Supplementary Data

sum_orthologue_transcript_counts.py - python script to sum read counts and TPM values after using kallisto to pseudoalign RNA-Seq reads to the pantranscriptome reference. CS_plus_1to1_orthologues_cds.fasta - pantranscriptome reference containing transcripts from the Chinese Spring RefSeq v1.1 high-confidence annotation and transcripts from genes from the pangenome cultivars that exist in a 1-to-1 relationship with a Chinese Spring gene. CS_1to1_orthologue_pairs.tsv - Genes in a 1-to-1 relationship with a Chinese Spring, determined using OrthoFinder with proteins from Chinese Spring and the nine chromosome-level genome assemblies from the wheat pangenome project (Walkowiak et al., 2020). RefSeqv1.1_hc_triad_ids.tsv - Gene IDs of each triad identified by Ramírez-González et al., 2018. accessions_with_chr1D_introgression.tsv - Table showing which accessions from He et al. (2022) contain the chr1D introgression. He_et_al_expression_matrix_CS_reference.tsv - expression matrix generated by pseuoaligning the RNA-Seq data from He et al. (2022) to the Chinese Spring RefSeq v.1.1 high-confidence transcripts. He_et_al_expression_matrix_pantranscriptome_reference.tsv - expression matrix generated by pseuoaligning the RNA-Seq data from He et al. (2022) to the pantranscriptome reference and processed using sum_orthologue_transcript_counts.py