A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons

Due to their history of domestication and breed formation, dogs are a powerful system for studying the phenotypic impact of genetic variation. Comparison of canine genome assemblies show that retrotransposons, mobile elements which mobilize through an RNA intermediate, are a major contributor to canine genetic diversity with an eightfold and 17-fold increase of LINE-1 and SINE differences, respectively, in dogs relative to that found among humans. The frequency of dimorphic retrotransposon insertions among dogs suggests these elements have mobilized at a high rate over recent canine evolution. However, the rate at which new insertions arise has yet to be determined.

We aligned a collection of genome assemblies derived from four breed dogs, a Dingo, and an American grey wolf to a Greenland grey wolf to identify dimorphic LINE-1 and SINEC insertions. Across our panel of seven canine assemblies, we identified a total of 7,428 dimorphic LINE-1s and 51,572 dimorphic SINECs. Each assembly differs from the Greenland wolf genome by an average of 3,497 LINE-1s and 25,558 SINECs. Analysis of allele sharing among samples recapitulates known relationships and reveals substantial within-breed variation. Calibrating estimates using a previously estimated single nucleotide mutation rate of 4.5×10^-9 per base pair per generation, we estimate that new LINE-1 and SINEC and insertions have occurred at a rate of 1/184 and 1/22 births over recent canine evolution. These estimates are largely consistent across assemblies and breeds.

Our phylogenetic estimate of SINEC retrotransposition in canines is approximately twice as large as that estimated for Alu in humans, while the canine LINE-1 insertion rate is within the range of human estimates. These data suggest that although SINEC has been an outsized driver of canine genome evolution, the striking levels of canine LINE-1 and SINEC dimorphism mainly reflect high levels of long-standing genetic variation.