Genomic data of the Downy Woodpecker (Picoides pubescens).

Dataset type: Genomic
Data released on April 28, 2014

Zhang G; Li B; Li C; Gilbert MTP; Jarvis ED; The Avian Genome Consortium ; Wang J (2014): Genomic data of the Downy Woodpecker (Picoides pubescens). GigaScience Database. http://dx.doi.org/10.5524/101012

DOI10.5524/101012

The Downy Woodpecker (Picoides pubescens (Linnaeus, 1766)) is the smallest of its kind in North America. It uses a number of vocalizations, including a short 'pik' call and produces a slow drumming sound while it pecks into trees compared with other North American woodpeckers.
These data have been produced as part of the G10K and Avian Phylogenomics Project. DNA was collected from a vouchered tissue sample (B-21955) from the Louisiana State University Museum, of a female caught in Marcum Mountain, Cowell County, Montana, USA. We sequenced the genome to a depth of approximately 105X 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 1.17Gb, with the contig and scaffold N50 values of 20kb and 2Mb respectively. We identified 15,576 protein-coding genes with a mean length of 20kb.

Additional details

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:10.5524/101012 IsSupplementTo doi:10.5524/101000

Accessions (data generated as part of this study):

BioProject: PRJNA212874
SRA: SRP028625

Projects:







Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Downy Woodpecker-B-21955, B-21955118200Downy WoodpeckerDowny WoodpeckerPicoides pubescens Source material identifiers:Erich Jarvis
Estimated genome size:unknown size
Funding source:BGI
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Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Downy Woodpecker-B-21955, B-21955Coding sequenceFASTA6.5 MB2014-04-28
Downy Woodpecker-B-21955, B-21955Sequence assemblyFASTA331.82 MB2014-04-28
Downy Woodpecker-B-21955, B-21955AnnotationGFF1.62 MB2014-04-28
Downy Woodpecker-B-21955, B-21955Protein sequenceFASTA4.24 MB2014-04-28
Downy Woodpecker-B-21955, B-21955OtherUNKNOWN22.99 MB2014-04-28
Displaying 1-5 of 5 File(s).
Date Action
October 30, 2015 File Picoides_pubescens.cds.gz updated
October 30, 2015 File Picoides_pubescens.fa.gz updated
October 30, 2015 File Picoides_pubescens.gff.gz updated
October 30, 2015 File Picoides_pubescens.pep.gz updated