High-coverage sequencing and annotated assemblies of the budgerigar genome

Ganapathy, G., Howard, J. T., Ward, J. M., Li, J., Li, B., Li, Y., Xiong, Y., Zhang, Y., Zhou, S., Schwartz, D. C., Schatz, M., Aboukhalil, R., Fedrigo, O., Bukovnik, L., Wang, T., Wray, G., Rasolonjatovo, I., Winer, R., Knight, J. R., Koren, S., Warren, W. C., Zhang, G., Phillippy, A. M., Jarvis, E. D. (July 2014) High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience, 3. p. 11. ISSN 2047-217x

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URL: http://www.ncbi.nlm.nih.gov/pubmed/25061512
DOI: 10.1186/2047-217x-3-11

Abstract

BACKGROUND: Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a rhythmic beat, and understand complex concepts of referential meaning to sounds. However, little is known about the genetics of these traits. Elucidating the genetic bases would require whole genome sequencing and a robust assembly of a parrot genome. FINDINGS: We present a genomic resource for the budgerigar, an Australian Parakeet (Melopsittacus undulatus) -- the most widely studied parrot species in neuroscience and behavior. We present genomic sequence data that includes over 300x raw read coverage from multiple sequencing technologies and chromosome optical maps from a single male animal. The reads and optical maps were used to create three hybrid assemblies representing some of the largest genomic scaffolds to date for a bird; two of which were annotated based on similarities to reference sets of non-redundant human, zebra finch and chicken proteins, and budgerigar transcriptome sequence assemblies. The sequence reads for this project were in part generated and used for both the Assemblathon 2 competition and the first de novo assembly of a giga-scale vertebrate genome utilizing PacBio single-molecule sequencing. CONCLUSIONS: Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble, including those not yet assembled in prior bird genomes, and promoter regions of genes differentially regulated in vocal learning brain regions. This work provides valuable data and material for genome technology development and for investigating the genomics of complex behavioral traits.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > de novo assembly
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > genome annotation
Investigative techniques and equipment > assays > next generation sequencing
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Atwal lab
CSHL labs > Schatz lab
Watson School > Publications
Depositing User: Matt Covey
Date: 8 July 2014
Date Deposited: 01 Aug 2014 16:24
Last Modified: 23 Sep 2014 14:04
PMCID: PMC4109783
Related URLs:
URI: http://repository.cshl.edu/id/eprint/30659

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