Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed

Longbiao Guo, Jie Qiu, Chuyu Ye, Gulei Jin, Lingfeng Mao, Haiqiang Zhang, Xuefang Yang, Qiong Peng, Yingying Wang, Lei Jia, Zhangxiang Lin, Gengmi Li, Fei Fu, Chen Liu, Li Chen, Enhui Shen, Weidi Wang, Qinjie Chu, Dongya Wu, Sanling Wu, Chenyang Xia, Yongfei Zhang, Xiaomao Zhou, Lifeng Wang, Lamei Wu, Weijie Song, Yunfei Wang, Qingyao Shu, Daisuke Aoki, Emi Yumoto, Takao Yokota, Koji Miyamoto, Kazunori Okada, Do-Soon Kim, Daguang Cai, Chulong Zhang, Yonggen Lou, Qian Qian, Hirofumi Yamaguchi, Hisakazu Yamane, Chui-Hua Kong, Michael P. Timko, Lianyang Bai, Longjiang Fan

Barnyardgrass (Echinochloa crus-galli) is a pernicious weed in agricultural fields worldwide. The molecular mechanisms underlying its success in the absence of human intervention are presently unknown. Here we report a draft genome sequence of the hexaploid species E. crus-galli, i.e., a 1.27 Gb assembly representing 90.7% of the predicted genome size. An extremely large repertoire of genes encoding cytochrome P450 monooxygenases and glutathione S-transferases associated with detoxification are found. Two gene clusters involved in the biosynthesis of an allelochemical 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and a phytoalexin momilactone A are found in the E. crus-galli genome, respectively. The allelochemical DIMBOA gene cluster is activated in response to co-cultivation with rice, while the phytoalexin momilactone A gene cluster specifically to infection by pathogenic Pyricularia oryzae. Our results provide a new understanding of the molecular mechanisms underlying the extreme adaptation of the weed.