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. In this study, 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 a significant loss of disease-resistance genes such as those encoding NB-ARC domain-containing proteins during Echinochloa polyploidization, contrary to their significant expansionduring wheat polyploidization, suggesting that natural selection might favor reduced investment in resistance in this weed to maximize its growth and reproduction. In contrast to the asymmetric patterns of genome evolution observed in wheat and other crops, no significant differences in selection pressure were detected between the subgenomes in E. oryzicola and E. crus-galli. In addition, distinctive differences in subgenome transcriptome dynamics during hexaploidization were observed between E. crus-galli and bread wheat. Collectively, our study documents genomic mechanisms underlying the adaptation of a major agricultural weed during polyploidization. The genomic and transcriptomic resources of three Echinochloa species and new insights into the polyploidization-driven adaptive evolution would be useful for future breeding cereal crops.

六倍体E草是农作物田中最有害的杂草之一，特别是在稻田中。它的进化历史与面包小麦相似，是通过四倍体和二倍体物种杂交后多倍体化而产生的。在这项研究中，我们产生和分析二倍体的高品质的基因组序列（Ë。haploclada），四倍体（ê。空心稗），和六倍体（Ë。稗）稗种。基因家族分析显示疾病抗性基因一个显著损失诸如在那些编码NB-ARC结构域的蛋白质稗多倍体化与小麦多倍体化期间的显着扩张相反，表明自然选择可能有利于减少对这种杂草的抗性投资，以使其繁殖和繁殖最大化。与在小麦和其他农作物中观察到的基因组进化的不对称模式相反，E的亚基因组之间的选择压力没有发现显着差异。空心稗和Ë。克鲁斯加利。另外，在E之间观察到六倍体化过程中亚基因组转录组动力学的显着差异。克鲁斯加利和面包小麦。总的来说，我们的研究记录了多倍体化过程中主要农业杂草适应的基因组机制。三种棘皮动物的基因组和转录组学资源以及多倍体化驱动的适应性进化的新见识对于将来的谷物作物育种将很有用。