A chromosome-level genome assembly for the Eastern Fence Lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology

Abstract

High-quality genomic resources facilitate population-level and species-level comparisons to answer questions about behavioral ecology, morphological and physiological adaptations, as well as the evolution of genomic architecture. Squamate reptiles (lizards and snakes) are particularly diverse in characteristics that have intrigued evolutionary biologists, but high-quality genomic resources for squamates are relatively sparse. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. We present a high-quality chromosome-level reference genome assembly, SceUnd1.0, (utilizing 10X Genomics Chromium, HiC, and PacBio data) and tissue/developmental stage transcriptomes for the Eastern Fence Lizard, Sceloporus undulatus. We performed synteny analysis with other available squamate chromosome-level assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes in S. undulatus. Using this new S. undulatus genome assembly we conducted reference-based assemblies for 34 other Sceloporus species to improve draft nuclear genomes assemblies from 1% coverage to 43% coverage on average. Across these species, typically >90% of reads mapped for species within 20 million years divergence from S. undulatus, this dropped to 75% reads mapped for species at 35 million years divergence. Finally we use RNAseq and whole genome resequencing data to compare the three assemblies as references, each representing an increased level of sequencing, cost and assembly efforts: Supernova Assembly with data from10X Genomics Chromium library; HiRise Assembly that added data from HiC library; and PBJelly Assembly that added data from PacBio sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq, but the chromosome-level scaffolds provided by the addition of the HiC data allowed the reference to be used for other whole genome analysis, including synteny and whole genome association mapping analyses. The addition of PacBio data provided negligible gains. Overall, these new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.

Chromosome-scale genome assembly of the brown anole (Anolis sagrei), a model species for evolution and ecology

“…2b). The eastern fence lizard 64 ( Sceloporus undulatus ) is slightly more contiguous than our assembly but less complete. These two genomes stand apart from other recent lepidosaur genome assemblies in being both highly complete and contiguous (Fig.…”

Characterization of a pericentric inversion in plateau fence lizards (Sceloporus tristichus): evidence from chromosome-scale genomes

“…Adding sequencing data to refine our assemblies would help to confirm the extent of the inversion, as chromosome 7 in HOL included two scaffolds. As we used S. undulatus as a reference to confirm our chromosome-scale assemblies, we expect to find 1:1 synteny with S. undulatus ( Westfall et al 2020 ). Therefore, the pericentric inversion could be much larger than reported here, since it is possible that either one or both of the chromosome 7 scaffolds in HOL are reversed.…”

“…The program was run with default “seed families” and default values for all other parameters. We determined the identity of large scaffolds by comparing S. tristichus assemblies to the assembled chromosome-scale genome of the closely related species S. undulatus ( Westfall et al 2020 ) (Table S3 and S4). Furthermore, HiCUP v0.8.0 ( Wingett et al 2015 ) was used to map the Hi-C paired end raw sequencing reads of HOL against the assembled chromosome 7 of SNOW using bowtie2 v.2.4.2.…”

“…While many species have the ancestral karyotype formula of 2 n = 36 chromosomes, Sceloporus exhibits substantial karyotype variation (ranging from 2 n = 22 to 46), sex chromosome evolution ( Lisachov et al 2020 ), and large genome rearrangements ( Leaché and Sites Jr. 2009 ). Existing genomic resources for Sceloporus include an annotated genome for S. undulatus ( Westfall et al 2020 ), a de novo assembled shotgun genome for S. occidentalis and partial genomes for 34 other species ( Arthofer et al . 2015 ).…”

Brain transcriptomic responses of Yarrow's spiny lizard, Sceloporus jarrovii, to conspecific visual or chemical signals

“…Although S. jarrovii and S. undulatus diverged $22 Mya, 48 estimates based on draft genomic data from several other Sceloporus species predicted that $85% of reads would map to the reference genome. 23 We generated read summarization with unique STAR aligned reads using featureCounts from the Subread package (v2.0.0). 49 Paired reads (fragments) were counted with option "-p" and multi-mapping and multi-overlapping reads were excluded by default.…”