The DNA methylomes of Echinochloa species provide insights into polyploidization‐driven adaptation and orphan crop domestication

SUMMARY The genus Echinochloa (Poaceae) contains problematic weeds worldwide and two domesticated orphan crops. In this study, through sequencing DNA methylomes and transcriptomes, we aimed to reveal the epigenome changes and their relationship with gene expression in Echinochloa species during their polyploidization and domestication. Compared with hexaploid crop bread wheat, we found common and distinctive methylation patterns in hexaploid Echinochloa crus‐galli . More diverse methylation patterns were uncovered during hexaploidization of E. crus‐galli , suggesting more plasticity of the weed genome, which might contribute to its environmental adaptation. In addition, less changes in DNA methylation were observed in the two cultivated Echinochloa species, as compared with rice, indicating incomplete domestication of the Echinochloa orphan crops. Our results provide new insights into plant polyploidization and orphan crop domestication from an epigenomic perspective.