Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis.
Anusha P Bishop, Erin P Westeen, Michael L Yuan, Merly Escalona, Eric Beraut, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Erin Toffelmier, Robert N Fisher, H Bradley Shaffer, Ian J Wang
Author Information
Anusha P Bishop: Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States. ORCID
Erin P Westeen: Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States. ORCID
Michael L Yuan: Center for Population Biology, University of California, Davis, Davis, CA, United States. ORCID
Merly Escalona: Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States. ORCID
Eric Beraut: Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States. ORCID
Colin Fairbairn: Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States.
Mohan P A Marimuthu: DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States. ORCID
Oanh Nguyen: DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States. ORCID
Noravit Chumchim: DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States. ORCID
Erin Toffelmier: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States. ORCID
Robert N Fisher: U.S. Geological Survey Western Ecological Research Center, San Diego, CA, United States.
H Bradley Shaffer: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States. ORCID
Ian J Wang: Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States. ORCID
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.
