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Data released on April 23, 2014

Genomic data of the Crested Ibis (Nipponia nippon).

Gilbert, M, P; Jarvis, E, D; Li, B; Li, C; The Avian Genome Consortium, ; Wang, J; Zhang, G (2014): Genomic data of the Crested Ibis (Nipponia nippon). GigaScience Database. http://dx.doi.org/10.5524/101003 RIS BibTeX Text

The Crested Ibis (Nipponia nippon (Temminck, 1855)) is the only member of the genus Nipponia and also known as the Japanese Crested Ibis (Toki). Originally widespread across China, Japan, Korea, Taiwan and Russia, by 1988 the species had disappeared from nearly all these places, except two surviving breeding pairs in Southern Qinling mountains of Yangxian County, China.
DNA was collected from a female that descended from one of these pairs, belonging to a population now rescued from near extinction. We sequenced the 1.6 Gb genome to a depth of approximately 105X 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 totaled 1.17 Gb, with the contig and scaffold N50 values of 22kb and 5.4Mb respectively. We identified 16,756 protein-coding genes with a mean length of 19.4 kb.

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Related datasets:

doi:10.5524/101003 IsSupplementTo doi:10.5524/101000

Accessions (data included in GigaDB):

BioProject: PRJNA232572
SRA: SRP035852
BioProject: PRJNA308878
SRA: SRP068541

Projects:



Genomic

http://gigadb.org/images/data/cropped/101003.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Crested Ibis128390Crested IbisCrested IbisNipponia nippon Source material identifiers:Shengbin Li & BGI
Estimated genome size:1.6
Funding source:Xian Jiaotong University
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SZYD11111235_A128390Crested IbisCrested IbisNipponia nippon Alternative accession-biosample:SAMN04419254
Tissue type:UBERON:0000178(blood)
Collection date:40893
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SZYD11111236_A128390Crested IbisCrested IbisNipponia nippon Alternative accession-biosample:SAMN04419255
Tissue type:UBERON:0000178(blood)
Collection date:40893
...
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SZYD11111237_A128390Crested IbisCrested IbisNipponia nippon Alternative accession-biosample:SAMN04419260
Tissue type:UBERON:0000178(blood)
Collection date:40893
...
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SZYD11111238_A128390Crested IbisCrested IbisNipponia nippon Alternative accession-biosample:SAMN04419258
Tissue type:UBERON:0000178(blood)
Collection date:40893
...
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SZYD11111239_A128390Crested IbisCrested IbisNipponia nippon Alternative accession-biosample:SAMN04419259
Tissue type:UBERON:0000178(blood)
Collection date:40893
...
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SZYD11111240_A128390Crested IbisCrested IbisNipponia nippon Alternative accession-biosample:SAMN04419256
Tissue type:UBERON:0000178(blood)
Collection date:40893
...
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SZYD11111242_A128390Crested IbisCrested IbisNipponia nippon Alternative accession-biosample:SAMN04419253
Tissue type:UBERON:0000178(blood)
Collection date:40893
...
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SZYD11111243_A128390Crested IbisCrested IbisNipponia nippon Alternative accession-biosample:SAMN04419257
Tissue type:UBERON:0000178(blood)
Collection date:40893
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Displaying 1-9 of 9 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 
Crested IbisCoding sequenceFASTA6.88 MB2014-04-23
Crested IbisSequence assemblyFASTA359.76 MB2014-04-23
Crested IbisAnnotationGFF1.71 MB2014-04-23
Crested IbisProtein sequenceFASTA4.46 MB2014-04-23
Crested IbisRepeat sequenceUNKNOWN8.17 MB2014-04-23
Displaying 1-5 of 5 File(s).

History:

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