Agronomically important weeds cause tremendous worldwide losses of crop yields estimated at over $95 billion annually according to UN Food and Agriculture Organization (http://www.fao.org/). Within the short period of agricultural history, weedy plants have evolved to survive in agroecosystems under natural and unintentionally human-mediated selections, leading to a distinct evolutionary state that has proceeded in parallel to crop domestication. Therefore, agricultural weeds are ideal models for the study of environmental adaption of plants from an evolutionary perspective. Uncovering how weeds evolve and how crop and weed interact are crucial for weeds management and protection of the global food supply.
In contrast to numerous food and forage crops where the genomes of many important domesticated forms and their wild relatives have been sequenced, little genomic scale analysis has taken place on agricultural weeds despite their economic significance. Up to now, limited numbers of weed species, such as the monocot barnyardgrass (Echinochloa crus-galli) and dicot horseweed (Conyza canadensis), have had its whole genome sequenced.
We initiated a database (Weedomes at http://ibi.zju.edu.cn/weedomes/ or http://weedgenome.org/) for weed genomes and crop-weed interactions, which provides genome assembly, gene and gene family annotations (including non-target herbicide genes), genome-wide variations, transcriptomic profiles of crop-weed interactions of agricultural weeds. In the current version, the database includes E. crus-galli, C. canadensis and weedy rice.
The current database mainly based on the genomic data from the following papers:
Peng, Y., Lai, Z., Lane, T., Nageswara-Rao, M., Okada, M., Jasieniuk, M., et al. (2014). De Novo Genome Assembly of the Economically Important Weed Horseweed Using Integrated Data from Multiple Sequencing Platforms. Plant Physiol. 166:1241-1254.
Guo, L., Qiu, J., Ye, C., Jin, G., Mao, L., Zhang, H., et al. (2017). Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed. Nat. Commun. 8:1031.
Qiu, J., Zhou, Y., Mao, L., Ye, C., Wang, W., Zhang, J., et al. (2017). Genomic variation associated with local adaptation of weedy rice during de-domestication. Nat. Commun. 8:15323.
Li, L. F., Li, Y. L., Jia, Y., Caicedo, A. L., and Olsen, K. M. (2017). Signatures of adaptation in the weedy rice genome. Nat. Genet. 49:811-814.
How to cite this database:
Lingfeng Mao, Most Humaira Sultana, Qinjie Chu, Jie Qiu, Xiangdong Kong, Dongya Wu, Lei Jia, Longjiang Fan, Chu-yu Ye. 2017. Weedomes: a database for weed genomes and crop-weed interactions. Unpublished