A Beary Good Genome: Haplotype-Resolved, Chromosome-Level Assembly of the Brown Bear (<i>Ursus arctos</i>)

Armstrong, Ellie E.; Perry, Blair W.; Huang, Yongqing; Garimella, Kiran; Jansen, Heiko T.; Robbins, Charles T.; Tucker, Nathan R; Kelley, Joanna L.

doi:10.1093/gbe/evac125

Cited by 2 publications

References 51 publications

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Divergent reference genomes compromise the reconstruction of demographic histories, selection scans, and population genetic summary statistics

Akopyan,

Genchev,

Armstrong

et al. 2024

Preprint

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Characterizing genetic variation in natural populations is central to evolutionary biology. However, most non-model organisms lack integral genomic resources such as reference genomes and recombination maps, limiting accurate evolutionary inference. Here, we explore the consequences of reference genome bias on the inference of genetic diversity, demographic histories, and recombination rates using gray foxes (Urocyon cinereoargenteus), which, like most members of Canidae, are traditionally mapped to the dog (Canis lupus familiaris) reference genome. Whole genome sequence data from gray foxes were mapped to the gray fox reference genome and two heterospecific canid references (dog and Arctic fox; Vulpes lagopus). Our results reveal that reference bias significantly affects population genomic analyses. Mapping to the conspecific gray fox genome improved read pairing, increased detection of SNPs, especially rare variants, and reduced spurious variants. Estimates of nucleotide diversity (π) and genetic differentiation (FST) were higher using the gray fox genome. We observed that mapping to heterospecific references leads to underestimates of population sizes, distorted demographic trajectories, and more variable recombination rates. These effects are further complicated by population-specific biases, which vary in their magnitude and direction across populations, highlighting the need for tailored approaches to mitigate reference bias. Importantly, FST outlier detection also differed among references, affecting functional interpretations. Collectively, this work addresses a critical gap in the rapidly expanding field of non-model species genomics by demonstrating the importance of using conspecific genomic resources in evolutionary research and illustrating how reliance on distantly related reference genomes can distort population genetic analyses.

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Divergent reference genomes compromise the reconstruction of demographic histories, selection scans, and population genetic summary statistics

Akopyan,

Genchev,

Armstrong

et al. 2024

Preprint

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Feeding during hibernation shifts gene expression toward active season levels in brown bears (Ursus arctos)

Perry

McDonald

Trojahn

et al. 2023

Physiological Genomics

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Hibernation in bears involves a suite of metabolic and physiological changes, including the onset of insulin resistance, that are driven in part by sweeping changes in gene expression in multiple tissues. Feeding bears glucose during hibernation partially restores active season physiological phenotypes, including partial re-sensitization to insulin, but the molecular mechanisms underlying this transition remain poorly understood. Here, we analyze tissue-level gene expression in adipose, liver, and muscle to identify genes that respond to mid-hibernation glucose feeding and thus potentially drive post-feeding metabolic and physiological shifts. We show that mid-hibernation feeding stimulates differential expression in all analyzed tissues of hibernating bears, and that a subset of these genes respond specifically by shifting expression towards levels typical of the active season. Inferences of upstream regulatory molecules potentially driving these post-feeding responses implicate PPARG and other known regulators of insulin sensitivity, providing new insight into high-level regulatory mechanisms involved in shifting metabolic phenotypes between hibernation and active states.

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A Beary Good Genome: Haplotype-Resolved, Chromosome-Level Assembly of the Brown Bear (Ursus arctos)

Cited by 2 publications

References 51 publications

Divergent reference genomes compromise the reconstruction of demographic histories, selection scans, and population genetic summary statistics

Divergent reference genomes compromise the reconstruction of demographic histories, selection scans, and population genetic summary statistics

Feeding during hibernation shifts gene expression toward active season levels in brown bears (Ursus arctos)

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