Variant calling and mapping accuracies
A total of 40 samples were mapped to the reference genome, resulting in 1,505,327 SNPs. After filtering out SNPs with a minor allele frequency of less than 0.05 and more than10% of missingness and removing the linkage disequilibrium within a 50kb window size and 10kb step size, we obtained 81,566 biallelic variant sites. These sites were used to construct a nuclear phylogenetic tree, and to perform PCA analysis forP. australis lineages. For the chloroplast phylogenetic trees, 211 sites were retained after filtering out those with a minor allele frequency of less than 0.05, and a missing rate higher than 50%. To assess the transcriptomic response to heavy metal exposure among the hybrid lineages, we prepared 18 RNAseq libraries, including control, low cadmium treatment, and high cadmium treatment groups. A total of 128.92 Gb of clean RNA-seq data was obtained from the 18 samples, with each sample producing 5.88Gb of clean data. The percentage of Q30 bases exceeded 94.31% across all samples. All reads from the 18 libraries were mapped to the reference genome with high accuracy, with unique mapping rates ranging from 85.94 to 93.96% (Supplementary Table S2 ). After filtering out genes with a count number of less than 1, a total of 40,089 genes were retained.