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

GND
142510254
Affiliation
Julius Kühn-Institute (JKI), Institute for Breeding Research on Fruit Crops, Germany
Wöhner, Thomas;
GND
1211645738
Affiliation
Julius Kühn-Institute (JKI), Institute for Breeding Research on Fruit Crops, Germany
Emeriewen, Ofere F.;
Affiliation
Keygene N. V., Netherlands
Wittenberg, Alexander;
Affiliation
Keygene N. V., Netherlands
Schneiders, Harrie;
Affiliation
Keygene N. V., Netherlands
Vrijenhoek, Ilse;
Affiliation
Szent István University, Department of Genetics and Plant Breeding, Faculty of Horticultural Science, Hungary
Halász, Júlia;
Affiliation
Hungarian University of Agriculture and Life Science, Department of Floriculture and Dendrology, Institute of Landscape Architecture, 15 Urban Planning and Ornamental Horticulture, Hungary
Hrotkó, Károly;
Affiliation
University of Greifswald, Institute of Mathematics and Computer Science, Germany ; University of Greifswald, Center for Functional Genomics of Microbes, Germany
Hoff, Katharina J.;
Affiliation
University of Greifswald, Institute of Mathematics and Computer Science, Germany ; University of Greifswald, Center for Functional Genomics of Microbes, Germany
Gabriel, Lars;
GND
1013858662
Affiliation
Julius Kühn-Institute (JKI), Institute for Biosafety in Plant Biotechnology, Germany
Keilwagen, Jens;
GND
1172920559
Affiliation
Julius Kühn-Institute (JKI), Institute for Biosafety in Plant Biotechnology, Germany
Berner, Thomas;
GND
1059103494
Affiliation
Julius Kühn-Institute (JKI), Institute for Breeding Research on Fruit Crops, Germany
Schuster, Mirko;
GND
172861896
Affiliation
Julius Kühn-Institute (JKI), Institute for Breeding Research on Fruit Crops, Germany
Peil, Andreas;
GND
172687926
Affiliation
University of Hohenheim, Institute of Special Crops and Crop Physiology, Germany
Wünsche, Jens;
Affiliation
Germany
Kropop, Stephan;
GND
128593652
Affiliation
Julius Kühn-Institute (JKI), Institute for Breeding Research on Fruit Crops, Germany
Flachowsky, Henryk

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 43 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.

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