The extent of structural variants (SVs), in particular copy number variations (CNVs) in plant and animal genomes remains unknown, mainly due to the lack of population-scale truly high-quality genomes. Here, we de novo assembled and annotated 31 gold-standard reference genomes from varieties representing all major cultivated rice subtypes, and accurately detected 107,251 non-redundant SVs affecting 644.91Mbp. A position-resolved pan-genome comprising 66,636 genes enabled our discovery that more than 38% of protein-coding genes in cultivated rice harbor CNVs, a far greater proportion than previous estimate. Illustrating functional consequences of these variations, CNVs of Awn3-1, OsVIL1 and OsMADS18, as well as a 345kb inversion likely contributed to major events in rice evolution, domestication and environmental adaptation. Beyond fully resolving the SVs of cultivated rice and comprehensively cataloguing CNVs among protein-coding genes, our study suggests that SVs-affected genes likely contribute to many mechanisms underlying domestication and phenotypic variation in rice.
Qin, Peng and Lu, Hongwei and Du, Huilong and Chen, Weilan and Wang, Hao and Ou, Shujun and Chen, Zhuo 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 Qiang, Yangwen and Fan, Shijun and Li, Weitao and Wang, Jiang and He, Min and Yin, Junjie and Jiang, Ning and Chen, Xuewei and Liang, Chengzhi and Li, Shigui, A Catalog of Structural and Gene Copy Number Variations of Cultivated Rice. Available at SSRN: https://ssrn.com/abstract=3525548 or http://dx.doi.org/10.2139/ssrn.3525548
This version of the paper has not been formally peer reviewed.
Subscribe to this free journal for more curated articles on this topic
FOLLOWERS
20
PAPERS
9,160
Feedback
Feedback to SSRN
If you need immediate assistance, call 877-SSRNHelp (877 777 6435) in the United States, or +1 212 448 2500 outside of the United States, 8:30AM to 6:00PM U.S. Eastern, Monday - Friday.