Sample information, library construction, and genome sequencing

DNA samples were harvested from the leaf tissues of an individual opium poppy plant, which was provided by Wuhan Botanical Garden, Chinese Academy of Sciences (Supplementary Fig. S1). High-quality genomic DNA was extracted from frozen leaf samples by a modified CTAB method³⁸. The quality and quantity of the isolated DNA were checked by electrophoresis on a 0.8% agarose gel and a NanoDrop D-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) as well as a Qubit Fluorometer, respectively. With the qualified DNA, three types of short-insert paired-end libraries (250, 300, and 450 bp) were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, USA), and four types of mate-pair libraries (2, 5, 10, and 20 kb) were prepared using Illumina’s DNA library preparation kits (TruSeq PE Cluster Kit v3, cBot, HS; and TruSeq SBS Kit v3, HS [200 cycles]) according to the manufacturer’s protocol. The Hi-C library was also constructed using fresh leaves according to the manufacturer’s instructions. Illumina paired-end sequencing libraries were generated following the manufacturer’s standard protocol (Illumina) and sequenced on the Illumina HiSeq platform (Illumina, San Diego, CA).