Abstract
BackgroundGeckos are among the most species-rich reptile groups and the sister clade to all other lizards and snakes. Geckos possess a suite of distinctive characteristics, including adhesive digits, nocturnal activity, hard, calcareous eggshells, and a lack of eyelids. However, one gecko clade, the Eublepharidae, appears to be the exception to most of these ‘rules’ and lacks adhesive toe pads, has eyelids, and lays eggs with soft, leathery eggshells. These differences make eublepharids an important component of any investigation into the underlying genomic innovations contributing to the distinctive phenotypes in ‘typical’ geckos.FindingsWe report high-depth genome sequencing, assembly, and annotation for a male leopard gecko, Eublepharis macularius (Eublepharidae). Illumina sequence data were generated from seven insert libraries (ranging from 170 to 20 kb), representing a raw sequencing depth of 136X from 303 Gb of data, reduced to 84X and 187 Gb after filtering. The assembled genome of 2.02 Gb was close to the 2.23 Gb estimated by k-mer analysis. Scaffold and contig N50 sizes of 664 and 20 kb, respectively, were comparable to the previously published Gekko japonicus genome. Repetitive elements accounted for 42 % of the genome. Gene annotation yielded 24,755 protein-coding genes, of which 93 % were functionally annotated. CEGMA and BUSCO assessment showed that our assembly captured 91 % (225 of 248) of the core eukaryotic genes, and 76 % of vertebrate universal single-copy orthologs.ConclusionsAssembly of the leopard gecko genome provides a valuable resource for future comparative genomic studies of geckos and other squamate reptiles.Electronic supplementary materialThe online version of this article (doi:10.1186/s13742-016-0151-4) contains supplementary material, which is available to authorized users.
Highlights
Geckos are among the most species-rich reptile groups and the sister clade to all other lizards and snakes
Assembly of the leopard gecko genome provides a valuable resource for future comparative genomic studies of geckos and other squamate reptiles
Sample collection and sequencing Genomic DNA was extracted from the tail tissue of a male leopard gecko (Eublepharis macularius: NCBI taxonomy ID 481883; specimen ID TG1477) (Fig. 1)
Summary
Sample collection and sequencing Genomic DNA was extracted from the tail tissue of a male leopard gecko (Eublepharis macularius: NCBI taxonomy ID 481883; specimen ID TG1477) (Fig. 1). Genome assembly We first performed a 17-mer analysis [2] to estimate the leopard gecko genome size using 54 Gb clean sequences from 170 and 500 bp insert size libraries. We assembled a high-quality leopard gecko genome using SOAPdenovo (version 2.0) [2] in three steps: contig construction, scaffolding, and gap filling. In the contig construction step, SOAPdenovo was used to a de Bruijn graph by dividing high-quality reads from short insert libraries into kmers in which paired-end information was ignored, and kmers were merged, tips clipped, bubbles merged, and low coverage links removed. The end result was a leopard gecko genome assembly with a total length of 2.0 Gb and scaffold and contig N50s of 664 and 20 kb, respectively, which is comparable to the previously reported Gekko japonicus genome assembly (Table 3) [4]. High-quality data were obtained by filtering raw data for low-quality and duplicate reads and correcting sequencing errors
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