Visualization software for plant gene editing identification

doi:10.3969/j.issn.1004-1524.2022.12.19

Acta Agriculturae Zhejiangensis ›› 2022, Vol. 34 ›› Issue (12): 2759-2766.DOI: 10.3969/j.issn.1004-1524.2022.12.19

• Biosystems Engineering • Previous Articles Next Articles

Visualization software for plant gene editing identification

YOU Qi(), WU Wenwen, JIANG Yi

Key Laboratory of Plant Functional Genomics of Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co-innovation Center for Modern Production Technology of Grain Crops of Jiangsu, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China

Received:2021-11-24 Online:2022-12-25 Published:2022-12-26

Abstract

Abstract:

The CRISPR editing system together with high-throughput sequencing can evaluate the efficiency and accuracy of mutation efficiently. At present, they have been widely used in genetics, biology, medicine and others. However, a one-click visualization tool was lack to evaluate mutation efficiency and accuracy of high-throughput sequencing data. Here, a Python-based visualization tool was developed, named as the visualization software for plant gene editing identification. The software can calculate high-throughput gene editing data together, and can realize data preprocessing (split and merge), detection of mutation and efficiency, visualization outputs of charts with one click. The software was an interface program, data input and results output could be realized by clicking the mouse. The outputs had a variety of formats, including images zooming and color change, which was convenient for post-processing results and writing papers. In addition, the tool supported multiple operating systems (Windows, Linux and MacOS) and was easy to install and use. At present, the user manual and program package of the software had been uploaded to the open software platform.

Key words: high-throughput data, visualization interface, mutation calculation, genome editing efficiency

CLC Number:

S126

YOU Qi, WU Wenwen, JIANG Yi. Visualization software for plant gene editing identification[J]. Acta Agriculturae Zhejiangensis, 2022, 34(12): 2759-2766.

Figures/Tables 5

Fig.1 The work flow of the visualization software for plant gene editing identification

Fig.2 Example of input files A, Information table of gene editing sample group; B, Sample information table; C, Edit range of target sequence.

Fig.3 Introduction of outputs A, The summary of the editing results. The upper part was the link to a single sample and the lower part was the link to the comparison between the experimental group and the control group; B, The deletion histogram of a single sample (AsCpf1-OsPDS-crRNA01_rep1). The x-axis was nucleotide sequence of the target gene, the PAM sequence was red, and the y-axis was the deletion frequency; C, The x-axis of the colorful matrix was detected reads (or alleles) after editing, and the numbers were occurrences of the alleles. The four base ATCGs were represented in different colors. The following part was a fasta format of the editing result; D, The comparison deletion histograms of the editing group (duplicate) and the control sample (AsCpf1-OsPDS-crRNA01 control); E, Deletion length distribution of target sites (sample AsCpf1-OsPDS-crRNA01). The x-axis was the deletion length of target gene sequence, and the y-axis was the frequency of deletion length.

Fig.4 The diversified format of results The software supported customizable editing of result format. Users could zoom in or out to view the editing area, or change the color ratio. The changed results could be directly saved in pdf format.

Table 1 Comparison of functions between visual editing software and other software for crop gene editing

项目Item	1	2	3	4	5	6
网络界面Network interface	√	√			√
GUI			√	√	√	√
数据预处理Data preprocessing	√					√
一键分析One-click analysis		√	√			√
数据批量分析	√		√	√		√
Batch analysis of data
可视化Visualization		√		√	√	√

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Visualization software for plant gene editing identification

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