The transcript and genome assembly data generated in this study have been deposited in the NCBI databases under the BioProject PRJNA770669. Raw RNA-seq and DNA reads are available under the accession numbers SRR16389878–SRR16389886, SRR16690173, SRR16690174 and SRR16591802–SRR16591806. Assembled RNA-seq datasets are available under the following accession numbers GJOO00000000–GJOY00000000. Annotated genomes are available under the following accessions (JAJJMA000000000, JAJJMB000000000, JAJJMC000000000, JAJJWW000000000, and JAJJWX000000000. Annotated genomes have also been made available at ORCAE68 (Online Resource for Community Annotation of Eukaryotes) [https://bioinformatics.psb.ugent.be/gdb/poppy/]. Individual sequences of STORR gene have been deposited at NCBI under accessions OK631703–OK631705. In addition, individual sequences of Papaver nudicaule COR-L gene have been deposited at NCBI under accessions OK631706–OK631710, OK999969–OK999970, and OL452058. Source data are provided with this paper.