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Data released on February 16, 2015

Genomic data from the Tibetan Plateau frog (Nanorana parkeri).

Che, J; Liu, S; Sun, Y; Wang, J; Xiong, Z; Zhang, G; Zhang, X; Zhang, Y (2015): Genomic data from the Tibetan Plateau frog (Nanorana parkeri). GigaScience Database. http://dx.doi.org/10.5524/100132 RIS BibTeX Text

Nanorana parkeri (also known as the high Himalaya frog, Xizang Plateau frog, Parker's slow frog, or mountain slow frog) is a common frog living across the Tibetan Plateau. It occurs at elevations ranging from 2,850 to 5,000m. Because this species lives at such high elevations, it provides an additional excellent biological model to study the frog’s adaptations to extreme conditions.
A female frog was collected from the Qinghai-Tibetan Plateau at an elevation of 4,900m, and genomic DNA was extracted from muscle tissue. Paired end DNA libraries with different insert-size lengths (170 bp to 20 kb) were sequenced on the Illumina HiSeq 2000 platform. After performing filtering steps to remove artificial duplication, adapter contamination and low-quality reads, 190 Gbp of high-quality data (83× genome coverage) was obtained. This was assembled using SOAPdenovo and SSPACE, producing a final draft assembly of 2.0Gb with an N50 scaffold size of 1.05Mb. More than 20,000 genes were predicted. The Nanorana parkeri genome should help offer new insights into the amphibian evolution and Tibetan high-altitude adaptation.

Contact Submitter

Related manuscripts:

doi:10.1073/pnas.1501764112

Accessions (data included in GigaDB):

PROJECT: PRJNA243398

Accessions (data not in GigaDB):

SRA: SRA151427

Genomic

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Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
01125878  Nanorana parkeri Altitude:4900
Life stage:adult
Geographic location (country and/or sea,region):Ti...
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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 
01TextTEXT-0 KB2015-02-11
01Coding sequenceFASTA9.84 MB2015-02-11
01AnnotationGFF1.88 MB2015-02-11
01Protein sequenceFASTA6.4 MB2015-02-11
01Sequence assemblyFASTA534.98 MB2015-02-11
01Repeat sequenceGFF215.6 MB2015-02-11
01Repeat sequenceGFF93.67 MB2015-02-11
01Repeat sequenceUNKNOWN184.06 MB2015-02-11
01Repeat sequenceGFF22.82 MB2015-02-11
01Repeat sequenceUNKNOWN28 MB2015-02-11
Displaying 1-10 of 17 File(s).

History:

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