Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Qin, P., Lu, H., Du, H., Wang, H., Chen, W., Chen, Z., He, Q., Ou, S., Zhang, H., Li, X., Li, X., Li, Y., Liao, Y., Gao, Q., Tu, B., Yuan, H., Ma, B., Wang, Y., Qian, Y., Fan, S., Li, W., Wang, J., He, M., Yin, J., Li, T., Jiang, N., Chen, X., Liang, C., & Li, S. Cell, 184(13):3542–3558.e16, June, 2021.
Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations [link]Paper  doi  abstract   bibtex   
Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population. Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication. Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly. Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research.
@article{qin_pan-genome_2021,
	title = {Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations},
	volume = {184},
	issn = {0092-8674},
	url = {https://www.sciencedirect.com/science/article/pii/S009286742100581X},
	doi = {10.1016/j.cell.2021.04.046},
	abstract = {Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population. Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication. Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly. Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research.},
	language = {en},
	number = {13},
	urldate = {2022-09-13},
	journal = {Cell},
	author = {Qin, Peng and Lu, Hongwei and Du, Huilong and Wang, Hao and Chen, Weilan and Chen, Zhuo and He, Qiang and Ou, Shujun and Zhang, Hongyu and Li, Xuanzhao and Li, Xiuxiu and Li, Yan and Liao, Yi and Gao, Qiang and Tu, Bin and Yuan, Hua and Ma, Bingtian and Wang, Yuping and Qian, Yangwen and Fan, Shijun and Li, Weitao and Wang, Jing and He, Min and Yin, Junjie and Li, Ting and Jiang, Ning and Chen, Xuewei and Liang, Chengzhi and Li, Shigui},
	month = jun,
	year = {2021},
	keywords = {high-level, pangenome},
	pages = {3542--3558.e16},
}

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