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Data released on January 23, 2014

Genome sequence of the duck (Anas platyrhynchos).

Burt, D, W; Chen, H; Gan, S; Huang, Y; Kim, H; Li, J; Li, Y; Qian, W; Zhang, Y; Zhao, Y; Feng, H; Yi, K; Zhu, P; Li, B; Liu, Q; Du, Z; Fairley, S; Hu, X; Magor, K, E; Goodman, L; Tafer, H; Vignal, A; Lee, T; Kim, K; Sheng, Z; An, Y; Searle, S; Herrero, J; Groenen, M, A; Crooijmans, R, P; Faraut, T; Cai, Q; Webster, R, G; Aldridge, J, R; Warren, W, C; Bartschat, S; Kehr, S; Marz, M; Stadler, P, F; Smith, J; Kraus, R, H; Zhao, Y; Ren, L; Fei, J; Morisson, M; Kaiser, P; Griffin, D, K; Rao, M; Pitel, F; Wang, J; Li, N (2014): Genome sequence of the duck (Anas platyrhynchos). GigaScience Database. http://dx.doi.org/10.5524/101001 RIS BibTeX Text

Available here is the first draft genomic sequence of the duck (Anas platyrhynchos). Duck is a member of Anatidae, a family of birds that include geese and swans. However, duck is an economically important waterfowl serving as a source of meat, eggs and feathers; though, of special interest to agriculture and medicine is that fact that the duck is a principal natural host of influenza A viruses and harbours all subtypes of 16 haemagglutinin and 9 neuraminidase subtypes currently known, except for H13 and H16 subtypes.
Using llumina Genome Analyser sequencing technology the genome of a 10-week old female Beijing duck was sequenced and a total 77 Gb of paired-end reads (approximately 64-fold coverage of the whole genome) was generated with an average length of 50 bp. Using SOAPdenovo to combine short reads, a draft genome assembly was constructed consisting of 78,487 scaffolds and covered 1.1 Gb. The contig N50 and scaffold N50 values were 26 kb and 1.2 Mb respectively. Super scaffolds were constructed and chromosomal sequences created according to the duck genetic map – this resulted in 47 superscaffolds which contained 225 scaffolds and spanned 289 Mb. Transcriptomes were also generated from several different tissues, comprising 1.87 million ESTs, and approximately 121 million 75-bp and 917 million 90-bp paired-end reads, which were generated using either the 454/Roche Life Sciences Analyzer or Illumina Genome sequencing technology.

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Related manuscripts:

doi:10.1038/ng.2657 (PubMed: 23749191)
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Related datasets:

doi:10.5524/101001 IsSupplementTo doi:10.5524/101000

Genome browser:

http://asia.ensembl.org/Anas_platyrhynchos/Info/Index

Accessions (data included in GigaDB):

BioProject: PRJNA46621

Accessions (data not in GigaDB):

BioProject: PRJNA194464
GEO: GSE22967

Projects:



Genomic

http://gigadb.org/images/data/cropped/101001_Duck.png

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Pekin duck8839Mallard duckmallardAnas platyrhynchos Estimated genome size:1.4
Funding source:China Agriculctural University
Geographic location (country and/or sea,region):Ch...
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Displaying 1-1 of 1 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
Pekin duckCoding sequenceFASTA21.5 MB2015-08-03
Pekin duckOtherUNKNOWN7.79 MB2015-03-23
Pekin duckAnnotationGFF10.1 MB2015-08-03
Pekin duckProtein sequenceFASTA7.8 MB2015-08-03
Pekin duckSequence assemblyFASTA1.03 GB2013-01-23
DirectoryUNKNOWN50 MB2015-08-03
ReadmeTEXT0.33 KB2013-01-23
Displaying 1-7 of 7 File(s).

History:

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