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Data released on October 20, 2016

Supporting data for "Draft genome of the leopard gecko, Eublepharis macularius"

Xiong, Z; Li, F; Li, Q; Zhou, L; Gamble, T; Zheng, J; Kui, L; Li, C; Li, S; Yang, H; Zhang, G (2016): Supporting data for "Draft genome of the leopard gecko, Eublepharis macularius" GigaScience Database. http://dx.doi.org/10.5524/100246 RIS BibTeX Text

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 lack of eyelids. However, one gecko clade, the Eublepharidae, seems to be the exception to most of these “rules” and lack adhesive toe pads, have eyelids, and lay 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 the 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 bp 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 size was 2.02 Gb, close to the 2.23 Gb estimated by k-mer analysis. Scaffold and contig N50 sizes were 664 kb and 20 kb, respectively, comparable to the previously published Gekko japonicus genome. Repetitive elements made up 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 eukaryotic core genes and 76% of the vertebrate universal single-copy orthologs.
The leopard gecko genome assembly provides a valuable resource for future comparative genomic studies of geckos and other squamate reptiles.

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Related manuscripts:

doi:10.1186/s13742-016-0151-4

Additional information:

https://github.com/gigascience/paper-xiong2016

Genomic

http://gigadb.org/images/data/cropped/100246.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Gecko481883Eublepharis macularius Description:This leopard gecko was captive born fr...
Alternative names:TG1477
Tissue type:Tail (UBERON:0002415)
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Displaying 1-1 of 1 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
Tabular dataUNKNOWN50.69 KB2016-10-03
Tabular dataUNKNOWN50.03 KB2016-10-03
Tabular dataUNKNOWN0.34 KB2016-10-03
Tabular dataUNKNOWN0.35 KB2016-10-03
Tabular dataUNKNOWN0.6 KB2016-10-03
otherUNKNOWN2.25 MB2016-10-03
fastaFASTA94.49 KB2016-10-03
annotationGFF66.1 KB2016-10-03
Coding sequenceFASTA11.65 MB2016-10-03
annotationGFF2.51 MB2016-10-03
Displaying 1-10 of 33 File(s).

History:

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