Dataset Information

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 investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. 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 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length. These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.

SUBMITTER: Westfall AK

PROVIDER: S-EPMC8486681 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

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Publications

A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology.

Westfall Aundrea K AK Telemeco Rory S RS Grizante Mariana B MB Waits Damien S DS Clark Amanda D AD Simpson Dasia Y DY Klabacka Randy L RL Sullivan Alexis P AP Perry George H GH Sears Michael W MW Cox Christian L CL Cox Robert M RM Gifford Matthew E ME John-Alder Henry B HB Langkilde Tracy T Angilletta Michael J MJ Leaché Adam D AD Tollis Marc M Kusumi Kenro K Schwartz Tonia S TS

GigaScience 20211001 10

<h4>Background</h4>High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. 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.<h4>Findings</h4>We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromi ...[more]

PMID: 34599334

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Dataset Information

A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology.

Publications

A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology.

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