Efficient and highly continuous chromosome-level genome assembly of a diploid amniote genome

Most amniote genomes are diploid, moderate in size (approximately 1–6 g), and contain a large proportion of repetitive sequences. The development of next-generation sequencing technology has made it possible to resolve the genome assembly of non-model species. However, traditional genome assembly methods usually involve the acquisition of a large amount of sequencing data and complex calculations, making the de novo genome for non-model species expensive and difficult for most projects. The development of long-read sequencing, especially the emergence of high-fidelity (HiFi) long-read data, has made it possible to assemble genomes efficiently, but how to obtain high-quality reference genomes economically and quickly still lacks practical evaluation. Here we de novo assembled the first chameleon genome, the panther chameleon (Furcifer pardalis). We obtained chromosome-level contigs using only HiFi data, and further combined Hi-C data to assemble all contigs to pseudochromosomes. 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. Our results provide an accurate and efficient de novo assembly strategy for reference genomes of non-model species.