Efficient and highly continuous chromosome-level genome assembly of the first chameleon genome.

Most amniote genomes are diploid, moderate in size (approximately 1-6 Gbp), and contain a large proportion of repetitive sequences. The development of next-generation sequencing technology, especially the emergence of high-fidelity (HiFi) long-read data, has made it feasible to resolve high-quality genome assembly for non-model species efficiently. However, reference genomes for squamate reptiles has lagged behind other amniote lineages. Here we de novo assembled the first genome from the Chameleonidae family, the panther chameleon (Furcifer pardalis). We obtained telomere-to-telomere contigs using only HiFi data, reaching a contig N50 of 158.72 Mbp. The final chromosome-level assembly is 1.61 Gbp in size and 100% of primary contigs were placed to pseudochromosomes using Hi-C interaction data. We also found that sequencing depth > 30 folds can ensure both the integrity and accuracy of the genome, while insufficient depth led to false increase in genome size and proportion of duplicated genes. We provide a high-quality reference genome valuable for evolutionary and ecological studies in chameleons as well as providing comparative genomic resources for squamate reptiles.