Genomic data of the Great-crested grebe (Podiceps cristatus).

Dataset type: Genomic
Data released on May 20, 2014

Zhang G; Li B; Li C; Gilbert MTP; Jarvis ED; The Avian Genome Consortium ; Wang J (2014): Genomic data of the Great-crested grebe (Podiceps cristatus). GigaScience Database. http://dx.doi.org/10.5524/101036

DOI10.5524/101036

The Great Crested Grebe (Podiceps cristatus cristatus (Linnaeus, 1758)) is known for its elaborate mating display and is the largest member of the Grebe family in the Old World. In the 19th century, the species was almost hunted to extinction in the UK for its head plumes, which were used to decorate hats and other female attire.
These data have been produced as part of the Avian Phylogenomics Project. DNA was collected from a vouchered tissue sample (137837) at the Natural History Museum of Denmark, of a male caught in Denmark. We sequenced the genome to a depth of approximately 30X.
The assembled scaffolds of high quality sequences total 1.15Gb, with the contig and scaffold N50 values of 13kb and 30kb respectively. We identified 13,913 protein-coding genes with a mean length of 10.4kb.

Additional details

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

Related datasets:

doi:10.5524/101036 IsSupplementTo doi:10.5524/101000

Accessions (data generated as part of this study):

BioProject: PRJNA212905
SRA: SRP029346

Projects:







Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Great-crested grebe -137837345573Great-crested grebegreat crested grebePodiceps cristatus Source material identifiers:Tom Gilbert
Estimated genome size:unknown size
Funding source:BGI
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Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Great-crested grebe -137837Coding sequenceFASTA4.84 MB2014-02-07
Great-crested grebe -137837Sequence assemblyFASTA341.24 MB2014-02-07
Great-crested grebe -137837AnnotationGFF1.2 MB2014-02-07
Great-crested grebe -137837Protein sequenceFASTA3.15 MB2014-02-07
Great-crested grebe -137837Repeat sequenceUNKNOWN8.39 MB2014-02-07
Displaying 1-5 of 5 File(s).
Date Action
October 30, 2015 File Podiceps_cristatus.cds.gz updated
October 30, 2015 File Podiceps_cristatus.cds.gz updated
October 30, 2015 File Podiceps_cristatus.gff.gz updated
October 30, 2015 File Podiceps_cristatus.pep.gz updated
October 30, 2015 File Podiceps_cristatus.pep.gz updated
October 30, 2015 File Podiceps_cristatus.pep.gz updated
October 30, 2015 File Podiceps_cristatus.cds.gz updated
October 30, 2015 File Podiceps_cristatus.cds.gz updated
October 30, 2015 File Podiceps_cristatus.cds.gz updated
October 30, 2015 File Podiceps_cristatus.cds.gz updated
October 30, 2015 File Podiceps_cristatus.gff.gz updated
October 30, 2015 File Podiceps_cristatus.pep.gz updated