Biology subjects

Slippers, B.

Publications and source records attributed to Slippers, B..

6 recordsLinked to original sources

bioRxiv2025

Annotated genome of the Eucalyptus snout beetle, Gonipterus sp. n. 2 (Coleoptera, Curculionidae)

Gonipterus species, or Eucalyptus snout beetles, are defoliators that damage Eucalyptus trees in plantations globally. The Gonipterus sp. n. 2 genome was sequenced using both Oxford Nanopore and Illumina sequencing platforms which produced 76.41 Gb long-read and 57.1 Gb short-read sequence data, respectively. Genome assembly using these data resulted in 1,023 contigs, with an N50 of 2.78 Mb and a genome size of roughly 1.54 Gb. Genome completeness analysis using BUSCO resulted in a score of 98.2%. We used Braker3 to annotate the assembled Gonipterus sp. n. 2 genome using transcriptomic data from gut and reproductive tissues, as well as and available protein sequences from selected Coleoptera species. Genome annotation resulted in 42,343 protein coding gene models and a proteome BUSCO completeness score of 99%. Protein clustering with 13 other insect species using OrthoFinder identified 22,245 families with 1,398 families unique to Gonipterus sp. n. 2. The number of cytochrome P450 monooxygenase genes in Gonipterus sp. n. 2 (n = 119) was greater than the other 13 insect species used in comparison. The genome of Gonipterus sp. n. 2 will be a valuable resource to assist in unravelling various aspects of the weevils life history, such as the metabolism of xenobiotics or the production of pheromones, and to develop alternative pest control methods.

genomics↗

bioRxiv2025

The influence of biosecurity on the diversity and management of a 120-year old joint insect-fungus pest invasion

The woodwasp, Sirex noctilio, and its mutualistic fungal symbiont, Amylostereum areolatum, are native to Eurasia and northern Africa. Sirex noctilio was first reported outside its native range in New Zealand in 1900, Tasmania in 1952 and mainland Australia in 1961. In this study, we consider the invasion history of these organisms across Australasia through population genetic analysis using mitochondrial sequence data and microsatellite markers and compared them with a previously published dataset from global collections. The study included contemporary (n=461) and historical (n=41) samples of S. noctilio dating back to 1952 and fungal (n=176) samples from across the range. No population structure was found in Australian and New Zealand populations of S. noctilio or the fungal symbiont A. areolatum reflecting both the natural (within the countries) and human-assisted (between the countries) spread of these symbionts. The S. noctilio populations in these countries had lower genetic diversity than other populations sampled globally. Amylostereum areolatum populations from Australia and New Zealand clustered separately from all other countries and were highly clonal. While the results suggested multiple early introductions in these two countries, it also reflected an efficient recent quarantine system that isolated these populations and reduced their complexity compared to other parts of the world. The findings also have relevance to the application of biological control for the pest complex.

ecology↗

bioRxiv2025

Mathematically modelling the population dynamics of CRISPR gene drive systems in the pine pest Sirex noctilio

Sirex noctilio is an invasive pest of pine that has caused significant economic damage in South Africa and many other Southern Hemisphere countries. Current management tools are not efficient in all cases and consequently there is a need for more efficient and targeted control measures. An emerging tool for pest management is the use of gene editing and associated gene drive systems. In this study, we aim to investigate the use of CRISPR-Cas gene drive systems in the management of S. noctilio in South Africa. As a first step, we developed a model for the population dynamics of S. noctilio, using historical national population monitoring data and incorporating the influence of two main biological control agents of the pest. We then modelled the influence of two different CRISPR-Cas systems on the population dynamics of S. noctilio namely, a baseline CRISPR model and Complementary Sex Determination CRISPR (CSD) model. Each model is used to simulate a male and female only introduction strategy to estimate the effectiveness of different methods of introducing the gene drive system. The model calibration was achieved by optimizing the model fit to existing data using the least squares technique. Results suggest that both CRISPR gene drive systems would be effective at controlling the population growth of S. noctilio at high levels of introduction, but overall population control would be hindered by practical limitations. Although only two CRISPR models were explored, the underlying population model serves as a framework for further studies into the population dynamics of Sirex noctilio, as well as many other CRISPR-Cas gene drive systems.

ecology↗

bioRxiv2025

Chromosome-level genome assemblies for the latent pine pathogen, Diplodia sapinea, reveal two rapidly evolving accessory chromosomes

