The structure of the tetraploid sour cherry 'Schattenmorelle' (Prunus cerasus L.) genome reveals insights into its segmental allopolyploid nature

Sour cherry (Prunus cerasus L.) is an economically important allotetraploid cherry species believed to have evolved in the Caspian Sea and Black Sea regions. How, when and where exactly the evolution of this species took place is unclear. It resulted from a hybridization of the tetraploid ground cherry (Prunus fruticosa Pall.) and an unreduced (2n) pollen of the diploid ancestor sweet cherry (P. avium L.). Some indications implement that the genome of sour cherry is segmental allopolyploid, but how it is structured and to what extent is unknown. To get an insight, the genome of the sour cherry cultivar Schattenmorelle was sequenced at ~400x using Illumina NovaSeqTM short-read and Oxford Nanopore long-read technologies (ONT R9.4.1 PromethION). Additionally, the transcriptome of Schattenmorelle was sequenced using PacBio Sequel II SMRT cell sequencing at ~300x. The final assembly resulted in a ~629 Mbp long pseudomolecule reference genome, which could be separated into two subgenomes each split into eight chromosomes. Subgenome PceS_a which originates from P. avium has a length of 269 Mbp, whereas subgenome PceS_f which originates from P. fruticosa has a length of 299.5 Mbp. The length of unassembled contigs was 60 Mbp. The genome of the sour cherry shows a size-reduction compared to the genomes of its ancestral species. It also shows traces of homoeologous sequence exchanges throughout the genome. Comparative positional sequence and protein analyses provided evidence that the genome of sour cherry is segmental allotetraploid and that it has evolved in a very recent event in the past.