title: Draft genome of the leopard gecko, Eublepharis macularius.
abstract: 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.
  
  
  
  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 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.
  
  
  
  Assembly of the leopard gecko genome provides a valuable resource for future comparative genomic studies of geckos and other squamate reptiles.
authors: College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.|China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China.|State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
authors: Zijun
authors: Z
authors: Xiong
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China.
authors: Fang
authors: F
authors: Li
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China.|State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.|Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.
authors: Qiye
authors: Q
authors: Li
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China.
authors: Long
authors: L
authors: Zhou
authors: Department of Biological Sciences, Marquette University, Milwaukee, WI, 53201, USA.
authors: Tony
authors: T
authors: Gamble
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China.
authors: Jiao
authors: J
authors: Zheng
authors: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
authors: Ling
authors: L
authors: Kui
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China.
authors: Cai
authors: C
authors: Li
authors: College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
authors: Shengbin
authors: S
authors: Li
authors: BGI-Shenzhen, Shenzhen, 518083, China.|James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China.
authors: Huanming
authors: H
authors: Yang
authors: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China. zhanggj@genomics.cn.|State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China. zhanggj@genomics.cn.|Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark. zhanggj@genomics.cn.
authors: Guojie
authors: G
authors: Zhang
mesh_terms: D000818:Animals; D020451:Contig Mapping; D016678:Genome; D059646:Genome Size; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008116:Lizards / Q000235:genetics*; D008297:Male; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: Assembly; Eublepharis macularius; Gekkota; Genome sequencing; Leopard gecko