Genomic data of the Golden-collared Manakin (Manacus vitellinus).

Dataset type: Genomic
Data released on April 26, 2014

Zhang G; Li B; Li C; Gilbert MTP; Schlinger B; Jarvis ED; The Avian Genome Consortium ; Wang J (2014): Genomic data of the Golden-collared Manakin (Manacus vitellinus). GigaScience Database. http://dx.doi.org/10.5524/101010

DOI10.5524/101010

The Golden-collared Manakin (Manacus vitellinus (Gould, 1843)) belongs to the Pipridae family of suboscine passseriform birds. It is commonly found in Colombia, Costa Rica and Panama.
These data have been produced as part of the G10K and Avian Phylogenomics Project. DNA was collected from a male obtained in Gamboa, Panama, with the sample obtained by Barney Schlinger of UCLA. We sequenced the 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 1.12Gb, with the contig and scaffold N50 values of 34kb and 2.5Mb respectively. We identified 15,285 protein-coding genes with a mean length of 18.8kb.

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:10.5524/101010 IsSupplementTo doi:10.5524/101000

Accessions (data generated as part of this study):

BioProject: PRJNA212872
SRA: SRP028393

Projects:







Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Golden-collared Manakin328815Golden-collared ManakinGolden-collared ManakinManacus vitellinus Source material identifiers:Erich Jarvis
Estimated genome size:unknown size
Funding source:BGI
...
+
Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Golden-collared ManakinCoding sequenceFASTA6.41 MB2014-04-26
Golden-collared ManakinSequence assemblyFASTA335.18 MB2014-04-26
Golden-collared ManakinAnnotationGFF1.6 MB2014-04-26
Golden-collared ManakinProtein sequenceFASTA4.17 MB2014-04-26
Golden-collared ManakinRepeat sequenceUNKNOWN9.53 MB2014-04-26
Displaying 1-5 of 5 File(s).
Date Action
October 28, 2015 File Manacus_vitellinus.gff.gz updated