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-le...

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Published in:G3 : genes - genomes - genetics Vol. 14; no. 4
Main Authors: Armstrong, Ellie E, Bissell, Ky L, Fatima, H Sophia, Heikkinen, Maya A, Jessup, Anika, Junaid, Maryam O, Lee, Dong H, Lieb, Emily C, Liem, Josef T, Martin, Estelle M, Moreno, Mauricio, Otgonbayar, Khuslen, Romans, Betsy W, Royar, Kim, Adler, Mary Beth, Needle, David B, Harkess, Alex, Kelley, Joanna L, Mooney, Jazlyn A, Mychajliw, Alexis M
Format: Journal Article
Language:English
Published: US Oxford University Press 03-04-2024
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Summary: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. 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, Armstrong et al. 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 (Mb), 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 US 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.
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Ky L. Bissell, H. Sophia Fatima, Maya A. Heikkinen, Anika Jessup, Maryam O. Junaid, Dong H. Lee, Emily C. Lieb, Josef T. Liem, Estelle M. Martin, Mauricio Moreno, Khuslen Otgonbayar, Betsy W. Romans, Jazlyn A. Mooney and Alexis M. Mychajliw contributed equally to this work
Conflicts of interest. The author(s) declare no conflicts of interest.
ISSN:2160-1836
2160-1836
DOI:10.1093/g3journal/jkae034