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Data released on May 05, 2014

Genomic data of the Little Egret (Egretta garzetta).

Gilbert, M, P; Jarvis, E, D; Li, B; Li, C; The Avian Genome Consortium, ; Wang, J; Zhang, G (2014): Genomic data of the Little Egret (Egretta garzetta). GigaScience Database. http://dx.doi.org/10.5524/101002 RIS BibTeX Text

The Little Egret (Egretta garzetta (Linnaeus, 1766)) is a small white heron. An adult's average size is 55–65 cm long with an 88–106 cm wingspan, and weighs 350–550 grams. Little egret's are mostly silent birds, but make various croaking and bubbling calls at their breeding colonies and produce a harsh alarm call when disturbed.
These data have been produced as part of a project on deciphering the genomics of near extinction events, with the egret as a control species for the Ibis. DNA from a male in the Southern Qinling Mountains, Yangxian County Reserve, China. We sequenced the genome to a depth of approximately 74X 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 24 kb and 3.1Mb respectively. We identified 16,585 protein-coding genes with a mean length of 18.6 kb.

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Related manuscripts:

doi:10.1186/2047-217X-3-26
doi:10.1126/science.1251385
doi:10.1126/science.1253451

Related datasets:

doi:10.5524/101002 IsSupplementTo doi:10.5524/101000

Accessions (data included in GigaDB):

BioProject: PRJNA232959
SRA: SRP035853
BioProject: PRJNA309350
SRA: SRP068698

Projects:



Genomic

http://gigadb.org/images/data/cropped/bird/egretta_garzetta.png

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Little egret188379Little egretLittle egretEgretta garzetta Source material identifiers:BGI
Estimated genome size:unknown size
Funding source:BGI
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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 
Little egretCoding sequenceFASTA6.34 MB2014-05-05
Little egretSequence assemblyFASTA345.81 MB2014-05-05
Little egretAnnotationGFF1.59 MB2014-05-05
Little egretProtein sequenceFASTA4.09 MB2014-05-05
Little egretRepeat sequenceUNKNOWN8.51 MB2014-05-05
Displaying 1-5 of 5 File(s).

History:

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