The revised reference genome of the leopard gecko (Eublepharis macularius) provides insight into the considerations of genome phasing and assembly

Author:

Pinto Brendan J123ORCID,Gamble Tony345ORCID,Smith Chase H6ORCID,Keating Shannon E4ORCID,Havird Justin C6ORCID,Chiari Ylenia7ORCID

Affiliation:

1. School of Life Sciences, Arizona State University , Tempe, AZ , USA

2. Center for Evolution and Medicine, Arizona State University , Tempe, AZ , USA

3. Department of Zoology, Milwaukee Public Museum , Milwaukee, WI , USA

4. Department of Biological Sciences, Marquette University , Milwaukee WI , USA

5. Bell Museum of Natural History, University of Minnesota , St Paul, MN , USA

6. Department of Integrative Biology, University of Texas at Austin , Austin, TX , USA

7. Department of Biology, George Mason University , Fairfax, VA , USA

Abstract

Abstract Genomic resources across squamate reptiles (lizards and snakes) have lagged behind other vertebrate systems and high-quality reference genomes remain scarce. Of the 23 chromosome-scale reference genomes across the order, only 12 of the ~60 squamate families are represented. Within geckos (infraorder Gekkota), a species-rich clade of lizards, chromosome-level genomes are exceptionally sparse representing only two of the seven extant families. Using the latest advances in genome sequencing and assembly methods, we generated one of the highest-quality squamate genomes to date for the leopard gecko, Eublepharis macularius (Eublepharidae). We compared this assembly to the previous, short-read only, E. macularius reference genome published in 2016 and examined potential factors within the assembly influencing contiguity of genome assemblies using PacBio HiFi data. Briefly, the read N50 of the PacBio HiFi reads generated for this study was equal to the contig N50 of the previous E. macularius reference genome at 20.4 kilobases. The HiFi reads were assembled into a total of 132 contigs, which was further scaffolded using HiC data into 75 total sequences representing all 19 chromosomes. We identified 9 of the 19 chromosomal scaffolds were assembled as a near-single contig, whereas the other 10 chromosomes were each scaffolded together from multiple contigs. We qualitatively identified that the percent repeat content within a chromosome broadly affects its assembly contiguity prior to scaffolding. This genome assembly signifies a new age for squamate genomics where high-quality reference genomes rivaling some of the best vertebrate genome assemblies can be generated for a fraction of previous cost estimates. This new E. macularius reference assembly is available on NCBI at JAOPLA010000000.

Funder

National Science Foundation

National Institutes of Health

Publisher

Oxford University Press (OUP)

Subject

Genetics (clinical),Genetics,Molecular Biology,Biotechnology

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