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Long-read assemblies reveal structural diversity in genomes of organelles - an example with Acacia pycnantha

View ORCID ProfileAnna E. Syme, Todd G.B. McLay, Frank Udovicic, David J. Cantrill, Daniel J. Murphy
doi: https://doi.org/10.1101/2020.12.22.423164
Anna E. Syme
1Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne 3004, Australia
2Melbourne Bioinformatics, The University of Melbourne, Parkville 3010, Australia
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  • ORCID record for Anna E. Syme
  • For correspondence: anna.syme@unimelb.edu.au
Todd G.B. McLay
1Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne 3004, Australia
3School of BioSciences, The University of Melbourne, Parkville 3010, Australia
4Centre for Australian National Biodiversity Research, CSIRO, GPO Box 1700, Canberra 2601, Australia
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Frank Udovicic
1Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne 3004, Australia
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David J. Cantrill
1Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne 3004, Australia
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Daniel J. Murphy
1Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne 3004, Australia
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Abstract

Although organelle genomes are typically represented as single, static, circular molecules, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms. We sequenced and assembled chloroplast and mitochondrial genomes of the Golden Wattle, Acacia pycnantha, using long reads, iterative baiting to extract organelle-only reads, and several assembly algorithms to explore genomic structure. Using a de novo assembly approach agnostic to previous hypotheses about structure, we found different assemblies revealed contrasting arrangements of genomic segments; a hypothesis supported by mapped reads spanning alternate paths.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://doi.org/10.5281/zenodo.4330088

  • Abbreviations

    bp
    base pair
    SSC
    short single copy region
    LSC
    long single copy region
    IR
    inverted repeat
    plastome
    chloroplast genome
    mitome
    mitochondrial genome
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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    Posted December 23, 2020.
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    Long-read assemblies reveal structural diversity in genomes of organelles - an example with Acacia pycnantha
    Anna E. Syme, Todd G.B. McLay, Frank Udovicic, David J. Cantrill, Daniel J. Murphy
    bioRxiv 2020.12.22.423164; doi: https://doi.org/10.1101/2020.12.22.423164
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    Long-read assemblies reveal structural diversity in genomes of organelles - an example with Acacia pycnantha
    Anna E. Syme, Todd G.B. McLay, Frank Udovicic, David J. Cantrill, Daniel J. Murphy
    bioRxiv 2020.12.22.423164; doi: https://doi.org/10.1101/2020.12.22.423164

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