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Data released on April 29, 2014

Genomic data of the Ostrich (Struthio camelus australis).

Gilbert, M, P; Jarvis, E, D; Li, B; Li, C; Ryder, O; The Avian Genome Consortium, ; Wang, J; Zhang, G (2014): Genomic data of the Ostrich (Struthio camelus australis). GigaScience Database. http://dx.doi.org/10.5524/101013 RIS BibTeX Text

The Southern Ostrich (Struthio camelus australis (Gurney, 1868)) is a sub-species of The Common Ostrich (Struthio camelus) and found in southern Africa, south of the Zambezi and Cunene rivers. It is a flightless bird native to Africa and the only living member of the genus, Struthio. The Ostrich is farmed throughout the world for its meat, feathers and leather.
These data have been produced as part of the G10K and Avian Phylogenomics Project. DNA was collected from a female at the San Diego Zoo in California by Oliver Ryder, of an animal originally from Botswana, Africa (ISIS ID: 202443). We sequenced the 2.16Gb genome to a depth of approximately 85X with short reads from a series of libraries with various insert sizes (170bp, 500bp, 800bp, 2kb, 5kb, 10kb and 20kb).
The assembled scaffolds of high quality sequences total 1.23Gb, with the contig and scaffold N50 values of 29kb and 3.5Mb respectively. We identified 16,178 protein-coding genes with a mean length of 19.5kb.
Update - 13-AUG-2014 - A new assembly making use of the optical mapping data has been release, this improves the assembled scaffolds N50 to 17.7 Mb, the protein count is unchanged.

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Related manuscripts:

doi:10.1186/2047-217X-3-26
doi:10.1126/science.1251385
doi:10.1126/science.1253451
doi:10.1186/s13742-015-0062-9

Related datasets:

doi:10.5524/101013 IsSupplementTo doi:10.5524/101000

Accessions (data included in GigaDB):

BioProject: PRJNA212875
SRA: SRP028745

Projects:



Genomic, Genome-Mapping

http://gigadb.org/images/data/cropped/bird/struthio_camelus.png

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Ostrich- 202443441894OstrichStruthio camelus australis Source material identifiers:Oliver Ryder (San Dieg...
Estimated genome size:2.16
Funding source:BGI
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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 
DirectoryUNKNOWN0 KB2014-04-29
Ostrich- 202443Optical mapUNKNOWN123.98 MB2014-08-14
Ostrich- 202443AnnotationGFF10.17 KB2014-08-14
ReadmeTEXT2.46 KB2014-08-14
Ostrich- 202443Sequence assemblyFASTA327.49 MB2014-08-13
Ostrich- 202443Coding sequenceFASTA6.52 MB2014-08-13
Ostrich- 202443AnnotationGFF1.61 MB2014-08-13
Ostrich- 202443Protein sequenceFASTA4.28 MB2014-08-13
Ostrich- 202443OtherUNKNOWN4.83 MB2014-08-13
Displaying 1-9 of 9 File(s).

History:

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