RNAseq reads obtained from NCBI database
We obtained RNAseq data of 32 individuals and whole genome sequencing reads for two samples from the NCBI database, representing different geographic origins (Supplementary Table S1 ). Identifications of brackish water and freshwater ecotypes were justified in the original publications (Supplementary Table S1 ). Of these, RNAseq data from 13 individuals were generated from a common garden in Shandong University in July 2020, allowing for direct comparison of gene expression profiles. Ploidy level information was sourced from previous studies, determined either through flow cytometry or predicted using alternative allele frequency after genome mapping (C. Wang, Liu, Yin, Eller, Brix, Wang, Salojarvi, et al., 2021). Specifically, individuals in the AU lineage are octoploid, while those in the USnat, EU, Med, and CN lineages are tetraploid. The reference genome sequence of P. australis was obtained from our previous work (NCBI accession: ASM4037322v1)(C. Wang et al., 2024). For phylogenetic analysis, we included the 34 samples as well as the six RNAseq samples of the Heze and Panjin genotype control samples.