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Data released on February 18, 2014

Genomic data for the Tibetan ground tit (Pseudopoces humilis).

Cai, Q; Cai, Y; Gou, C; Hao, M; He, R; Hui, Y; Lang, Y; Li, Y; Liu, J; Luo, L; Luo, Y; Pan, S; Qian, X; Wang, J; Wang, S; Wang, Z; Xu, J; Zhang, X; Zhao, J (2014): Genomic data for the Tibetan ground tit (Pseudopoces humilis). GigaScience Database. http://dx.doi.org/10.5524/100088 RIS BibTeX Text

Available here is the first draft genome sequence of the Tibetan ground tit (Pseudopodoces humilis) also known as Hume’s Groundpecker. This bird is native to the Qinghai-Tibet Plateau (QTP) or ‘the roof of the world’, which has become a focus for many biological studies due to the extreme environmental conditions, and the genetic mechanisms of high-altitude adaptation has never been studied. Controversy also exists regarding the ground tit’s phylogeny – formerly thought to be part of the Corvidae family, recent phylogenetic analysis have determined this to not be the case.
A 1.04 Gb assembled draft genome sequence was generated that covered 95.4% of the whole genome. The scaffold N50 and contig N50 values were 16.3 Mb and 164.7 Kb respectively. High accuracy at the sequencing level was ensured, where the average sequencing depth of the ground tit assembly was 96×, and 99% of the assembly had at least 20× coverage. This data contributes to the study of avian evolutionary history and provides new insights into the tit’s adaptation to extreme environmental conditions.

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Related manuscripts:

doi:10.1186/gb-2013-14-3-r29 (PubMed: 23537097)
doi:10.1186/gb-2014-15-2-r33

Accessions (data included in GigaDB):

BioProject: PRJNA175930
BioProject: PRJNA179234

Genomic

http://gigadb.org/images/data/cropped/100088.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN01925482181119Tibetan Ground TitTibetan ground-titPseudopodoces humilis Geographic location (country and/or sea,region):Ti...
IUCN Red List:LC
Sex:male
...
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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 
SAMN01925482Coding sequenceFASTA23.7 MB2013-02-18
SAMN01925482Protein sequenceFASTA8.69 MB2013-02-18
SAMN01925482AnnotationGFF16.75 MB2013-02-18
SAMN01925482Sequence assemblyFASTA1007.6 MB2013-02-18
ReadmeUNKNOWN0.31 KB2013-02-18
Displaying 1-5 of 5 File(s).

History:

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