Efficient and Highly Continuous Chromosome-Level Genome Assembly of the First Chameleon Genome

Abstract

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.

Heteromorphic ZZ/ZW sex chromosomes sharing gene content with mammalian XX/XY are conserved in Madagascan chameleons of the genus Furcifer

“…For the first time, we uncovered the partial gene content of sex chromosomes in the chameleons of the genus Furcifer . The genome of a male F. pardalis was recently sequenced and assembled in chromosome level, resulting in 11 scaffolds, but sex chromosomes were not identified 52 . A local Blast search 53 of the Z-specific genes revealed by coverage analysis and the Z/W-linked genes revealed from sequencing the microdissected chromosomes allowed us to assign the Z 1 chromosome to the scaffold no 10 of the assemblies published by Xie and co-authors 52 .…”

“…The genome of a male F. pardalis was recently sequenced and assembled in chromosome level, resulting in 11 scaffolds, but sex chromosomes were not identified 52 . A local Blast search 53 of the Z-specific genes revealed by coverage analysis and the Z/W-linked genes revealed from sequencing the microdissected chromosomes allowed us to assign the Z 1 chromosome to the scaffold no 10 of the assemblies published by Xie and co-authors 52 . This assignment is further supported by previous cytogenetic analysis, where the Z 1 chromosome was identified as the 10th pair of the male karyotype 23 .…”

The first complete assembly for a lungless urodelan with a "miniaturized" genome, the Northern Dusky Salamander (Plethodontidae: Desmognathus fuscus)

“…Increasing coverage has been shown to result in dramatically higher-quality assemblies up to a threshold of ∼30x, at least in some species with smaller (∼1.6GB) genomes (Xie et al . 2023).…”