A Catalog of CSINE3A Retrotransposons in the Genome of the Domestic Rabbit, Oryctolagus cuniculus

Short interspersed elements (SINEs) are retrotransposons often found at copy numbers in excess of 100,000 per genome. SINE retrotransposition into a gene can disrupt the gene’s normal patterns of splicing or expression; examples of such disruption have been reported in many species including man, mouse and domestic dog. Domestic mammals, including the rabbit, typically feature extreme variation in certain obvious traits that can be readily selected for or against by breeders. For example, distinct sub-populations (breeds) of rabbit feature a nearly ten-fold range in adult mean body mass and also exhibit a wide variation in hair colors, patterns and lengths. We hypothesize that gene disruptions by polymorphic CSINE3A retrotransposons explain some of these stark phenotypic variations in rabbits, as is the case for merle-coated dogs carrying a SINE insertion mutation in the SILV gene. With the immediate goal of cataloging novel CSINE3A insertions in the rabbit genome, we have created inverse-PCR libraries highly enriched for CSINE3A copies with flanking sequence. A total of 328 such libraries have been subjected to Illumina Hi-Seq sequencing from rabbits representing 47 breeds.  SINE insertion loci have been identified in the sample libraries that are not present in the rabbit reference genome assembly. Our catalog provides a resource for investigating the genomic patterns of SINE insertion in the domestic rabbit.