TY - JOUR

T1 - High-coverage sequencing and annotated assemblies of the budgerigar genome

AU - Ganapathy, Ganeshkumar

AU - Howard, Jason T.

AU - Ward, James M.

AU - Li, Jianwen

AU - Li, Bo

AU - Li, Yingrui

AU - Xiong, Yingqi

AU - Zhang, Yong

AU - Zhou, Shiguo

AU - Schwartz, David C.

AU - Schatz, Michael

AU - Aboukhalil, Robert

AU - Fedrigo, Olivier

AU - Bukovnik, Lisa

AU - Wang, Ty

AU - Wray, Greg

AU - Rasolonjatovo, Isabelle

AU - Winer, Roger

AU - Knight, James R.

AU - Koren, Sergey

AU - Warren, Wesley C.

AU - Zhang, Guojie

AU - Phillippy, Adam M.

AU - Jarvis, Erich D.

PY - 2014/7/8

Y1 - 2014/7/8

N2 - 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.

AB - 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.

KW - Budgerigar

KW - Hybrid assemblies

KW - Melopsittacus undulatus

KW - Next-generation sequencing

KW - Optical maps

KW - Parakeet

KW - Vocal learning

U2 - 10.1186/2047-217X-3-11

DO - 10.1186/2047-217X-3-11

M3 - Journal article

AN - SCOPUS:84921918950

VL - 3

JO - GigaScience

JF - GigaScience

SN - 2047-217X

IS - 1

M1 - 11

ER -