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

 Abstract : 
 Sour cherry ( Prunus cerasus ) is an important fruit crop that is widely cultivated within the northern hemisphere . Its fruits are rich in nutrients and bioactive compounds that have been linked to numerous health benefits , including anti - inflammatory , antioxidant , and anti - cancer properties . The demand for sour cherry has been increasing due to its use in the food , pharmaceutical , and cosmetic industries . Breeding of sour cherry has been a major focus of research and development in recent years , aiming to improve yield , fruit quality , and disease resistance . One of the main challenges in sour cherry breeding is the genetic complexity of the species , which makes it difficult to identify and select desirable traits . 
  However , advances in molecular biology and genomics have provided new tools and resources for sour cherry breeders , enabling them to identify and characterize important genes and markers associated with desirable traits . Rapid progress in third - generation sequencing technologies enables breeders to explore and exploit the genomic information underlying economical important traits . We used Oxford Nanopore Technology PromethION platform and R9.4.1 pore type and Illumina NovaSeqTM to sequence the genome of tetraploid sour cherry ( Prunus cerasus ) . The genome and annotation visualization is permanently hosted at an assembly hub http://bioinf.uni-greifswald.de/private-hubs/pcer/hub.txt . 
  The data on this platform includes 28 files , supporting the assembling , annotation procedure , and additional data used to characterize the segmental allopolyploid structure of the genome . 
  As a result , a genome sequence has been processed ( 20_WGS_PCE_2_0.fa ) . 
  The final genome sequence was annotated using Braker 1 and Braker 2 and the GeMoMa pipeline and 14 reference datasets from other Prunus species ( Prunus_cerasus_families_fa.gz , genome_chr_fa_masked.gz , rm1_genome_chr_fa_out.gz , rm1_genome_chr_fa_tbl.gz , rm2_genome_chr_fa_out.gz , rm2_genome_chr_fa_tbl.gz , tsebra_braker1_2_gmst_v4_aa.gz , tsebra_braker1_2_gmst_v4_codingseq.gz , tsebra_braker1_2_gmst_v4-gtf.gz , final_annotation_1.gff ) . 
  The final structural annotation and protein predictions are provided for future studies ( final_annotation_proteins.fasta ) . 
  The functional prediction was performed with InterProScan ( Results IPS_PCE_A.xlsx , Results IPS_PCE_F.xlsx ) . 
  In addition , the sequences and annotation of the chloroplast ( PCE_chloroplast_1_0.fa , GeSeqJob_20220901_192228_PCE_chloroplast_GFF3.gff3 ) and mitochondrion ( PCE_mitochondria_1_0.fa , GeSeqJob_20230103_105327_PCE_mitochondria_GFF3.gff3 ) are presented . 
  Moreover , we used percentage of base coverage from rna - seq reads ( RNAseq_avium.tsv , RNAseq_fruticosa.tsv ) , genomic reads ( percentages_125.tsv ) and % IAA ( best_iAA_all_transcripts_PA_PF_only.xlsx , suppl_data_TabS5.csv ) to evaluate the structure of the genome sequence on the occurrence of homoeologous exchanges . 
  We also determined the position of molecular markers ( suppl_data_FigS5.xlsx ) and LTRs ( From_PCE_Prunus_avium_fna_mod_pass.list , From_PCE_Prunus_fruticosa_fna_mod_pass.list ) on both subgenomes . Furthermore , the position of LTRs was determined on the genomes of P. avium ( Prunus_avium_NCBI_fna_mod_pass.list ) and P. fruticosa ( Prunus_fruticosa_NCBI_fna_mod_pass.list ) .