Misidentifications of Echinochloa crus‐galli var. formosensis as Echinochloa oryzicola as a result of similar cpDNA sequences

Echinochloa crus‐galli (L.) Beauv. var. formosensis Ohwi (2n = 6x = 54, AABBCC genomes) and Echinochloa oryzicola (Vasinger) Vasinger (2n = 4x = 36, AABB) are major paddy weeds in East and Southeast Asia. E. oryzicola has been generally considered to be a paternal genome donor of E. crus‐galli s. l., which includes E. crus‐galli var. formosensis based on cpDNA sequences. Thus, molecular characterization using polymerase chain reaction‐restriction fragment length polymorphism analysis of cpDNA has been proposed as a reliable method for discriminating between the two species. In this study, we report that four accessions of E. crus‐galli var. formosensis from Okinawa, Nagasaki, Shizuoka and Tokyo had similar cpDNA sequences to E. oryzicola and had been misidentified as E. oryzicola using molecular methods. In addition, our results demonstrated that these accessions likely inherited their chloroplast genomes from E. oryzicola and not from an anonymous diploid species during polyploidization. Our findings provide new insights into the evolution of E. crus‐galli s. l. and suggest that identification using the cpDNA molecular method alone is not an appropriate approach to differentiate E. crus‐galli var. formosensis and E. oryzicola.