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

Dataset type: Genomic
Data released on February 16, 2015

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

DOI10.5524/100132

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.

Additional details

Read the peer-reviewed publication(s):


Accessions (data generated as part of this study):

PROJECT: PRJNA243398

Accessions (data referenced by this study):

SRA: SRA151427





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).




File NameSample IDData TypeFile FormatSizeRelease Date 
01TextTEXT1.07 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).
Date Action
October 18, 2015 File Nanorana_parkeri.gene.v2.cds.gz updated
October 18, 2015 File Nanorana_parkeri.gene.v2.cds.gz updated
October 18, 2015 File Nanorana_parkeri.gene.v2.cds.gz updated
October 18, 2015 File Nanorana_parkeri.gene.v2.pep.gz updated
October 18, 2015 File Nanorana_parkeri.gene.v2.cds.gz updated
October 18, 2015 File Nanorana_parkeri.gene.v2.cds.gz updated
October 18, 2015 File Nanorana_parkeri.gene.v2.cds.gz updated
October 23, 2015 File Nanorana_parkeri.genome.v2.fa.gz updated
October 27, 2015 File Nanorana_parkeri.genome.v2.fa.gz updated
October 27, 2015 File Nanorana_parkeri.genome.v2.fa.gz updated
November 3, 2015 File Nanorana_parkeri.genome.v2.fa.gz updated
November 3, 2015 File md5.txt updated
November 3, 2015 File Nanorana_parkeri.genome.v2.fa.gz updated
November 4, 2015 File Nanorana_parkeri.genome.v2.fa.gz updated
November 4, 2015 File Nanorana_parkeri.genome.v2.fa.gz updated
November 4, 2015 File Nanorana_parkeri.genome.v2.fa.gz updated
November 5, 2015 File Nanorana_parkeri.genome.v2.fa.gz updated
November 5, 2015 File Nanorana_parkeri.gene.v2.cds.gz updated
November 7, 2015 File Nanorana_parkeri.gene.v2.gff.gz updated
November 7, 2015 File Nanorana_parkeri.gene.v2.cds.gz updated
November 7, 2015 File Nanorana_parkeri.gene.v2.pep.gz updated
May 2, 2017 Additional file N_parkeri_gene_GeneSymbol.list.tsv added
May 2, 2017 Additional file N_parkeri_X_tropicalis_orthologs.list.tsv added
May 2, 2017 File N_parkeri_gene_GeneSymbol.list.tsv updated
November 3, 2017 File N_parkeri_gene_GeneSymbol.lst.gz updated
November 3, 2017 File N_parkeri_X_tropicalis_orthologs.lst.gz updated
April 28, 2020 File size of md5.txt updated