Help Login Create account

Data released on April 24, 2014

Genomic

Genomic data of the Anna's Hummingbird (Calypte anna).

Zhang, G; Li, B; Li, C; Gilbert,M.T.P.; Mello, C.V. ; Jarvis, E.D.; The Avian Genome Consortium; Wang,J (2014): Genomic data of the Anna's Hummingbird (Calypte anna). GigaScience Database. http://dx.doi.org/10.5524/101004 RIS BibTeX Text

The Anna's Hummingbird (Calypte anna (Lesson, 1829)) is a medium-sized hummingbird native to the west coast of North America and is the only North American hummingbird species with a red crown. It belongs to one of the rare groups of vocal learning birds. The bird was named after Anna Massena, Duchess of Rivoli.
These data have been produced as part of the G10K and Avian Phylogenomics Project. DNA was collected from from a female, which was caught in Portland, Oregan, USA by Claudio Mello and Pete Lovell. We sequenced the 1 Gb genome to a depth of approximately 110X 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 1.1Gb, with the contig and scaffold N50 values of 23 kb and 4Mb respectively. We identified 16,000 protein-coding genes with a mean length of 18.5kb.

Related manuscripts:

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

Related datasets:

doi:10.5524/101004 IsSupplementTo doi:10.5524/101000

Accessions (data included in GigaDB):

BioProject: PRJNA212866
SRA: SRP028275

Projects:



Samples:

Sample ID Taxonomic ID Common name Genbank name Scientific name Sample attributes
Annas hummingbird -A9 9244 Annas hummingbird Annas hummingbird Calypte anna short_name="CALAN"
BioMaterial_ref="Erich Jarvis & Claudio Mello"
funding_source="BGI"
sample_source=""
source material identifiers="CNN11DN01"
est_genome_size="1"
ploidy="diploid"
tissue_type="UBERON:0000178(blood), UBERON:0002107(liver), UBERON:0001015(muscle)"
geographic location (country and/or sea,region)="USA, Oregan, Portland"
geographic location (latitude and longitude)="not recorded"
sex="F"
IUNC_Red_List="LC"
Sample_contact="Claudio Mello & Christopher Olson OHSU"

Files (FTP site) (Aspera):Aspera user name: gigadb , password: gigadb Table Settings
Items per page:

File Name Sample ID File Type File Format Size Release Date

Calypte_anna.cds.gz

Anna's hummingbird -A9 Coding sequence FASTA 2 7 69850166.66 MB 2014-04-24

Calypte_anna.fa.gz

Anna's hummingbird -A9 Genome assembly FASTA 2 9 332584370317.18 MB 2014-04-24

Calypte_anna.gff.gz

Anna's hummingbird -A9 Annotation GFF 2 7 17343171.65 MB 2014-04-24

Calypte_anna.pep.gz

Anna's hummingbird -A9 Protein sequence FASTA 2 7 45548044.34 MB 2014-04-24

Caprimugus_Carolinensis.RepeatMasker.out.gz

Anna's hummingbird -A9 other UNKNOWN 2 8 100223919.56 MB 2014-04-24