TY - JOUR
T1 - A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology
AU - Westfall, Aundrea K.
AU - Telemeco, Rory S.
AU - Grizante, Mariana B.
AU - Waits, Damien S.
AU - Clark, Amanda D.
AU - Simpson, Dasia Y.
AU - Klabacka, Randy L.
AU - Sullivan, Alexis P.
AU - Perry, George H.
AU - Sears, Michael W.
AU - Cox, Christian L.
AU - Cox, Robert M.
AU - Gifford, Matthew E.
AU - John-Alder, Henry B.
AU - Langkilde, Tracy
AU - Angilletta, Michael J.
AU - Leaché, Adam D.
AU - Tollis, Marc
AU - Kusumi, Kenro
AU - Schwartz, Tonia S.
N1 - Funding Information:
This work was supported by National Science Foundation Graduate Research Fellowship Program (DGE 1414475 to A.C.; DGE 1255832 to A.P.S.); National Science Foundation BCS-1554834 to GHP; National Science Foundation IOS-PMB 1855845 to A.D.L.; National Science Foundation IOS-1456655 to T.L.; Clemson University lab funds to M.S.; Georgia Southern Startup Funds to C.L.C.; University of Virginia start-up funding to R.M.C.; Hatch Multistate W3045 project no. NJ17240 to H.P.J.A.; Grant for Postdoctoral Interdisciplinary Research in the Life Sciences from the School of Life Sciences at Arizona State University to M.T.; Auburn University Start-up Funds to T.S.S.
Publisher Copyright:
© 2021 The Author(s). Published by Oxford University Press GigaScience.
PY - 2021/10/1
Y1 - 2021/10/1
N2 - Background: 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. Findings: 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. Conclusions: These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.
AB - Background: 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. Findings: 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. Conclusions: These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.
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U2 - 10.1093/gigascience/giab066
DO - 10.1093/gigascience/giab066
M3 - Article
C2 - 34599334
AN - SCOPUS:85117497824
SN - 2047-217X
VL - 10
JO - GigaScience
JF - GigaScience
IS - 10
ER -