Genomic data of the Killdeer (Charadrius vociferus).

Dataset type: Genomic
Data released on April 25, 2014

Gilbert MTP; Jarvis ED; Li B; Li C; The Avian Genome Consortium ; Wang J; Zhang G (2014): Genomic data of the Killdeer (Charadrius vociferus). GigaScience Database. http://dx.doi.org/10.5524/101007

DOI10.5524/101007

The Killdeer (Charadrius vociferus vociferus (Linnaeus, 1758)) is a medium-sized plover (a wading bird belonging to the subfamily Charadriinae), and often uses a "broken wing act" to distract predators from their nests.
These data have been produced as part of the G10K and Avian Phylogenomics Project. DNA was collected from a vouchered tissue sample (B-66055) from the Louisiana State University Museum, of a female, subspecies peruvianus, caught in Loreto, Peru. 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 1.2 Gb, with the contig and scaffold N50 values of 32 kb and 3.6Mb respectively. We identified 16,856 protein-coding genes with a mean length of 19.1kb.

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:10.5524/101007 IsSupplementTo doi:10.5524/101000

Accessions (data included in GigaDB):

BioProject: PRJNA212867
SRA: SRP028286

Projects:







Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Killdeer -B-6605550402Killdeer Charadrius vociferus Source material identifiers:Erich Jarvis
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 
Killdeer -B-66055Coding sequenceFASTA6.74 MB2014-04-25
Killdeer -B-66055Sequence assemblyFASTA354.94 MB2014-04-25
Killdeer -B-66055AnnotationGFF1.67 MB2014-04-25
Killdeer -B-66055Protein sequenceFASTA4.36 MB2014-04-25
Killdeer -B-66055Repeat sequenceUNKNOWN8.23 MB2014-04-25
Displaying 1-5 of 5 File(s).
Date Action
October 14, 2015 File Charadrius_vociferus.cds.gz updated
October 14, 2015 File Charadrius_vociferus.fa.gz updated
October 14, 2015 File Charadrius_vociferus.gff.gz updated
October 14, 2015 File Charadrius_vociferus.pep.gz updated