotypes in the UK, resolving individuals to a higher resolution than using microsatellite data. The work presented here will provide useful information for integrated pest management of potato aphids, elaborating on the relationship between genotype diversity and functional traits such as parasitism and insecticide resistance, and host plant use, as well as providing more resources for further comparative genomics studies within the Aphididae.

genomics↗

bioRxiv2020

White pupae genes in the Tephritids Ceratitis capitata, Bactrocera dorsalis and Zeugodacus cucurbitae: a story of parallel mutations

Mass releases of sterilized male insects, in the frame of sterile insect technique programs, have helped suppress insect pest populations since the 1950s. In the major horticultural pests Bactrocera dorsalis, Ceratitis capitata, and Zeugodacus cucurbitae, a key phenotype white pupae (wp) has been used for decades to selectively remove females before releases, yet the gene responsible remained unknown. Here we use classical and modern genetic approaches to identify and functionally characterize causal wp− mutations in these distantly related fruit fly species. We find that the wp phenotype is produced by parallel mutations in a single, conserved gene. CRISPR/Cas9-mediated knockout of the wp gene leads to the rapid generation of novel white pupae strains in C. capitata and B. tryoni. The conserved phenotype and independent nature of the wp− mutations suggest that this technique can provide a generic approach to produce sexing strains in other major medical and agricultural insect pests.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genetics↗