Biology subjects

Peers, J. A.

Publications and source records attributed to Peers, J. A..

3 recordsLinked to original sources

bioRxiv2026

Over-representation of sperm-associated deleterious mutations across wild and ex situ cheetah (Acinonyx jubatus) populations

As purifying selection becomes less effective and inbreeding increases, small populations frequently develop an increased load of genome-wide deleterious mutations. Reflecting this pattern, deleterious mutations in genes associated with fertility and immunity have previously been identified in the cheetah (Acinonyx jubatus), which has had a low effective population size for at least the last 10,000 years. However, the distribution of deleterious mutations across cheetah populations is currently unknown. Here, we analysed novel whole genome resequencing data from 30 ex situ and 9 wild cheetahs. We investigated variation in genetic diversity, genomic measures of inbreeding, and the distribution of deleterious mutations across cheetah populations. South Sudanese and Tanzanian cheetahs showed higher inbreeding and realized load, while Namibian cheetahs had a higher proportion of population-specific deleterious mutations. Genes containing high- or moderate-impact deleterious mutations were significantly enriched for sperm-related functions, highlighting putative causative loci associated with poor sperm quality in cheetahs. Similar levels of genetic diversity and inbreeding were observed in ex situ cheetahs compared to their wild counterparts, providing empirical evidence of the efficacy of captive breeding programmes in maintaining genetic variation in ex situ populations.

genomics↗

bioRxiv2024

Gene pseudogenization in fertility-associated genes in cheetah (Acinonyx jubatus), a species with long-term low effective population size

The ongoing global biodiversity crisis is placing an increasing number of mammalian populations at risk of decline. Species that have survived severe historic bottlenecks, such as the cheetah (Acinonyx jubatus) exhibit symptoms of inbreeding depression including reproductive and developmental defects. Although it has long been suggested that such defects stem from an accumulation of weakly deleterious mutations, the implications of such mutations leading to pseudogenization has not been assessed. Here, we use comparative analysis of eight felid genomes to better understand the impacts of deleterious mutations in the cheetah. We find novel pseudogenization events specific to the cheetah. Through careful curation, we identify 89 genes with previously unreported premature termination codons that likely affect gene function, 65 of which are caused by point mutations. With the addition of population data, we find 22 PTCs fixed in wild populations, four of which (DEFB116, ARL13A, CFAP119 and NC5TD4) are also found in a more recent reference genome. Mutations within three of these genes are linked with sterility, including azoospermia, which is common in cheetahs. Our results highlight the power of comparative genomic approaches for the discovery of novel causative variants in declining species.

genomics↗

bioRxiv2023

Endophytic fungi related to the ash dieback causal agent encode signatures of pathogenicity on European ash

Tree diseases constitute a significant threat to biodiversity worldwide. Pathogen discovery in natural habitats is of vital importance to understanding current and future threats and prioritising efforts towards developing disease management strategies. Ash dieback is a fungal disease of major conservational concern that is infecting common ash trees, Fraxinus excelsior, in Europe. The disease is caused by a non-native fungal pathogen, Hymenoscyphus fraxineus. Other dieback causing-species have not previously been identified in the genus Hymenoscyphus. Here, we discover the pathogenicity potential of two newly identified related species of Asian origin, H. koreanus and H. occultus, and one Europe-native related species, H. albidus. We sequence the genomes of all three Hymenoscyphus species and compare them to that of H. fraxineus. Phylogenetic analysis of core eukaryotic genes identified H. albidus and H. koreanus as sister species, whilst H. occultus diverged prior these and H. fraxineus. All four Hymenoscyphus genomes are of comparable sizes (55-62 Mbp) and GC contents (42-44%) and encode for polymorphic secretomes. Surprisingly, 1,133 predicted secreted proteins are shared between the ash dieback pathogen H. fraxineus and the three related Hymenoscyphus endophytes. Amongst shared secreted proteins are cell death-inducing effector candidates, such as necrosis, and ethylene-inducing peptide 1-like proteins, NLPs, that are upregulated during in planta growth of all Hymenoscyphus species. Indeed, pathogenicity tests showed that all four related Hymenoscyphus species develop pathogenic growth on European ash stems, with native H. albidus being the least virulent. Our results identify the threat Hymenoscypohus species pose to the survival of European ash trees, and highlight the importance of promoting pathogen surveillance in environmental landscapes. Identifying new pathogens and including them in the screening for durable immunity of common ash trees is key to the long-term survival of ash.

plant biology↗