Diplodia sapinea (Dothideomycetes) is a latent fungal pathogen with a global distribution that predominantly infects Pinus species. The impact of the fungus is increasing due to climate-driven range expansion and thus wide-scale disease outbreaks. With the aim of developing high quality genome resources, we generated chromosome-level genome assemblies for three D. sapinea isolates and low-coverage Illumina genome data for six additional isolates. By comparing these genome assemblies, we identified 14 core chromosomes and two accessory chromosomes (ACs) in the pathogen. The ACs encode 80 and 155 proteins, respectively, while 11374 - 11609 genes were identified in the core chromosomes. Both ACs had lower gene density and higher proportions of transposable elements compared to the core chromosomes. Sequence analysis indicated that genes on the ACs are rapidly evolving, suggesting they serve as evolutionary hotspots in the species. Sequence homology analyses suggested that the ACs were likely acquired horizontally, probably from a species in the Dothideomycetes. We designed PCR-based assays to aid in the detection of the ACs and applied these on a set of 37 isolates from 14 countries. One of the ACs was detected in 33 isolates from 13 countries, while the other AC was absent in all isolates tested. Pathogenicity trials on Pinus patula seedlings showed no correlation between the presence of ACs and isolate aggressiveness. The high-quality genomes provided here offer important resources for future research on this globally important pathogen, including the biological roles of the ACs.

genomics↗

bioRxiv2021

Female and male Sirex noctilio use age and size to select a mate

While male mate choice in insects is a widely accepted concept, there is still limited evidence showing that lek formation is compatible with the evolution of male mate choice. In the woodwasp Sirex noctilio, males form leks that are used by females to select a mate. However, males have been observed to ignore certain females, suggesting the presence of male mate choice despite the presence of a lek mating system. In this study we demonstrate that males only attempt to mate with certain females. To understand the criteria used by males and females to select a mate, we also tested the effect of age, size, and male to female size ratio on the number of mating attempts made by males and on female receptivity. We demonstrate that size and age play a role in both male and female mate choice. Our results suggest that males must reach sexual maturity after emergence and are neither receptive nor attractive to females during the first few days of their lives. We also show that older females become less attractive to males, suggesting that female S. noctilio switch to a strict host location phase sometime after emergence. Our results show that male and female size, and the ratio between them, play a role in mate choice. While larger males are more motivated to mate, their large size can physically prevent them from mating with small females. Small females are also more attractive and more receptive to males, consistent with the presence of convenience polyandry in S. noctilio.

animal behavior and cognition↗

bioRxiv2021

Abundant secreted hydrolytic enzymes and secondary metabolite gene clusters in genomes of the Botryosphaeriaceae reflect their role as important plant pathogens

The Botryosphaeriaceae are important plant pathogens, but unique in their ability to establish asymptomatic infections that persist for extended periods in a latent state. In this study, we used comparative analyses to consider elements that might shed light on the genetic basis of the interactions of these fungi with their plant hosts. For this purpose, we characterised secreted hydrolytic enzymes, secondary metabolite biosynthetic gene clusters and considered general trends in genomic architecture using all available Botryosphaeriaceae genomes, and selected Dothideomycetes genomes. The Botryosphaeriaceae genomes were rich in carbohydrate-active enzymes (CAZymes), proteases, lipases and secondary metabolic biosynthetic gene clusters (BGCs) compared to other Dothideomycete genomes. The genomes of Botryosphaeria, Macrophomina, Lasiodiplodia and Neofusicoccum, in particular, had gene expansions of the major constituents of the secretome, notably CAZymes involved in plant cell wall degradation. The Botryosphaeriaceae genomes were shown to have moderate to high GC contents and most had low levels of repetitive DNA. The genomes were not compartmentalized based on gene and repeat densities, but genes of secreted enzymes were slightly more abundant in gene-sparse regions. The abundance of secreted hydrolytic enzymes and secondary metabolite BGCs in the genomes of Botryosphaeria, Macrophomina, Lasiodiplodia, and Neofusicoccum were similar to those in necrotrophic plant pathogens, but also endophytes of woody plants. The results provide a foundation for future comparative genomic analyses and hypothesis to explore the mechanisms underlying Botryosphaeriaceae host-plant interactions.

genomics↗