Draft genome of the leopard gecko, Eublepharis macularius

Authors

Zijun Xiong, Xi'an Jiaotong University, China National GeneBank, Chinese Academy of Sciences
Fang Li, China National GeneBankFollow
Qiye Li, China National GeneBank, Chinese Academy of Sciences, University of Copenhagen
Long Zhou, China National GeneBank
Jiao Zheng, China National GeneBank
Tony Gamble, Marquette UniversityFollow
Ling Kui, Chinese Academy of Sciences
Cai Li, China National GeneBankFollow
Shengbin Li, Xi'an Jiaotong University
Huanming Yang, BGI-Shenzhen, James D. Watson Institute of Genome SciencesFollow
Guojie Zhang, China National GeneBank, Chinese Academy of Sciences, University of CopenhagenFollow

Document Type

Article

Language

eng

Publication Date

12-1-2016

Publisher

Oxford University Press

Source Publication

GigaScience

Source ISSN

2047-217X

Abstract

Background

Geckos 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.

Findings

We 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 compble 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.

Conclusions

Assembly of the leopard gecko genome provides a valuable resource for future comptive genomic studies of geckos and other squamate reptiles.

Comments

Published Version. GigaScience, Vol. 5, No. 1 (December 2016): 1-6. DOI. © 2016 Oxford University Press. Used with permission.

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Recommended Citation

Xiong, Zijun; Li, Fang; Li, Qiye; Zhou, Long; Zheng, Jiao; Gamble, Tony; Kui, Ling; Li, Cai; Li, Shengbin; Yang, Huanming; and Zhang, Guojie, "Draft genome of the leopard gecko, Eublepharis macularius" (2016). Biological Sciences Faculty Research and Publications. 623.
https://epublications.marquette.edu/bio_fac/623