Dataset Information

Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae.

ABSTRACT: Reference genome assemblies have been created from multiple lineages within the Canidae family; however, despite its phylogenetic relevance as a basal genus within the clade, there is currently no reference genome for the gray fox (Urocyon cinereoargenteus). Here, we present a chromosome-level assembly for the gray fox (U. cinereoargenteus), which represents the most contiguous, non-domestic canid reference genome available to date, with 90% of the genome contained in just 34 scaffolds and a contig N50 and scaffold N50 of 59.4 and 72.9 Megabases, respectively. Repeat analyses identified an increased number of simple repeats relative to other canids. Based on mitochondrial DNA, our Vermont sample clusters with other gray fox samples from the northeastern United States and contains slightly lower levels of heterozygosity than gray foxes on the west coast of California. This new assembly lays the groundwork for future studies to describe past and present population dynamics, including the delineation of evolutionarily significant units of management relevance. Importantly, the phylogenetic position of Urocyon allows us to verify the loss of PRDM9 functionality in the basal canid lineage, confirming that pseudogenization occurred at least 10 million years ago.

SUBMITTER: Armstrong EE

PROVIDER: S-EPMC10989890 | biostudies-literature | 2024 Apr

REPOSITORIES: biostudies-literature

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Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae.

Armstrong Ellie E EE Bissell Ky L KL Fatima H Sophia HS Heikkinen Maya A MA Jessup Anika A Junaid Maryam O MO Lee Dong H DH Lieb Emily C EC Liem Josef T JT Martin Estelle M EM Moreno Mauricio M Otgonbayar Khuslen K Romans Betsy W BW Royar Kim K Adler Mary Beth MB Needle David B DB Harkess Alex A Kelley Joanna L JL Mooney Jazlyn A JA Mychajliw Alexis M AM

G3 (Bethesda, Md.) 20240401 4

Reference genome assemblies have been created from multiple lineages within the Canidae family; however, despite its phylogenetic relevance as a basal genus within the clade, there is currently no reference genome for the gray fox (Urocyon cinereoargenteus). Here, we present a chromosome-level assembly for the gray fox (U. cinereoargenteus), which represents the most contiguous, non-domestic canid reference genome available to date, with 90% of the genome contained in just 34 scaffolds and a con ...[more]

PMID: 38366575

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Project description:Disease transmission and epidemic prevention are top conservation concerns for wildlife managers, especially for small, isolated populations. Previous studies have shown that the course of an epidemic within a heterogeneous host population is strongly influenced by whether pathogens are introduced to regions of relatively high or low host densities. This raises the question of how disease monitoring and vaccination programs are influenced by spatial heterogeneity in host distributions. We addressed this question by modeling vaccination and monitoring strategies for the Channel Island fox (Urocyon littoralis), which has a history of substantial population decline due to introduced disease. We simulated various strategies to detect and prevent epidemics of rabies and canine distemper using a spatially explicit model, which was parameterized from field studies. Increasing sentinel monitoring frequency, and to a lesser degree, the number of monitored sentinels from 50 to 150 radio collared animals, reduced the time to epidemic detection and percentage of the fox population infected at the time of detection for both pathogens. Fox density at the location of pathogen introduction had little influence on the time to detection, but a large influence on how many foxes had become infected by the detection day, especially when sentinels were monitored relatively infrequently. The efficacy of different vaccination strategies was heavily influenced by local host density at the site of pathogen entry. Generally, creating a vaccine firewall far away from the site of pathogen entry was the least effective strategy. A firewall close to the site of pathogen entry was generally more effective than a random distribution of vaccinated animals when pathogens entered regions of high host density, but not when pathogens entered regions of low host density. These results highlight the importance of considering host densities at likely locations of pathogen invasion when designing disease management plans.

Project description:Pleistocene aridification in central North America caused many temperate forest-associated vertebrates to split into eastern and western lineages. Such divisions can be cryptic when Holocene expansions have closed the gaps between once-disjunct ranges or when local morphological variation obscures deeper regional divergences. We investigated such cryptic divergence in the gray fox (Urocyon cinereoargenteus), the most basal extant canid in the world. We also investigated the phylogeography of this species and its diminutive relative, the island fox (U. littoralis), in California. The California Floristic Province was a significant source of Pleistocene diversification for a wide range of taxa and, we hypothesized, for the gray fox as well. Alternatively, gray foxes in California potentially reflected a recent Holocene expansion from further south. We sequenced mitochondrial DNA from 169 gray foxes from the southeastern and southwestern United States and 11 island foxes from three of the Channel Islands. We estimated a 1.3% sequence divergence in the cytochrome b gene between eastern and western foxes and used coalescent simulations to date the divergence to approximately 500,000 years before present (YBP), which is comparable to that between recognized sister species within the Canidae. Gray fox samples collected from throughout California exhibited high haplotype diversity, phylogeographic structure, and genetic signatures of a late-Holocene population decline. Bayesian skyline analysis also indicated an earlier population increase dating to the early Wisconsin glaciation (~70,000 YBP) and a root height extending back to the previous interglacial (~100,000 YBP). Together these findings support California's role as a long-term Pleistocene refugium for western Urocyon. Lastly, based both on our results and re-interpretation of those of another study, we conclude that island foxes of the Channel Islands trace their origins to at least 3 distinct female founders from the mainland rather than to a single matriline, as previously suggested.

Dataset Information

Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae.

Publications

Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae.

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