De Novo Genome Assembly

K-mer frequency analysis was performed using Jellyfish V2.0 (Marçais and Kingsford, 2011) to estimate the P. grandiflorus genome size, heterozygosity and repeat content. The NextDenovo (https://github.com/Nextomics/NextDenovo) was used to assemble the P. grandiflorus genome with ONT long reads, and then the Nanopore-assembled genome was polished using the Illumina DNA short reads by NextPolish V1.3.1 (Hu et al., 2020) to improve base accuracy using default parameters. Next, the ALLHiC V0.9.8 (Zhang et al., 2019) was used to reorder and anchor preliminarily assembled contigs into chromosomes based on Hi-C data using default parameters. Finally, we use the Juicerbox V1.1 (Robinson et al., 2018) to adjust the heatmap and assemble it into a chromosome version of the genome. To assess the accuracy and completeness of the assemblies, Illumina clean reads were mapped to our assembly using BWA (Li and Durbin, 2009). In addition, BUSCO (Simão et al., 2015) was used to access the completeness of the genome assembly.