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Hybrid de novo assembly of the draft genome of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida)

View ORCID ProfileSébastien Renaut, View ORCID ProfileDavide Guerra, Walter R. Hoeh, Donald T. Stewart, Arthur E. Bogan, Fabrizio Ghiselli, Liliana Milani, Marco Passamonti, View ORCID ProfileSophie Breton
doi: https://doi.org/10.1101/265157
Sébastien Renaut
1Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, Canada
2Quebec Centre for Biodiversity Science, Montréal, QC, Canada
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  • ORCID record for Sébastien Renaut
  • For correspondence: sebastien.renaut@umontreal.ca s.breton@umontreal.ca
Davide Guerra
3Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
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Walter R. Hoeh
4Department of Biological Sciences, Kent State University, Kent, OH, USA
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Donald T. Stewart
5Department of Biology, Acadia University, Wolfville, NS, Canada
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Arthur E. Bogan
6North Carolina Museum of Natural Sciences, Raleigh, NC, USA
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Fabrizio Ghiselli
7Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Bologna, Italy
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Liliana Milani
7Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Bologna, Italy
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Marco Passamonti
7Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Bologna, Italy
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Sophie Breton
2Quebec Centre for Biodiversity Science, Montréal, QC, Canada
3Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
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  • For correspondence: sebastien.renaut@umontreal.ca s.breton@umontreal.ca
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Abstract

Freshwater mussels (Bivalvia: Unionida) serve an important role as aquatic ecosystem engineers but are one of the most critically imperilled groups of animals. An assembled and annotated genome for freshwater mussels has the potential to be utilized as a valuable resource for many researchers given their ecological value and threatened status. In addition, a sequenced genome will help to answer more fundamental questions of sex-determination and genome evolution in bivalves exhibiting a unique “doubly uniparental inheritance” mode of mitochondrial DNA transmission through comparative genomics approaches. Here, we used a combination of sequencing strategies to assemble and annotate a draft genome of the freshwater mussel Venustaconcha ellipsiformis. The genome described here was obtained by combining high coverage short reads (65X genome coverage of Illumina paired-end and 11X genome coverage of mate-pairs sequences) with low coverage Pacific Biosciences long reads (0.3X genome coverage). Briefly, the final scaffold assembly accounted for a total size of 1.54Gb (366,926 scaffolds, N50 = 6.5Kb, with 2.3% of "N" nucleotides), representing 93% of the predicted genome size of 1.66Gb. Over one third of the genome (37.5%) consisted of repeated elements and more than 85% of the core eukaryotic genes were recovered. Finally, we reassembled the full mitochondrial genome and found six polymorphic sites with respect to the previously published reference. This resource opens the way to comparative genomics studies to identify genes related to the unique adaptations of freshwater mussels and their distinctive mitochondrial inheritance mechanism.

  • Abbreviations

    BLAST
    Basic Local Alignment Search Tool
    b
    base pairs
    Kb
    Kilobases
    M
    Million
    Gb
    Gigabases
    GB
    gigabytes
    CPU
    Central Processing Unit
    DNA
    Deoxyribonucleic acid
    LINEs
    Long interspersed elements
    LTR
    Long terminal repeats
    ORF
    Open Reading Frames
    N80/50/20
    weighted median statistic such that 80/50/20% of the entire assembly is contained in contigs/scaffolds equal to or larger than this value.
    L50
    minimum number of sequences required to represent 50% of the entire assembly
    RAM
    Random Access Memory
    SINEs
    Short interspersed elements
  • Copyright 
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    Posted February 15, 2018.
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    Hybrid de novo assembly of the draft genome of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida)
    Sébastien Renaut, Davide Guerra, Walter R. Hoeh, Donald T. Stewart, Arthur E. Bogan, Fabrizio Ghiselli, Liliana Milani, Marco Passamonti, Sophie Breton
    bioRxiv 265157; doi: https://doi.org/10.1101/265157
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    Hybrid de novo assembly of the draft genome of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida)
    Sébastien Renaut, Davide Guerra, Walter R. Hoeh, Donald T. Stewart, Arthur E. Bogan, Fabrizio Ghiselli, Liliana Milani, Marco Passamonti, Sophie Breton
    bioRxiv 265157; doi: https://doi.org/10.1101/265157

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