Chromosome-level genome assembly and Oligo-FISH confirmation of chromosome models for the Tasmanian snow skink Carinascincus ocellatus (Scincidae, Eugongylinae).

Abstract

Background: Skinks (Scincidae) are one of the most diverse and ecologically versatile lizard families, making them key models for studying major evolutionary transitions including viviparity, limb reduction, and shifts between modes of sex determination. Despite their diversity and research potential, skinks remain underrepresented in genome databases, limiting comparative studies and our ability to investigate the genetic foundations of their evolutionary diversity.

Results: We generated a high-quality chromosome-level genome assembly for the Tasmanian snow skink, Carinascincus ocellatus, using PacBio long-read sequencing and Hi-C scaffolding. We validated the accuracy of chromosome models in this genome using an innovative application of Oligo-FISH, designing thousands of short probes directly from the genome assembly and hybridizing them to a single C. ocellatus metaphase slide. This single-step approach provides direct and independent cytogenetic validation of all 15 chromosomes in the assembly, including microchromosomes, which are broadly recognized as more susceptible to misassembly. We further demonstrate the approach's cross-species utility through comparative cytogenomics and in silico probe alignment to multiple other skink genomes, highlighting its potential for multi-genome validation and comparative analyses.

Conclusions: Our study establishes C. ocellatus as a genomic model for skinks and positions Oligo-FISH as a scalable, cost-effective, and broadly applicable approach for chromosome-level genome validation. By applying it across species, we demonstrate the method's potential to support more reliable genome reconstruction and comparative genomic analyses.