The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation

Abstract The hexaploid species Echinochloa crus-galli is one of the most detrimental weeds in crop fields, especially in rice paddies. Its evolutionary history is similar to that of bread wheat, arising through polyploidization after hybridization between a tetraploid and a diploid species. Here we generated and analyzed high quality genome sequences of diploid (E. haploclada), tetraploid (E. oryzicola) and hexaploid (E. crus-galli) Echinochloa species. Gene family analysis showed that disease resistance genes such as those containing the NB-ARC domain have been significantly lost during Echinochloa polyploidization, which is contrary to significant expansion of those genes during wheat polyploidization. The result suggests that natural selection might favor reduced investment in resistance in the weed to maximize its growth and reproduction. In contrast to the asymmetric patterns of genome evolution shown in wheat and other crops, no significant differences in selection pressure were detected between the subgenomes in E. oryzicola and E. crus-galli. Additionally, distinctive differences of transcriptomic dynamics in subgenome expression during hexaploidization were observed between E. crus-galli and bread wheat. This study documents genomic mechanisms for adaptation during polyploidization in a major agricultural weed and provides insights for crop breeding.