Genomic data of the Common Cuckoo (Cuculus canorus).

Dataset type: Genomic
Data released on April 26, 2014

Zhang G; Li B; Li C; Gilbert MTP; Jarvis ED; The Avian Genome Consortium ; Wang J (2014): Genomic data of the Common Cuckoo (Cuculus canorus). GigaScience Database. http://dx.doi.org/10.5524/101009

DOI10.5524/101009

The Common Cuckoo (Cuculus canorus canorus (Linnaeus, 1758)), also known as the European Cuckoo, is a widespread summer migrant to Europe and Asia. It is a brood parasite, meaning it lays eggs in other birds' nests; particularly in Dunnock's, Meadow Pipit's, and Eurasian Reed Warbler's nests.
These data have been produced as part of the G10K and Avian Phylogenomics Projects. DNA was collected from a male specimen in Denmark; voucher 137750 in the Natural History Museum of Denmark. We sequenced the genome to a depth of approximately 100X 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 1.15Gb, with the contig and scaffold N50 values of 31kb and 3Mb respectively. We identified 15,889 protein-coding genes with a mean length of 20kb.

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:10.5524/101009 IsSupplementTo doi:10.5524/101000

Accessions (data included in GigaDB):

BioProject: PRJNA212869
SRA: SRP028317

Projects:







Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Cuckoo -B-45971, TG7, TG855661Common CuckooCommon CuckooCuculus canorus Source material identifiers:Erich Jarvis & Tom Gil...
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 
Cuckoo -B-45971, TG7, TG8Coding sequenceFASTA6.72 MB2014-04-26
Cuckoo -B-45971, TG7, TG8Sequence assemblyFASTA334.25 MB2014-04-26
Cuckoo -B-45971, TG7, TG8AnnotationGFF1.66 MB2014-04-26
Cuckoo -B-45971, TG7, TG8Protein sequenceFASTA4.36 MB2014-04-26
Cuckoo -B-45971, TG7, TG8Repeat sequenceUNKNOWN10.87 MB2014-04-26
Displaying 1-5 of 5 File(s).
Date Action
October 30, 2015 File Cuculus_canorus.cds.gz updated
October 30, 2015 File Cuculus_canorus.gff.gz updated
October 30, 2015 File Cuculus_canorus.pep.gz updated
October 30, 2015 File Cuculus_canorus.pep.gz updated
October 31, 2015 File Cuculus_canorus.cds.gz updated