Data files

coverage and uniquely mapped spliced reads summary

samtools coverage https://www.htslib.org/doc/samtools-coverage.html

Number of transcripts from de novo assemblies contributing to cultivar Désirée, transcriptome and number of complete BUSCOs found in assemblies. Proportion of all contigs in de novo assembly (blue bars) and proportion of EvidentialGene okay set (green bars), and the number of complete BUSCOs (dots) using https://busco.ezlab.org/datasets/embryophyta_odb9.tar.gz set are shown. Assembly software abbreviations: CLCdn - CLC Genomics Workbench, Vdn - Velvet.

Supplementary Table S6 - EvidentialGene Summary Statistics for PacBio sequences. Layer _p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.2_assembly-contribution-count/reports/

Supplementary Table S5 - Rywal biological evidence filtering results. Output of 1st filtering step by biological evidence for cv. Rywal. Layer _p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.1_filtering/reports/

Supplementary Table S4 - PW363 biological evidence filtering results. Output of 1st filtering step by biological evidence for breeding clone PW363. Layer _p_stRT/ _I_STRT/_S_03_stCuSTr/_A_03.1_filtering/reports/,

Supplementary Table S3 - Désirée biological evidence filtering results. Output of 1st filtering step by biological evidence for cv. Désirée. Layer _p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.1_filtering/reports/

Number of transcripts from de novo assemblies contributing to breeding clone PW363, transcriptome and number of complete BUSCOs found in assemblies. Proportion of all contigs in de novo assembly (blue bars) and proportion of EvidentialGene okay set (green bars), and the number of complete BUSCOs (dots) using https://busco.ezlab.org/datasets/embryophyta_odb9.tar.gz set are shown. Assembly software abbreviations: CLCdn - CLC Genomics Workbench, Vdn - Velvet, Sdn - SPAdes.

Number of transcripts from de novo assemblies contributing to cultivar Rywal, transcriptome and number of complete BUSCOs found in assemblies. Proportion of all contigs in de novo assembly (blue bars) and proportion of EvidentialGene okay set (green bars), and the number of complete BUSCOs (dots) using https://busco.ezlab.org/datasets/embryophyta_odb9.tar.gz set are shown. Assembly software abbreviations: CLCdn - CLC Genomics Workbench, Vdn - Velvet, Sdn - SPAdes, PBdn - PacBio.

Supplementary Table S5 Rywal biological evidence filtering results. Output of 1st filtering step by biological evidence for cv. Rywal.

Supplementary Table S3 Désirée biological evidence filtering results. Output of 1st filtering step by biological evidence for cv. Désirée.

Supplementary Table S4 PW363 biological evidence filtering results. Output of 1st filtering step by biological evidence for breeding clone PW363.