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Data released on April 25, 2014

Genomic

Genomic data of the Killdeer (Charadrius vociferus).

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

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.

Related manuscripts:

doi:10.1186/2047-217X-3-26
doi:10.1126/science.1251385
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:



Samples:

Sample ID Taxonomic ID Common name Genbank name Scientific name Sample attributes
Killdeer -B-66055 50402 Killdeer Charadrius vociferus short_name="CHAVO"
BioMaterial_ref="Erich Jarvis"
funding_source="BGI"
sample_source="Peru: Loreto Department: Tumbes 25km SE Zorritos, 3° 49' 1"
80° 29' 19" W", source material identifiers="CVC11DN01"
est_genome_size="unknown size"
ploidy="diploid"
tissue_type="UBERON:0000479(tissue)"
geographic location (country and/or sea,region)="Peru, Loreto Department"
geographic location (latitude and longitude)=" -3.816944, -80.488611"
sex="F"
IUNC_Red_List="LC"
Sample_contact="Elizabeth Derryberry -LSU"

Files (FTP site) (Aspera):Aspera user name: gigadb , password: gigadb Table Settings
Items per page:

File Name Sample ID File Type File Format Size Release Date

Charadrius_vociferus.cds.gz

Killdeer -B-66055 Coding sequence FASTA 2 7 70682526.74 MB 2014-04-25

Charadrius_vociferus.fa.gz

Killdeer -B-66055 Genome assembly FASTA 2 9 372181513354.94 MB 2014-04-25

Charadrius_vociferus.gff.gz

Killdeer -B-66055 Annotation GFF 2 7 17553611.67 MB 2014-04-25

Charadrius_vociferus.pep.gz

Killdeer -B-66055 Protein sequence FASTA 2 7 45755404.36 MB 2014-04-25

Charadrius_vociferus.RepeatMasker.out.gz

Killdeer -B-66055 other UNKNOWN 2 7 86246608.23 MB 2014-04-25