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

Autor: Wu D; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China., Shen E; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China.; Zhejiang University Zhongyuan Institute, Zhengzhou, 450000, China., Jiang B; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China., Feng Y; Institute of Ecology, Zhejiang University, Hangzhou, 310058, China.; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China., Tang W; State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China., Lao S; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China., Jia L; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China., Lin HY; Institute of Ecology, Zhejiang University, Hangzhou, 310058, China., Xie L; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China., Weng X; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China., Dong C; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China., Qian Q; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China., Lin F; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China., Xu H; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China., Lu H; Institute of Maize and Upland Grain, Zhejiang Academy of Agricultural Sciences, Dongyang, 322105, China., Cutti L; Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91540-000, Brazil., Chen H; College of Computer Science and Technology, Zhejiang University, Hangzhou, 310058, China., Deng S; College of Computer Science and Technology, Zhejiang University, Hangzhou, 310058, China., Guo L; State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China., Chuah TS; Faculty of Plantation and Agrotechnology, Universiti Teknologi MARA, 02600, Arau, Perlis, Malaysia., Song BK; School of Science, Monash University Malaysia, 46150, Bandar Sunway, Selangor, Malaysia., Scarabel L; Istituto per la Protezione Sostenibile delle Piante (IPSP), CNR, Viale dell'Università, 16, 35020, Legnaro (PD), Italy., Qiu J; Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200235, China., Zhu QH; CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia., Yu Q; Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Crawley, WA, 6009, Australia., Timko MP; Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA., Yamaguchi H; Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan., Merotto A Jr; Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91540-000, Brazil., Qiu Y; Institute of Ecology, Zhejiang University, Hangzhou, 310058, China., Olsen KM; Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA., Fan L; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China.; Zhejiang University Zhongyuan Institute, Zhengzhou, 450000, China., Ye CY; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China. yecy@zju.edu.cn.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2022 Feb 03; Vol. 13 (1), pp. 689. Date of Electronic Publication: 2022 Feb 03.
DOI: 10.1038/s41467-022-28359-9
Abstrakt: 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.
(© 2022. The Author(s).)
Databáze: MEDLINE
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