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SuperDecode: An integrated toolkit for analyzing mutations induced by genome editing

文献类型： 外文期刊

作者： Li, Fuquan 1 ; Tan, Xiyu 1 ; Li, Shengting 1 ; Chen, Shaotong 1 ; Liu, Lin 6 ; Huang, Jingjing 1 ; Li, Gufeng 1 ; Lu, Zijun 1 ; Wu, Jinwen 1 ; Zeng, Dongchang 1 ; Luo, Yanqiu 1 ; Dong, Xiaoou 6 ; Ma, Xingliang 7 ; Zhu, Qinlong 1 ; Chen, Letian 1 ; Liu, Yao-Guang 1 ; Chen, Chengjie 2 ; Xie, Xianrong 1 ;

作者机构： 1.South China Agr Univ, Coll Agr, Guangdong Basic Res Ctr Excellence Precise Breedin, Guangdong Lab Lingnan Modern Agr,State Key Lab Con, Guangzhou 510642, Peoples R China

2.Chinese Acad Trop Agr Sci, Trop Crops Genet Resources Inst, Haikou 571101, Peoples R China

3.Natl Key Lab Trop Crop Breeding, Haikou 571101, Peoples R China

4.Minist Agr & Rural Affairs, Lab Crop Gene Resources & Germplasm Enhancement So, Haikou 571101, Peoples R China

5.Key Lab Trop Crops Germplasm Resources Genet Impro, Haikou 571101, Peoples R China

6.Nanjing Agr Univ, State Key Lab Crop Genet & Germplasm Enhancement &, Zhongshan Biol Breeding Lab, Nanjing 210095, Peoples R China

7.Univ Saskatchewan, Dept Plant Sci, Saskatoon, SK S7H 0W9, Canada

8.Univ Saskatchewan, Crop Dev Ctr, Saskatoon, SK S7H 0W9, Canada

关键词： CRISPR/; Cas; genome editing; high throughput; mutation analysis; sequencing; SuperDecode

期刊名称：MOLECULAR PLANT （ 影响因子：24.1； 五年影响因子：25.8 ）

ISSN： 1674-2052

年卷期： 2025 年 18 卷 4 期

页码：

收录情况： SCI

摘要： Genome editing using CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPRassociated protein) or other systems has become a cornerstone of numerous biological and applied research fields. However, detecting the resulting mutations by analyzing sequencing data remains time consuming and inefficient. In response to this issue, we designed SuperDecode, an integrated software toolkit for analyzing editing outcomes using a range of sequencing strategies. SuperDecode comprises three modules, DSDecodeMS, HiDecode, and LaDecode, each designed to automatically decode mutations from Sanger, high-throughput short-read, and long-read sequencing data, respectively, from targeted PCR amplicons. By leveraging specific strategies for constructing sequencing libraries of pooled multiple amplicons, HiDecode and LaDecode facilitate large-scale identification of mutations induced by single or multiplex targetsite editing in a cost-effective manner. We demonstrate the efficacy of SuperDecode by analyzing mutations produced using different genome editing tools (CRISPR/Cas, base editing, and prime editing) in different materials (diploid and tetraploid rice and protoplasts), underscoring its versatility in decoding genome editing outcomes across different applications. Furthermore, this toolkit can be used to analyze other genetic variations, as exemplified by its ability to estimate the C-to-U editing rate of the cellular RNA of a mitochondrial gene. SuperDecode offers both a standalone software package and a web-based version, ensuring its easy access and broad compatibility across diverse computer systems. Thus, SuperDecode provides a comprehensive platform for analyzing a wide array of mutations, advancing the utility of genome editing for scientific research and genetic engineering.

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