Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis

Abstract

Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the California endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards.

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

“…However, compared with other amniote groups such as mammals and birds, squamate reptiles are lagging behind in terms of available reference genomes ( Hotaling et al 2021 ). Although new genomes are quickly emerging ( Bishop et al 2023 ; Gomez-Garrido et al 2023 ; Richmond et al 2023 ), there are still <100 genomes publicly available for the ∼11,549 squamate species ( Uetz et al 2021 ; Pinto et al 2023 ).…”