High-coverage sequencing and annotated assemblies of the budgerigar genome

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dc.contributor.authorGanapathy, Ganeshkumar
dc.contributor.authorHoward, Jason T
dc.contributor.authorWard, James M
dc.contributor.authorLi, Jianwen
dc.contributor.authorLi, Bo
dc.contributor.authorLi, Yingrui
dc.contributor.authorXiong, Yingqi
dc.contributor.authorZhang, Yong
dc.contributor.authorZhou, Shiguo
dc.contributor.authorSchwartz, David C
dc.contributor.authorSchatz, Michael
dc.contributor.authorAboukhalil, Robert
dc.contributor.authorFedrigo, Olivier
dc.contributor.authorBukovnik, Lisa
dc.contributor.authorWang, Ty
dc.contributor.authorWray, Greg
dc.contributor.authorRasolonjatovo, Isabelle
dc.contributor.authorWiner, Roger
dc.contributor.authorKnight, James R
dc.contributor.authorKoren, Sergey
dc.contributor.authorWarren, Wesley C
dc.contributor.authorZhang, Guojie
dc.contributor.authorPhillippy, Adam M
dc.contributor.authorJarvis, Erich D
dc.date.accessioned2021-10-25T15:12:18Z
dc.date.available2021-10-25T15:12:18Z
dc.date.issued2014-07-08
dc.description.abstractParrots 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. 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. 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.en_US
dc.description.urihttps://doi.org/10.1186/2047-217X-3-11
dc.identifierhttps://doi.org/10.13016/xoar-m25o
dc.identifier.citationGanapathy, G., Howard, J.T., Ward, J.M. et al. High-coverage sequencing and annotated assemblies of the budgerigar genome. GigaSci 3, 11 (2014).en_US
dc.identifier.urihttp://hdl.handle.net/1903/28060
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtCollege of Computer, Mathematical & Physical Sciencesen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtBiologyen_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectMelopsittacus undulatusen_US
dc.subjectBudgerigaren_US
dc.subjectParakeeten_US
dc.subjectNext-generation sequencingen_US
dc.subjectHybrid assembliesen_US
dc.subjectOptical mapsen_US
dc.subjectVocal learningen_US
dc.titleHigh-coverage sequencing and annotated assemblies of the budgerigar genomeen_US
dc.typeArticleen_US

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