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

Cherries are among the most popular fruits among consumers and are grown for industrial processing or fresh consumption. The cultivation and breeding of cherries faces new challenges in the future, not least due to climate change. Cultivation is becoming increasingly difficult due to changing climatic conditions, diseases and pests. Therefore, the market demands new varieties with high fruit quality and adaptation to locally changing conditions. Breeding for tree fruit is a long-term task, though, and tools to facilitate this process are unfortunately not yet available to a sufficient extent. 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 R10.3 pore type to sequence the genome of tetraploid ground cherry (Prunus fruticosa). The final sequence has been deposited at DDBJ/ENA/GenBank under the accession JAHHUK000000000. A specific description of the work can be viewed at https://biorxiv.org/cgi/content/short/2021.06.01.446499v1. The version described in this paper is version JAHHUK010000000. The data on this platform includes 17 files, supports the assembling and annotation procedure, and provides insights into this challenging work. As a result, five assemblies (MiniasmMinimap.fasta, medaka.fasta, raconpolished.fasta, purged.fasta, purged2.fasta) have been processed to generate a draft genome assembly. The final genome sequence was masked (genome.fa.masked.gz, genome.fa.out, genome.fa.tbl) and annotated using Braker 1 and Braker 2, GeMoMa pipeline and eight reference datasets from other Prunus species. The final structural annotation, coding sequences and protein predictions are provided for future studies (GeMoMa_Annotation_filtered_predictions_8ref_RNAseq_Braker.gff, GeMoMa_Annotation_filtered_predictions_8ref_RNAseq_Braker_assignment.tabular, GeMoMa_Annotation_filtered_predictions_8ref_RNAseq_Braker_cds-parts.fasta, GeMoMa_Annotation_filtered_predictions_8ref_RNAseq_Braker_proteins.fasta). The functional prediction was performed with InterProScan (Results IPS.xlsx). In addition, the sequences and annotation of the chloroplast (Pf_chloroplast_1.0.fasta, GeSeqJob-20210201-124142_utg000088l_segment0_1_GFF3.gff3) and mitochondrion (Pf_mitochondria_1.0, GeSeqJob-20210202-114557_utg001396l_trimmed_GFF3.gff3) are presented.