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Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes

View ORCID ProfileFernando A. Rabanal, Maike Gräff, Christa Lanz, Katrin Fritschi, View ORCID ProfileVictor Llaca, Michelle Lang, View ORCID ProfilePablo Carbonell-Bejerano, View ORCID ProfileIan Henderson, View ORCID ProfileDetlef Weigel
doi: https://doi.org/10.1101/2022.02.15.480579
Fernando A. Rabanal
1Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
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  • For correspondence: fernando.rabanal@tuebingen.mpg.de weigel@weigelworld.org
Maike Gräff
1Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
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Christa Lanz
1Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
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Katrin Fritschi
1Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
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Victor Llaca
2Genomics Technologies, Corteva Agriscience, Johnston, IA 50131, USA
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Michelle Lang
2Genomics Technologies, Corteva Agriscience, Johnston, IA 50131, USA
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Pablo Carbonell-Bejerano
1Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
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Ian Henderson
3Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
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  • ORCID record for Ian Henderson
Detlef Weigel
1Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
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  • ORCID record for Detlef Weigel
  • For correspondence: fernando.rabanal@tuebingen.mpg.de weigel@weigelworld.org
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ABSTRACT

Although long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model plant Arabidopsis thaliana, other than the reference accession Col-0, all other accessions de novo assembled with long-reads until now have used PacBio continuous long reads (CLR). Although these assemblies sometimes achieved chromosome-arm level contigs, they inevitably broke near the centromeres, excluding megabases of DNA from analysis in pan-genome projects. Since PacBio high-fidelity (HiFi) reads circumvent the high error rate of CLR technologies, albeit at the expense of read length, we compared a CLR assembly of accession Ey15-2 to HiFi assemblies of the same sample performed by five different assemblers starting from subsampled data sets, allowing us to evaluate the impact of coverage and read length. We found that centromeres and rDNA clusters are responsible for 71% of contig breaks in the CLR scaffolds, while relatively short stretches of GA/TC repeats are at the core of >85% of the unfilled gaps in our best HiFi assemblies. Since the HiFi technology consistently enabled us to reconstruct gapless centromeres and 5S rDNA clusters, we demonstrate the value of the approach by comparing these previously inaccessible regions of the genome between two A. thaliana accessions.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://keeper.mpdl.mpg.de/d/216caab287514b1ba2c5/

  • https://github.com/frabanal/A.thaliana_CLR_vs_HiFi

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 4.0 International license.
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Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes
Fernando A. Rabanal, Maike Gräff, Christa Lanz, Katrin Fritschi, Victor Llaca, Michelle Lang, Pablo Carbonell-Bejerano, Ian Henderson, Detlef Weigel
bioRxiv 2022.02.15.480579; doi: https://doi.org/10.1101/2022.02.15.480579
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Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes
Fernando A. Rabanal, Maike Gräff, Christa Lanz, Katrin Fritschi, Victor Llaca, Michelle Lang, Pablo Carbonell-Bejerano, Ian Henderson, Detlef Weigel
bioRxiv 2022.02.15.480579; doi: https://doi.org/10.1101/2022.02.15.480579

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