High-coverage sequencing and annotated assemblies of the budgerigar genome

Ganeshkumar Ganapathy; Jason T Howard; James M Ward; Jianwen Li; Bo Li; Yingrui Li; Yingqi Xiong; Yong Zhang; Shiguo Zhou; David C Schwartz; Michael Schatz; Robert Aboukhalil; Olivier Fedrigo; Lisa Bukovnik; Ty Wang; Greg Wray; Isabelle Rasolonjatovo; Roger Winer; James R Knight; Sergey Koren; Wesley C Warren; Guojie Zhang; Adam M Phillippy; Erich D Jarvis

doi:10.1186/2047-217X-3-11

High-coverage sequencing and annotated assemblies of the budgerigar genome

Gigascience. 2014 Jul 8:3:11. doi: 10.1186/2047-217X-3-11. eCollection 2014.

Authors

Ganeshkumar Ganapathy¹, Jason T Howard¹, James M Ward², Jianwen Li³, Bo Li³, Yingrui Li³, Yingqi Xiong³, Yong Zhang³, Shiguo Zhou⁴, David C Schwartz⁴, Michael Schatz⁵, Robert Aboukhalil⁵, Olivier Fedrigo⁶, Lisa Bukovnik⁷, Ty Wang², Greg Wray⁸, Isabelle Rasolonjatovo⁹, Roger Winer¹⁰, James R Knight¹⁰, Sergey Koren¹¹, Wesley C Warren¹², Guojie Zhang³, Adam M Phillippy¹¹, Erich D Jarvis¹

Affiliations

¹ Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
² National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Research Triangle Park, Raleigh, NC 27709, USA.
³ China National Genebank, BGI-Shenzhen, Shenzhen 518083, China.
⁴ Department of Chemistry, The Laboratory for Molecular and Computational Genomics, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, Madison, WI 53706, USA.
⁵ Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA.
⁶ Institute for Genome Sciences & Policy, Duke University, Durham, NC 27710, USA.
⁷ Institute for Genome Sciences & Policy, Duke University, Durham, NC 27710, USA ; Advanced Liquid Logic Morrisville, Morrisville, NC 27560, USA.
⁸ Department of Biology, Center for Systems Biology, Duke University, Durham, NC 27710, USA.
⁹ Illumina Cambridge Ltd, Cambridge, UK.
¹⁰ 454 Life Sciences, Branford, Connecticut 06405, USA.
¹¹ Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20740, USA ; National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702, USA.
¹² The Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA.

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.

Keywords: Budgerigar; Hybrid assemblies; Melopsittacus undulatus; Next-generation sequencing; Optical maps; Parakeet; Vocal learning.

Grants and funding

T32 GM065094/GM/NIGMS NIH HHS/United States