Genomic data from King penguin (Aptenodytes patagonicus).
Dataset type: Genomic
Data released on September 17, 2019
Pan H; Cole T; Couto A; Bi X; Machado AM; Brejova B; Fang M; Albertin CB; Zhou C; Silva F; Yang Z; Gardner P; Ksepka DT; Baril T; Hart T; Bouzat JL; Hayward A; Argilla LS; Campos A; Bertelsen MF; ; Barrio-Hernandez I; Boersma PD; Bost C; Hoving H; Cherel Y; Tafur-Jimenez R; Chu C; Dann P; Fiddaman SR; Frazão B; Howard P; Petersen B; Labuschagne K; Penaloza F; Mattern T; Musacchia F; Alexander Jr. GC; Miller G; Osório H; Parker P; Phillips RA; Winkelmann I; Quillfeldt P; Simakov O; Rasmussen S; Ryan PG; Rahman MZ; Taylor H; Pisani D; Thompson DR; Jarvis ED; Young MJ; Ellegaard MR; Zhang G; Gilbert MTP; Vinther J; Sinding MS; Strugnell JM; C. Castro LF; Pacheco G; Fedrigo O; Shepherd LD; D Tennyson AJ; Patricio M; Grosser S; Li Q; Kay E; Rocha S; Antunes A; Nupen LJ; Ellenberg U; Wu Y; Houston DM; Ma B; Reeve AH; Sanges R; Johnson K; Vinar T; Blagoev B; Masello JF; Sicheritz-Ponten T; Stracke T; McKinlay B; Nielsen R; García Borboroglu P; Gilbert MTP; Zhang DX; Zhang G (2019): Genomic data from King penguin (Aptenodytes patagonicus). GigaScience Database. https://doi.org/10.5524/102182
The King penguin is the second largest species of penguin. They have a circumpolar range, breeding on the subantarctic islands at the northern reaches of Antarctica, South Georgia, and other temperate islands. They were heavily hunted for oil on Macquarie Island. King penguins appear to have suffered a major population declines, and 70% are expected to disappear in the next eighty years, however they are still considered as Least Concern by the International Union for Conservation of Nature (IUCN).
We sequenced the genome of an adult King penguin from Fortuna Bay, South Georgia (provided by Tom Hart) to a depth of approximately 120x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.24Gb, with the contig and scaffold N50 values of 114.03Kb and 2.77Mb respectively. We identified 15195 protein-coding genes.
Keywords:
- genomics
- sphenisciformes
- comparative evolution
- phylogenetics
- speciation
- biogeography
- demography
- climate change
- antarctica
- evolution
Additional details
Related datasets:
doi:10.5524/102182 IsPartOf doi:10.5524/100649
Accessions (data included in GigaDB):
BioSample: SAMN12384866
Click on a table column to sort the results.
Table Settings| Sample ID | Common Name | Scientific Name | Sample Attributes | Taxonomic ID | Genbank Name |
|---|---|---|---|---|---|
| KP FORT 001 | Aptenodytes patagonicus | Description:DNA extracted from the blood of a wild... Common name:King Sample type:Wild ... |
9234 | king penguin |
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Table Settings| File Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
|---|---|---|---|---|---|---|---|---|
| Readme | TEXT | 2.48 kB | 2019-09-03 | MD5 checksum: e6818770a75618f5e25d73f08dd94b60 |
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| coding gene nucleotide sequences (fasta) | Coding sequence | FASTA | 22.21 MB | 2019-09-03 | MD5 checksum: 0ad837f95a360fc6c50e1ea6e0057df7 |
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| assembled genome from sequence data | Genome sequence | FASTA | 370.57 MB | 2019-09-03 | MD5 checksum: 183def2fae842a79dc49d7f84ae365a4 |
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| coding gene sequence annotations of assembled genome | Annotation | GFF | 12.42 MB | 2019-09-03 | MD5 checksum: ea426aec10287811b0d7db11e701af1e |
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| amino acid translation of the coding gene sequence predictions | Protein sequence | FASTA | 8.33 MB | 2019-09-03 | MD5 checksum: d73e72584e3f831fc04d6ee56363efd6 |
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| BUSCO output files | Other | UNKNOWN | 986 B | 2019-09-03 | MD5 checksum: 7f49ea2a9df7be5b289776430b64fe81 |
| 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 |
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