Hoffman, J. J.; Burbrink, F.; Pyron, R. A.; Raxworthy, C. J.

Although the publication of high-quality reference genomes is steadily increasing for vertebrate groups, many clades remain chronically neglected. Skinks (order: Squamata; family: Scincidae) are one of the most diverse lizard families (1,785 species), yet there are currently just four published chromosome-level skink genomes. Here, we present the first telomere-to-telomere, chromosome-level reference genome for one of the most abundant lizards in the eastern United States, the common five-lined skink (Plestiodon fasciatus). Through the sequencing of RNA, long-read DNA, and Hi-C chromatin interactions, we produced an annotated reference genome (N50 = 227MB, L50 = 3) consisting of 6 macrochromosome pairs and 7 microchromosome pairs with 98% of BUSCO genes (lineage: sauropsida; 7480 BUSCO markers) represented, providing one of the most complete skink genomes to date: rPleFas1.1. Functional annotation predicts 32,520 protein-coding genes (16,100 unique, named genes) with an average gene length of 9,372bp. Repeat annotations estimate that transposable elements comprise 46.7% of the genome, for which we show the amount and content is remarkably conserved across Scincidae.