Pangenome analyses uncover the scale and evolutionary consequences of structural variation in a wild mammal
Abstract
Pangenome methods reduce reference bias and reveal genomic variation that is inaccessible with a single reference genome, enabling new insights into genome evolution, particularly in species with high genetic diversity. Here, we constructed a pangenome for the deer mouse (Peromyscus maniculatus) - a premier model for studying local adaptation and a potent reservoir of zoonotic pathogens - using long-read assemblies from 14 ecologically and biogeographically distinct populations together with two outgroup species, representing 19 haplotypes. The resulting pangenome spans 3.9 Gb, yet only 1.4 Gb is shared across all deer mouse haplotypes, revealing extensive structural variation within the species. We identified approximately 108.3 million single-nucleotide polymorphisms (SNPs), 23.9 million indels (< 50 bp), and 2.4 million structural variants (> 50 bp), in addition to massive chromosomal rearrangements and an unprecedented diversity of centromeric satellite positions. We also uncovered widespread gene copy-number variation across deer mouse haplotypes, with copy numbers differing by more than an order of magnitude for some genes, and multiple gene-rich loci exhibiting exceptional structural complexity. These genes are enriched for functions related to sensory perception, environmental interaction, and immune responses, and many show signatures of diversifying selection, suggesting that structural variation has contributed to their functional diversification. Together, our results demonstrate the power of pangenome approaches to resolve the full spectrum of genomic variation and reveal a previously underappreciated degree of structural plasticity in mammalian genomes.
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BibTeX
@misc{gozashti2026pangenome,
title = {{Pangenome analyses uncover the scale and evolutionary consequences of structural variation in a wild mammal}},
author = {Landen Gozashti and Olivia Harringmeyer and Christopher Kirby and Peter H Sudmant and Andreas F Kautt and Hopi Hoekstra},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.01.27.701785},
url = {https://doi.org/10.64898/2026.01.27.701785},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - UNPB
TI - Pangenome analyses uncover the scale and evolutionary consequences of structural variation in a wild mammal
AU - Landen Gozashti
AU - Olivia Harringmeyer
AU - Christopher Kirby
AU - Peter H Sudmant
AU - Andreas F Kautt
AU - Hopi Hoekstra
PY - 2026
DA - 2026/10/13
PB - bioRxiv
DO - 10.64898/2026.01.27.701785
UR - https://doi.org/10.64898/2026.01.27.701785
AB - Pangenome methods reduce reference bias and reveal genomic variation that is inaccessible with a single reference genome, enabling new insights into genome evolution, particularly in species with high genetic diversity. Here, we constructed a pangenome for the deer mouse (Peromyscus maniculatus) - a premier model for studying local adaptation and a potent reservoir of zoonotic pathogens - using long-read assemblies from 14 ecologically and biogeographically distinct populations together with two outgroup species, representing 19 haplotypes. The resulting pangenome spans 3.9 Gb, yet only 1.4 Gb is shared across all deer mouse haplotypes, revealing extensive structural variation within the species. We identified approximately 108.3 million single-nucleotide polymorphisms (SNPs), 23.9 million indels (< 50 bp), and 2.4 million structural variants (> 50 bp), in addition to massive chromosomal rearrangements and an unprecedented diversity of centromeric satellite positions. We also uncovered widespread gene copy-number variation across deer mouse haplotypes, with copy numbers differing by more than an order of magnitude for some genes, and multiple gene-rich loci exhibiting exceptional structural complexity. These genes are enriched for functions related to sensory perception, environmental interaction, and immune responses, and many show signatures of diversifying selection, suggesting that structural variation has contributed to their functional diversification. Together, our results demonstrate the power of pangenome approaches to resolve the full spectrum of genomic variation and reveal a previously underappreciated degree of structural plasticity in mammalian genomes.
SN - 2692-8205
ER -