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De Novo PacBio long-read and phased avian genome assemblies correct and add to genes important in neuroscience research

Jonas Korlach, Gregory Gedman, Sarah B. Kingan, Chen-Shan Chin, Jason Howard, Lindsey Cantin, Erich D. Jarvis
doi: https://doi.org/10.1101/103911
Jonas Korlach
1Pacific Biosciences, Menlo Park, CA 94025, USA
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  • For correspondence: jkorlach@pacb.com ejarvis@rockefeller.edu
Gregory Gedman
2Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA
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Sarah B. Kingan
1Pacific Biosciences, Menlo Park, CA 94025, USA
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Chen-Shan Chin
1Pacific Biosciences, Menlo Park, CA 94025, USA
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Jason Howard
2Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA
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Lindsey Cantin
2Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA
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Erich D. Jarvis
2Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA
3Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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  • For correspondence: jkorlach@pacb.com ejarvis@rockefeller.edu
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Abstract

Reference quality genomes are expected to provide a resource for studying gene structure and function. However, often genes of interest are not completely or accurately assembled, leading to unknown errors in analyses or additional cloning efforts for the correct sequences. A promising solution to this problem is long-read sequencing. Here we tested PacBio-based long-read sequencing and diploid assembly for potential improvements to the Sanger-based intermediate-read zebra finch reference and Illumina-based short-read Anna’s hummingbird reference, two vocal learning avian species widely studied in neuroscience and genomics. With DNA of the same individuals used to generate the reference genomes, we generated diploid assemblies with the FALCON-Unzip assembler, resulting in contigs with no gaps in the megabase range (N50s of 5.4 and 7.7 Mb, respectively), and representing 150-fold and 200-fold improvements over the current zebra finch and hummingbird references, respectively. These long-read assemblies corrected and resolved what we discovered to be misassemblies, including due to erroneous sequences flanking gaps, complex repeat structure errors in the references, base call errors in difficult to sequence regions, and inaccurate resolution of allelic differences between the two haplotypes. We analyzed protein-coding genes widely studied in neuroscience and specialized in vocal learning species, and found numerous assembly and sequence errors in the reference genes that the PacBio-based assemblies resolved completely, validated by single long genomic reads and transcriptome reads. These findings demonstrate, for the first time in non-human vocal learning species, the impact of higher quality, phased and gap-less assemblies for understanding gene structure and function.

  • Abbreviations

    A1-L4
    primary auditory cortex – layer 4
    Am
    nucleus ambiguous
    Area X
    a vocal nucleus in the striatum
    aSt
    anterior striatum vocal region
    aT
    anterior thalamus speech area
    Av
    avalanche
    aDLM
    anterior dorsolateral nucleus of the thalamus
    DM
    dorsal medial nucleus of the midbrain
    HVC
    a vocal nucleus (no abbreviation)
    L2
    auditory area similar to human cortex layer 4
    LSC
    laryngeal somatosensory cortex
    LMC
    laryngeal motor cortex
    MAN
    magnocellular nucleus of the anterior nidopallium
    MO
    oval nucleus of the anterior mesopallium
    NIf
    interfacial nucleus of the nidopallium
    PAG
    peri-aqueductal gray
    RA
    robust nucleus of the arcopallium
    v
    ventricle space
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    Posted February 02, 2017.
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    De Novo PacBio long-read and phased avian genome assemblies correct and add to genes important in neuroscience research
    Jonas Korlach, Gregory Gedman, Sarah B. Kingan, Chen-Shan Chin, Jason Howard, Lindsey Cantin, Erich D. Jarvis
    bioRxiv 103911; doi: https://doi.org/10.1101/103911
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    De Novo PacBio long-read and phased avian genome assemblies correct and add to genes important in neuroscience research
    Jonas Korlach, Gregory Gedman, Sarah B. Kingan, Chen-Shan Chin, Jason Howard, Lindsey Cantin, Erich D. Jarvis
    bioRxiv 103911; doi: https://doi.org/10.1101/103911

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