Genomic and ecological characterization of unclassified tetraploid Echinochloa plants distributed in northern Japan

Understanding the evolutionary origins of globally noxious weeds provides insights into the genetic background of weediness. Among species of Echinochloa, the hexaploid E. crus-galli was previously thought to have arisen through hybridization and allopolyploidization between tetraploid E. oryzicola and an undiscovered diploid species, although they exhibit marked differences in both ecological and morphological characteristics. Recently, in Japan, unknown tetraploid Echinochloa plants were discovered that exhibit distinct ecological and morphological characteristics from those of E. oryzicola, with some traits showing greater similarity to those of E. crus-galli. In this study, we investigated the relationships between well-known Echinochloa species and these unknown tetraploid plants, hereafter referred to as ''ninja''. Subgenome-based read mapping analysis and phylogenetic analysis revealed that ninja possesses a distinct genomic composition, while showing close relationships to E. oryzicola in both its chloroplast and nuclear genomes. Furthermore, the identification of a very small number of ninja x E. oryzicola hybrids among field-collected individuals suggests that these two species rarely hybridize in the wild. Although ninja and E. oryzicola showed similar genomic compositions, ninja has a broader habitat range, partially overlapping with that of E. oryzicola and extending into areas occupied by E. crus-galli. Our findings indicate the possibility that hexaploid E. crus-galli may have originated from a tetraploid Echinochloa species other than E. oryzicola.