Data files

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Supplementary Table S1 - Detailed sample information table used to generate the de novo transcriptome assemblies. Raw and processed reads summary. Layer _p_stRT/_I_STRT/ _S_01_sequences/reports

Supplementary Table S2 - Detailed de novo assemblies information table. Primary potato transcriptome assemblies summary listing parameters used for short-read de novo assembly generation. Layer _p_stRT/_I_STRT/_S_02_denovo/reports/

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 File 1 - Merged ITAG/PGSC Phureja DM gene models. Archive containing GTF, CDS and peptide fasta files for merged ITAG and PGSC gene models for S. tuberosum Group Phureja DM genome v4.04

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 File 3 - Taxonomi cclassification of Désirée, PW363 and Rywal representative transcripts. Sequences were classified using Centrifuge and Sankey plots were generated using Pavian. Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_08_cdhit_centrifuge_3cvs-GFFmerged

Supplementary File 2 - Multiple sequence alignments using ClustalOmega v1.2.1 or MAFFT v7.271 and MView v1.66. Paralogue clusters on representative and alternative sequences, at least one from each of the four genotypes. Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_05_MSA_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_08_centrifuge_3cvs-GFFmerged