Genomic data of the Anna's Hummingbird (Calypte anna).
Dataset type: Genomic
Data released on April 24, 2014
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.
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
Accessions (data included in GigaDB):
|Sample ID||Taxonomic ID||Common Name||Genbank Name||Scientific Name||Sample Attributes|
|Annas hummingbird -A9||9244||Annas hummingbird||Annas hummingbird||Calypte anna|| Source material identifiers:Erich Jarvis & Claudio...|
Estimated genome size:1
... Source material identifiers:Erich Jarvis & Claudio Mello
Estimated genome size:1
Geographic location (country and/or sea,region):United States, Oregan, Portland
Geographic location (latitude and longitude):not recorded
IUCN Red List:LC
Sample contact:Claudio Mello & Christopher Olson OHSU
Source material identifiers:CNN11DN01
Tissue:UBERON:0000178(blood), UBERON:0002107(liver), UBERON:0001015(muscle)