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The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads

View ORCID ProfileThomas W. Wöhner, View ORCID ProfileOfere F. Emeriewen, Alexander H.J. Wittenberg, Harrie Schneiders, Ilse Vrijenhoek, View ORCID ProfileJúlia Halász, View ORCID ProfileKároly Hrotkó, View ORCID ProfileKatharina J. Hoff, Lars Gabriel, View ORCID ProfileJens Keilwagen, Thomas Berner, Mirko Schuster, Andreas Peil, Jens Wünsche, Stephan Kropop, View ORCID ProfileHenryk Flachowsky
doi: https://doi.org/10.1101/2021.06.01.446499
Thomas W. Wöhner
1Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, D-01326, Dresden, Germany
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  • For correspondence: thomas.woehner@julius-kuehn.de
Ofere F. Emeriewen
1Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, D-01326, Dresden, Germany
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Alexander H.J. Wittenberg
2Keygene N.V., P.O. Box 216, 6700 AE Wageningen, Netherlands
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Harrie Schneiders
2Keygene N.V., P.O. Box 216, 6700 AE Wageningen, Netherlands
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Ilse Vrijenhoek
2Keygene N.V., P.O. Box 216, 6700 AE Wageningen, Netherlands
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Júlia Halász
3Department of Genetics and Plant Breeding, Faculty of Horticultural Science, Szent István University, Ménesi Str. 44, Budapest 1118, Hungary
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Károly Hrotkó
4Department of Floriculture and Dendrology, Institute of Landscape Architecture, Urban Planning and Ornamental Horticulture, Hungarian University of Agriculture and Life Science, Villányi Str. 35-43, Budapest 1118, Hungary
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Katharina J. Hoff
5Institute of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Str. 47, 17489 Greifswald, Germany
8Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
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Lars Gabriel
5Institute of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Str. 47, 17489 Greifswald, Germany
8Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
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Jens Keilwagen
6Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, D-06484 Quedlinburg, Germany
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Thomas Berner
6Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, D-06484 Quedlinburg, Germany
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Mirko Schuster
1Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, D-01326, Dresden, Germany
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Andreas Peil
1Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, D-01326, Dresden, Germany
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Jens Wünsche
7University of Hohenheim, Institute of Special Crops and Crop Physiology, 70593 Stuttgart, Germany
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Stephan Kropop
9Jagdweg 1-3, 01159 Dresden, Germany
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Henryk Flachowsky
1Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, D-01326, Dresden, Germany
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Abstract

Background Cherries are stone fruits and belong to the economically important plant family of Rosaceae with worldwide cultivation of different species. The ground cherry, Prunus fruticosa Pall. is one ancestor of cultivated sour cherry, an important tetraploid cherry species. Here, we present a long read chromosome-level draft genome assembly and related plastid sequences using the Oxford Nanopore Technology PromethION platform and R10.3 pore type.

Finding The final assemblies obtained from 117.3 Gb cleaned reads representing 97x coverage of expected 1.2 Gb tetraploid (2n=4x=32) and 0.3 Gb haploid (1n=8) genome sequence of P. fruticosa were calculated. The N50 contig length ranged between 0.3 and 0.5 Mb with the longest contig being ∼6 Mb. BUSCO estimated a completeness between 98.7 % for the 4n and 96.1 % for the 1n datasets.

Using a homology and reference based scaffolding method, we generated a final consensus genome sequence of 366 Mb comprising eight chromosomes. The N50 scaffold was ∼44 Mb with the longest chromosome being 66.5 Mb.

The repeat content was estimated to ∼190 Mb (52 %) and 58,880 protein-coding genes were annotated. The chloroplast and mitochondrial genomes were 158,217 bp and 383,281 bp long, which is in accordance with previously published plastid sequences.

Conclusion This is the first report of the genome of ground cherry (P. fruticosa) sequenced by long read technology only. The datasets obtained from this study provide a foundation for future breeding, molecular and evolutionary analysis in Prunus studies.

Competing Interest Statement

The R10.3 flow cells were provided by Keygene for the project. Keygene wanted to gain experience with this new flow cells on a biologically difficult object. Keygene had no influence on the interpretation of the results and the writing of the manuscript.

Footnotes

  • https://www.openagrar.de/receive/openagrar_mods_00070329

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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The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads
Thomas W. Wöhner, Ofere F. Emeriewen, Alexander H.J. Wittenberg, Harrie Schneiders, Ilse Vrijenhoek, Júlia Halász, Károly Hrotkó, Katharina J. Hoff, Lars Gabriel, Jens Keilwagen, Thomas Berner, Mirko Schuster, Andreas Peil, Jens Wünsche, Stephan Kropop, Henryk Flachowsky
bioRxiv 2021.06.01.446499; doi: https://doi.org/10.1101/2021.06.01.446499
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The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads
Thomas W. Wöhner, Ofere F. Emeriewen, Alexander H.J. Wittenberg, Harrie Schneiders, Ilse Vrijenhoek, Júlia Halász, Károly Hrotkó, Katharina J. Hoff, Lars Gabriel, Jens Keilwagen, Thomas Berner, Mirko Schuster, Andreas Peil, Jens Wünsche, Stephan Kropop, Henryk Flachowsky
bioRxiv 2021.06.01.446499; doi: https://doi.org/10.1101/2021.06.01.446499

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