The Humboldt penguin inhabits coastal Chile and Peru. They nest on islands and rocky coasts, holes in guano and in caves. Humboldt penguin populations are declining, and the International Union for Conservation of Nature (IUCN) classifies them as vulnerable.
We sequenced the genome of an adult Humboldt penguin from Copenhagen Zoo, of Peru and Chile lineage (provided by Mads Bertelsen) to a depth of approximately 172x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.21Gb, with the contig and scaffold N50 values of 19.38Kb and 5.94Mb respectively. We identified 16587 protein-coding genes.

Additional details

Related datasets:

doi:10.5524/102176 IsPartOf doi:10.5524/100649

Accessions (data generated as part of this study):

BioSample: SAMN12384883





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Z-67-159240 Humboldt's penguinSpheniscus humboldti Description:DNA extracted from the blood of a capt...
Common name:Humboldt
Sample type:Captive
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Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Z-67-15otherUNKNOWN0.98 KB2019-09-03
readmeTEXT2.2 KB2019-09-03
Z-67-15Coding SequenceFASTA23.3 MB2019-09-03
Z-67-15Genome sequenceFASTA350.53 MB2019-09-03
Z-67-15annotationGFF14.15 MB2019-09-03
Z-67-15protein sequenceFASTA8.82 MB2019-09-03
Displaying 1-6 of 6 File(s).
Funding body Awardee Award ID Comments
Carlsbergfondet G Zhang CF CF16-0663
Ministry of Science and Technology (MOST) G Zhang 2018YFC1406901 National Key Research and Development Program
Chinese Academy of Sciences G Zhang XDB13000000 Strategic Priority Research Program
Chinese Academy of Sciences G Zhang XDB31020000 Strategic Priority Research Program
Lundbeckfonden G Zhang R190-2014-2827
Villum Fonden G Zhang 25900
European Research Council MTP Gilbert 681396 Extinction Genomics - Consolidator Grant
Shenzhen Municipality G Zhang JCYJ20170817150239127 Science Technology and Innovation Commission
Shenzhen Municipality G Zhang JCYJ20170817150721687 Science Technology and Innovation Commission
Date Action
September 17, 2019 Dataset publish