title: High-coverage sequencing and annotated assemblies of the budgerigar genome.
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.
  
  
  RESULTS
  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.
authors: Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
authors: Ganeshkumar
authors: G
authors: Ganapathy
authors: Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
authors: Jason T
authors: JT
authors: Howard
authors: National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Research Triangle Park, Raleigh, NC 27709, USA.
authors: James M
authors: JM
authors: Ward
authors: China National Genebank, BGI-Shenzhen, Shenzhen 518083, China.
authors: Jianwen
authors: J
authors: Li
authors: China National Genebank, BGI-Shenzhen, Shenzhen 518083, China.
authors: Bo
authors: B
authors: Li
authors: China National Genebank, BGI-Shenzhen, Shenzhen 518083, China.
authors: Yingrui
authors: Y
authors: Li
authors: China National Genebank, BGI-Shenzhen, Shenzhen 518083, China.
authors: Yingqi
authors: Y
authors: Xiong
authors: China National Genebank, BGI-Shenzhen, Shenzhen 518083, China.
authors: Yong
authors: Y
authors: Zhang
authors: Department of Chemistry, The Laboratory for Molecular and Computational Genomics, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, Madison, WI 53706, USA.
authors: Shiguo
authors: S
authors: Zhou
authors: Department of Chemistry, The Laboratory for Molecular and Computational Genomics, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, Madison, WI 53706, USA.
authors: David C
authors: DC
authors: Schwartz
authors: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA.
authors: Michael
authors: M
authors: Schatz
authors: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA.
authors: Robert
authors: R
authors: Aboukhalil
authors: Institute for Genome Sciences & Policy, Duke University, Durham, NC 27710, USA.
authors: Olivier
authors: O
authors: Fedrigo
authors: Institute for Genome Sciences & Policy, Duke University, Durham, NC 27710, USA ; Advanced Liquid Logic Morrisville, Morrisville, NC 27560, USA.
authors: Lisa
authors: L
authors: Bukovnik
authors: National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Research Triangle Park, Raleigh, NC 27709, USA.
authors: Ty
authors: T
authors: Wang
authors: Department of Biology, Center for Systems Biology, Duke University, Durham, NC 27710, USA.
authors: Greg
authors: G
authors: Wray
authors: Illumina Cambridge Ltd, Cambridge, UK.
authors: Isabelle
authors: I
authors: Rasolonjatovo
authors: 454 Life Sciences, Branford, Connecticut 06405, USA.
authors: Roger
authors: R
authors: Winer
authors: 454 Life Sciences, Branford, Connecticut 06405, USA.
authors: James R
authors: JR
authors: Knight
authors: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20740, USA ; National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702, USA.
authors: Sergey
authors: S
authors: Koren
authors: The Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA.
authors: Wesley C
authors: WC
authors: Warren
authors: China National Genebank, BGI-Shenzhen, Shenzhen 518083, China.
authors: Guojie
authors: G
authors: Zhang
authors: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20740, USA ; National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702, USA.
authors: Adam M
authors: AM
authors: Phillippy
authors: Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
authors: Erich D
authors: ED
authors: Jarvis
keywords: Budgerigar; Hybrid assemblies; Melopsittacus undulatus; Next-generation sequencing; Optical maps; Parakeet; Vocal learning