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 Chuah, Beng-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 and Chu-Yu Ye ()
Additional contact information
Dongya Wu: Zhejiang University
Enhui Shen: Zhejiang University
Bowen Jiang: Zhejiang University
Yu Feng: Zhejiang University
Wei Tang: China National Rice Research Institute
Sangting Lao: Zhejiang University
Lei Jia: Zhejiang University
Han-Yang Lin: Zhejiang University
Lingjuan Xie: Zhejiang University
Xifang Weng: Zhejiang University
Chenfeng Dong: Zhejiang University
Qinghong Qian: Zhejiang University
Feng Lin: Zhejiang University
Haiming Xu: Zhejiang University
Huabing Lu: Zhejiang Academy of Agricultural Sciences
Luan Cutti: Federal University of Rio Grande do Sul
Huajun Chen: Zhejiang University
Shuiguang Deng: Zhejiang University
Longbiao Guo: China National Rice Research Institute
Tse-Seng Chuah: Universiti Teknologi MARA
Beng-Kah Song: Monash University Malaysia
Laura Scarabel: Viale dell’Università, 16
Jie Qiu: Shanghai Normal University
Qian-Hao Zhu: CSIRO Agriculture and Food
Qin Yu: University of Western Australia
Michael P. Timko: University of Virginia
Hirofumi Yamaguchi: Osaka Prefecture University, Sakai
Aldo Merotto: Federal University of Rio Grande do Sul
Yingxiong Qiu: Zhejiang University
Kenneth M. Olsen: Washington University in St. Louis
Longjiang Fan: Zhejiang University
Chu-Yu Ye: Zhejiang University

Nature Communications, 2022, vol. 13, issue 1, 1-16

Abstract: Abstract 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.

Date: 2022
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DOI: 10.1038/s41467-022-28359-9

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