GigaDB Dataset - DOI 10.5524/101026 - Genomic data of the Red throated loon (Gavia stellata).

Data released on May 13, 2014

Genomic data of the Red throated loon (Gavia stellata).

Gilbert, M, P; Jarvis, E, D; Li, B; Li, C; The Avian Genome Consortium, ; Wang, J; Zhang, G (2014): Genomic data of the Red throated loon (Gavia stellata). GigaScience Database. http://dx.doi.org/10.5524/101026 RIS BibTeX Text

The Red-throated Loon (Gavia stellata (Pontoppidan, 1763)), also known as the Red-throated Diver, is a migratory aquatic bird that breeds mainly in the Arctic regions and spends winters in the northern coastal waters. The Red-throated loon has a large global population, making it the most widely distributed member of the Gaviidae (Loon or Diver) family.
These data have been produced as part of the Avian Phylogenomics Project. DNA was collected from a vouchered sample (137940) of Natural History Museum of Denmark from a male caught in Denmark. We sequenced the genome to a depth of approximately 33X.
The assembled scaffolds of high quality sequences total 1.15Gb, with the contig and scaffold N50 values of 16kb and 45kb respectively. We identified 13,454 protein-coding genes with a mean length of 13.2kb.

Read the peer-reviewed publication(s):

Zhang, G., Li, B., Li, C., Gilbert, M. T. P., Jarvis, E. D., & Wang, J. (2014). Comparative genomic data of the Avian Phylogenomics Project. GigaScience, 3(1). doi:10.1186/2047-217x-3-26
Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., … Meredith, R. W. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311–1320. doi:10.1126/science.1251385
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., … Howard, J. T. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320–1331. doi:10.1126/science.1253451

Related datasets:

doi:10.5524/101026 IsSupplementTo doi:10.5524/101000

Accessions (data included in GigaDB):

BioProject: PRJNA212895
SRA: SRP029187

Projects:

Genomic

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

Samples: Table Settings

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Scienfic Name

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Taxonomic ID

Genbank Name

Sample ID	Taxonomic ID	Common Name	Genbank Name	Scientific Name	Sample Attributes
Red throated loon -TG4	37040	Red throated loon		Gavia stellata	Source material identifiers:Tom Gilbert Estimated genome size:unknown size Funding source:BGI ... +

Displaying 1-1 of 1 Sample(s).

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Sample ID

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File Attributes

File Name	Sample ID	Data Type	File Format	Size	Release Date
Gavia_stellata.cds.gz	Red throated loon -TG4	Coding sequence	FASTA	5.14 MB	2014-02-07
Gavia_stellata.fa.gz	Red throated loon -TG4	Sequence assembly	FASTA	339.32 MB	2014-02-07
Gavia_stellata.gff.gz	Red throated loon -TG4	Annotation	GFF	1.27 MB	2014-02-07
Gavia_stellata.pep.gz	Red throated loon -TG4	Protein sequence	FASTA	3.35 MB	2014-02-07
Gavia_stellata.RepeatMasker.out.gz	Red throated loon -TG4	Repeat sequence	UNKNOWN	5.98 MB	2014-02-07