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Data released on November 13, 2014

Genomic data of the domestic goat (Capra hircus).

Bian, C; Chen, J; Chen, W; Dong, Y; Du, X; Hou, Y; Jiang, Y; Li, J; Li, Y; Liang, J; Liu, X; Moore, R; Nie, W; Pan, S; Sayre, B; Servin, B; Shen, Y; Sweeney, D; Tosser-Klopp, G; Wang, J; Wang, W; Xiao, N; Xie, M; Yang, S; Zeng, P; Zhang, G; Zhang, W; Zhao, R; Zhu, B; Faraut, T; Womack, J; Zhang, Y; Kijas, J; Cockett, N; Xu, X; Zhao, S; Wang, J; Wang, W (2014): Genomic data of the domestic goat (Capra hircus). GigaScience Database. http://dx.doi.org/10.5524/100082 RIS BibTeX Text

The domestic goat is one of the most important livestock species in the world, especially in China, India and other developing countries. Goats not only serve as an important source of meat, milk, fiber and pelts, and have fulfilled agricultural, economic, cultural and even religious roles from very early times in human civilization, but also are now used as animal models for biomedical research and transgene production of protein medicines.We would like to share all the genome data of goat. We hope the genome sequence of goat can provide a new resource for biological research and breeding of goat and other small ruminants.
We sequenced the 2.92 Gb genome to a depth of approximately 65.6 X with short reads from a series of libraries with various insert sizes ( 170 bp, 350 bp, 800 bp, 2 kb, 5 kb, 10 kb and 20 kb) on a HiSeq 2000 sequencer.
The assembled scaffolds of high quality sequences total 191.5 Gb, with the contig and scaffold N50 values of 18.7 kb and 2.21 Mb respectively. We identified 22,175 protein-coding genes. In addition, we also provide the restriction-enzyme fragment maps derived from the whole genome mapping (WGM) technology developed by the Argus System (method described in this paper).
Scaffolds derived from de novo assembly of next-generation sequencing data are converted into restriction maps by in silico restriction enzyme digestion. Then, the distance between restriction enzyme sites in the sequencing-derived scaffolds are matched to the lengths of the optical fragments in the single-molecule WGM restriction maps. Matches allow the scaffolds to be extended and linked into super-scaffolds.

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Related manuscripts:

doi:10.1038/nbt.2478 (PubMed: 23263233)

Accessions (data included in GigaDB):

SRA: SRP012150
BioProject: PRJNA158393

Projects:


Genomic, Genome-Mapping

http://gigadb.org/images/data/cropped/100082.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SRS3094789925domestic goatgoatCapra hircus Geographic location (country and/or sea,region):no...
Geographic location (latitude and longitude):not r...
Ploidy:diploid
...
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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 
SRS309478Coding sequenceFASTA30.54 MB2013-02-20
SRS309478AnnotationGFF14.39 MB2013-02-20
SRS309478Sequence assemblyFASTA2.52 GB2013-02-20
SRS309478Protein sequenceFASTA11.2 MB2013-02-20
SRS309478OtherTEXT244.14 MB2014-10-09
ReadmeTEXT0.33 KB2013-02-20
Displaying 1-6 of 6 File(s).

History:

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