Genomic insights into the evolution of Echinochloa species as weed and orphan crop

Dongya Wu, Enhui Shen, Bowen Jiang, Yu Feng, Wei Tang, Sangting Lao, Lei Jia, Han Yang Lin, Lingjuan Xie, Xifang Weng, Chenfeng Dong, Qinghong Qian, Feng Lin, Haiming Xu, Huabing Lu, Luan Cutti, Huajun Chen, Shuiguang Deng, Longbiao Guo, Tse Seng ChuahBeng Kah Song, Laura Scarabel, Jie Qiu, Qian Hao Zhu, Qin Yu, Michael P. Timko, Hirofumi Yamaguchi, Aldo Merotto, Yingxiong Qiu, Kenneth M. Olsen, Longjiang Fan, Chu Yu Ye

Research output: Contribution to journalArticlepeer-review

22 Scopus citations


As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.

Original languageEnglish
Article number689
JournalNature communications
Issue number1
StatePublished - Dec 2022


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