Genomic data from the domestic pigeon (Columba livia).

Dataset type: Genomic
Data released on July 06, 2011

Gilbert MTP; Li C; Wang J; Zhang G (2011): Genomic data from the domestic pigeon (Columba livia). GigaScience. http://dx.doi.org/10.5524/100007

DOI10.5524/100007

The domestic pigeon (Columba livia domestica) is one of the most common birds on planet Earth, located on every continent besides Antarctica. The sub-species sequenced was a breed known as the Danish Tumbler, a show pigeon with a distinct color markings. The domestic pigeon genome sequence provides a better understanding of such a widespread creature, including certain mechanisms that scientists still fail to understand fully, such as the magnetosensitivity. The sequencing data also presents insight into the species’ similarities to and differences from other birds, and to how breeding might have shaped its genome as this sub-species was taken from Asian colonies to Denmark 400 years ago and selectively bred. In 2010, BGI used the whole genome shotgun sequencing and IlluminaHiseq 2000 system to generate 98X short reads for a Danish Tumbler. The raw data was then used by the assembler SOAPdenovo to produce a draft assembly of 1.1 Gb with N50 scaffold length of 3.1Mb and N50 contig length of 22.4 Kb. Based on the k-mer distribution of sequencing data, the genome size of Columba livia is estimated to be 1.3 Gb, suggesting the current assembly is about 84% complete. The percentage of GC content (41.5%) and the percentage of repetitive content (8.7%) in the pigeon are also similar in nature to three other avian genomes (chicken, zebra finch, turkey); the uncovered regions of the genome appear to be enriched in repeats. A total of 17,300 protein-coding genes are predicted in the assembly.

Additional details

Read the peer-reviewed publication(s):

Shapiro, M. D., Kronenberg, Z., Li, C., Domyan, E. T., Pan, H., Campbell, M., … Wang, J. (2013). Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon. Science, 339(6123), 1063–1067. doi:10.1126/science.1230422 (PubMed: 23371554)
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

Accessions (data included in GigaDB):

GENBANK: AKCR00000000
BioProject: PRJNA167554

Accessions (data not in GigaDB):

SRA: SRA052637
GEO: GSE39333
SRA: SRA054391

Projects:







Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Danish Tumbler8932Domestic pigeonRock pigeonColumba livia Source material identifiers:Tom Gilbert
Estimated genome size:1.5
Funding source:BGI, Copenhagen
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Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Danish TumblerCoding sequenceFASTA6.83 MB2014-02-18
Danish TumblerSequence assemblyFASTA323.63 MB2014-02-18
Danish TumblerAnnotationGFF1.7 MB2014-02-18
Danish TumblerProtein sequenceFASTA4.43 MB2014-02-18
Danish TumblerTextFASTA8.09 MB2014-02-18
Danish TumblerSequence assemblyFASTA298.21 MB2011-07-06
Danish TumblerReadmeTEXT0.13 KB2011-07-06
Displaying 1-7 of 7 File(s).
Date Action
October 14, 2015 File Columba_livia.cds.gz updated
October 14, 2015 File Columba_livia.fa.gz updated
October 14, 2015 File Columba_livia.gff.gz updated
October 14, 2015 File Columba_livia.pep.gz updated
October 26, 2015 File Columba_livia.pep.gz updated
October 26, 2015 File Columba_livia.pep.gz updated