A genome assembly and annotation for the Australian alpine skink Bassiana duperreyi using long-read technologies.

Abstract

The eastern 3-lined skink (Bassiana duperreyi) inhabits the Australian high country in the southeast of the continent including Tasmania. It is a distinctive oviparous species because it undergoes sex reversal (from XX genotypic females to phenotypic males) at low incubation temperatures. We present a chromosome-scale genome assembly of a B. duperreyi XY male individual, constructed using PacBio HiFi and Oxford Nanopore Technologies long reads scaffolded using Illumina HiC data. The genome assembly length is 1.57 Gb with a scaffold N50 of 222 Mb, N90 of 26 Mb, 200 gaps, and 43.10% GC content. Most (95%) of the assembly is scaffolded into 6 macrochromosomes, 8 microchromosomes, and the X chromosome, corresponding to the karyotype. Fragmented Y chromosome scaffolds (n = 11 ≥ 1 Mb) were identified using Y-specific contigs generated by genome subtraction. We identified 2 novel alpha-satellite repeats of 187 and 199 bp in the putative centromeres that did not form higher-order repeats. The genome assembly exceeds the standard recommended by the Earth BioGenome Project: 0.02% false expansions, 99.63% k-mer completeness, 94.66% complete single-copy Benchmarking Universal Single-Copy Orthologs genes, and an average 98.42% of transcriptome data mappable to the genome assembly. The mitochondrial genome (17,506 bp) and the model rDNA repeat unit (15,154 bp) were assembled. The B. duperreyi genome assembly has high completeness for a skink and will provide a resource for research focused on sex determination and thermolabile sex reversal, as an oviparous foundation species for studies of the evolution of viviparity and for other comparative genomics studies of the Scincidae.