Chromosome-level genome assembly of Phrynocephalus forsythii using third-generation DNA sequencing and Hi-C analysis.

Phrynocephalus forsythii is a viviparous sand lizard that is endemic to the Tarim Basin with a broad altitudinal range of 872-3,100 m. Such variation in altitude and ecological variables can offer an opportunity to uncover genetic mechanisms of ectothermic adaptation to extreme environments at high- and low-altitude. Furthermore, the evolutionary relationship of karyotype with two different chromosome numbers (2n = 46 or 2n = 48) in the Chinese Phrynocephalus is unclear. In this study, a chromosome-level reference genome of P. forsythii was assembled. The genome assembly size was 1.82 Gb with a contig N50 length of 46.22 Mb, 20,194 protein-coding genes were predicted and 95.50% of these genes were annotated in functional public databases. After cluster contigs into chromosome level using Hi-C paired-end reads, we found that two chromosomes of P. forsythii were originated from one ancestral chromosome of species with 46 chromosomes. Comparative genomic analysis revealed that numerous characteristics associated with high- or low-altitude adaptation, including energy metabolism pathways, hypoxic adaptation, and immune, exhibit rapid changes or show signals of positive selection in the P. forsythii genome. This genome provides an excellent genome resource for the study of the karyotype evolution and ecological genomics of Phrynocephalus.