High-coverage sequencing and annotated assemblies of the budgerigar genome

Ganapathy, Ganeshkumar, Howard, Jason T., Ward, James M., Li, Jianwen, Li, Bo, Li, Yingrui, Xiong, Yingqi, Zhang, Yong, Zhou, Shiguo, Schwartz, David C, Schatz, Michael, Aboukhalil, Robert, Fedrigo, Olivier, Bukovnik, Lisa, Wang, Ty, Wray, Greg, Rasolonjatovo, Isabelle, Winer, Roger, Knight, James R., Koren, Sergey, Warren, Wesley C., Zhang, Guojie, Phillippy, Adam M. and Jarvis, Erich D. (2014) High-coverage sequencing and annotated assemblies of the budgerigar genome. GigaScience, 3 11: . doi:10.1186/2047-217X-3-11

Author Ganapathy, Ganeshkumar
Howard, Jason T.
Ward, James M.
Li, Jianwen
Li, Bo
Li, Yingrui
Xiong, Yingqi
Zhang, Yong
Zhou, Shiguo
Schwartz, David C
Schatz, Michael
Aboukhalil, Robert
Fedrigo, Olivier
Bukovnik, Lisa
Wang, Ty
Wray, Greg
Rasolonjatovo, Isabelle
Winer, Roger
Knight, James R.
Koren, Sergey
Warren, Wesley C.
Zhang, Guojie
Phillippy, Adam M.
Jarvis, Erich D.
Title High-coverage sequencing and annotated assemblies of the budgerigar genome
Journal name GigaScience   Check publisher's open access policy
ISSN 2047-217X
Publication date 2014-07-08
Sub-type Article (original research)
DOI 10.1186/2047-217X-3-11
Open Access Status DOI
Volume 3
Issue 11
Total pages 8
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
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 300× 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
Keyword Melopsittacus undulatus
Next-generation sequencing
Hybrid assemblies
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
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Created: Sat, 05 Sep 2015, 02:00:33 EST by Mr Mathew Carter on behalf of Institute for Molecular Bioscience