Construction and application of a graphic visualization tool for important forage omics data

doi:10.11686/cyxb2023166

Abstract

Abstract:

The post-genomic era in biological science has commenced with the publication of genome and transcriptome sequencing data for numerous forage grasses enabled by the rapid advancement of high-throughput sequencing technologies. The focus of genomics research has shifted from understanding genome structure to the level of identifying and validating gene functions. What’s more， gene expression in different tissues plays an important guiding role in the mining of gene function. In previous studies， most expression data across different tissues in the field of breeding research have only been presented in formats such as histograms， tables， or basic heatmaps. However， the visualizations conveyed by these methods are relatively simple in form， and the results are not visually compelling， making it difficult for readers to obtain relevant information quickly and effectively. In order to display combinatorial data more intuitively， aesthetically， and comprehensively， this study developed a forage data visualization workflow， which uses TBtools software and ten important forage grasses and legumes， including Medicago sativa， Medicago truncatula， Leymus chinensis， and Melilotus officinalis as the species for investigation. By combining with a file drawn by Adobe Illustrator， a set of forage omics data and visualization workflow was constructed. The expression pattern of the MsSAP gene in alfalfa and the changes in expression under different stresses was taken as a case study to illustrate data acquisition， heatmap generation and result visualization when using the workflow. Compared with the traditional graphic display method， it was found that by using the forage SVG graphics files and visualization processes provided by us to visualize multi-omics data， researchers can more rapidly， efficiently and aesthetically visualize their own multi-omics research results， so as to provide a basis for the subsequent in-depth mining of functional genes and functional verification.

Key words: forage grasses, breeding, gene expression, graphic drawing

Jia-hui CHEN, Wen-xian LIU. Construction and application of a graphic visualization tool for important forage omics data[J]. Acta Prataculturae Sinica, 2024, 33(2): 57-67.

Figures/Tables 10

Fig.1 10 species reference maps for drawing SVG images

Fig.2 The process of drawing SVG diagram of alfalfa

Fig.3 Results of SVG image generation for ten forage grasses

Fig.4 Acquisition of color code

Table 1 Color code for heatmap generation

器官Organ	颜色代码Color code
花Flower	187，72，253
叶Leaf	0，168，64
根瘤Nodule	107，105，44
根Root	225，228，98

Table 2 Expression matrix of different tissues of alfalfa

基因名称 Gene ID	花 Flower	叶 Leaf	根瘤 Nodule	根 Root
MsSAP7/13	9	5	7	13
MsSAP14	53	41	32	38
MsSAP6/18	76	36	23	55
MsSAP8/10/12	0	0	1	0
MsSAP19/20	38	46	38	51
MsSAP21/22	2	0	0	0

Fig.5 Interface of eFP Browers

Fig.6 TBtools cartoon heatmap result output interface

Fig.7 Analysis of the tissue expression pattern of alfalfa SAP members

Fig.8 Gene expression in root systems treated with different durations of aluminum stress

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