Genomic data of the Ostrich (Struthio camelus australis).
Dataset type: Genomic, Genome-Mapping
Data released on April 29, 2014
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.
Read the peer-reviewed publication(s):
Zhang, G., Li, B., Li, C., Gilbert, M. T. P., Jarvis, E. D., & Wang, J. (2014). Comparative genomic data of the Avian Phylogenomics Project. GigaScience, 3(1). doi:10.1186/2047-217x-3-26
Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., … Meredith, R. W. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311–1320. doi:10.1126/science.1251385
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., … Howard, J. T. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320–1331. doi:10.1126/science.1253451
Zhang, J., Li, C., Zhou, Q., & Zhang, G. (2015). Improving the ostrich genome assembly using optical mapping data. GigaScience, 4(1). doi:10.1186/s13742-015-0062-9
Accessions (data included in GigaDB):
|Sample ID||Taxonomic ID||Common Name||Genbank Name||Scientific Name||Sample Attributes|
|Ostrich- 202443||441894||Ostrich||Struthio camelus australis|| Source material identifiers:Oliver Ryder (San Dieg...|
Estimated genome size:2.16
... Source material identifiers:Oliver Ryder (San Diego Zoo)
Estimated genome size:2.16
Geographic location (country and/or sea,region):Botswana
Geographic location (latitude and longitude):not recorded
IUCN Red List:LC
Sample contact:Oliver Ryder
Sample source:San Diego Zoo (originally from Botswana)
Source material identifiers:San Diego Zoo ISIS ID: 202443