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. 2022 Nov 24;23(23):14676.
doi: 10.3390/ijms232314676.

Transcriptomics Profiling of Acer pseudosieboldianum Molecular Mechanism against Freezing Stress

Zhiming Han  1   2 , Xiangzhu Xu  3 , Shikai Zhang  1 , Qiushuang Zhao  1 , Hanxi Li  1 , Ying Cui  2 , Xiao Li  2 , Liran Wang  2 , Su Chen  1 , Xiyang Zhao  2
Affiliations

Transcriptomics Profiling of Acer pseudosieboldianum Molecular Mechanism against Freezing Stress

Zhiming Han et al. Int J Mol Sci. .

Abstract

Low temperature is an important environmental factor that affects the growth and development of trees and leads to the introduction of failure in the genetic improvement of trees. Acer pseudosieboldianum is a tree species that is well-known for its bright red autumn leaf color. These trees are widely used in landscaping in northeast China. However, due to their poor cold resistance, introduced A. pseudosieboldianum trees suffer severe freezing injury in many introduced environments. To elucidate the physiological indicators and molecular mechanisms associated with freezing damage, we analyzed the physiological indicators and transcriptome of A. pseudosieboldianum, using kits and RNA-Seq technology. The mechanism of A. pseudosieboldianum in response to freezing stress is an important scientific question. In this study, we used the shoots of four-year-old A. pseudosieboldianum twig seedlings, and the physiological index and the transcriptome of A. pseudosieboldianum under low temperature stress were investigated. The results showed that more than 20,000 genes were detected in A. pseudosieboldianum under low temperature (4 °C) and freezing temperatures (-10 °C, -20 °C, -30 °C, and -40 °C). There were 2505, 6021, 5125, and 3191 differential genes (DEGs) between -10 °C, -20°C, -30°C, -40 °C, and CK (4 °C), respectively. Among these differential genes, 48 genes are involved in the MAPK pathway and 533 genes are involved in the glucose metabolism pathway. In addition, the important transcription factors (MYB, AP2/ERF, and WRKY) involved in freezing stress were activated under different degrees of freezing stress. A total of 10 sets of physiological indicators of A. pseudosieboldianum were examined, including the activities of five enzymes and the accumulation of five hormones. All of the physiological indicators except SOD and GSH-Px reached their maximum values at -30 °C. The enzyme activity of SOD was highest at -10 °C, and that of GSH-Px was highest at -20 °C. Our study is the first to provide a more comprehensive understanding of the differential genes (DEGs) involved in A. pseudosieboldianum under freezing stress at different temperatures at the transcriptome level. These results may help to clarify the molecular mechanism of cold tolerance of A. pseudosieboldianum and provide new insights and candidate genes for the genetic improvement of the freezing tolerance of A. pseudosieboldianum.

Keywords: Acer pseudosieboldianum; DEGs; RNA-seq; freezing stress.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The expression of physiological indicators of A. pseudosieboldianum under freezing stress at different temperatures. (A) is the curve analysis of different physiological indicators to determine the accuracy of the test data; (B) is the activity and content expression of physiological indicators under freezing stress at different temperatures. These include the enzymatic activities of SOD, POD, CAT, APX and GSH-Px and the accumulation of ABA, MDA, H2O2, proline, and soluble sugar under freezing stress at different temperatures.
Figure 2
Figure 2
The number of DEGs caused by freezing of A. pseudosieboldianum at different temperatures. Map An is principal component analysis (PCA), which compresses the original data into five principal components to describe the characteristics of the original data set (A). PC1 represents the most obvious features in the multidimensional data matrix, PC2 represents the most significant features in the data matrix except PC1, (B) shows the clustering analysis of gene expression in five periods, and (C) shows the quantitative expression of differential genes in different periods. APCK, APA, APB, APC, and APD represent A. pseudosieboldianum, 4 °C, −10 °C, −20 °C, −30 °C and −40 °C, respectively.
Figure 3
Figure 3
Wayne diagram of A. pseudosieboldianum and DEGs of CK (4 °C) under different temperature freezing stress. They provide a comparison between −10 °C treatment and 4 °C treatment, −20 °C treatment and 4 °C treatment, −30 °C treatment and 4 °C treatment, and −40 °C treatment and 4°C treatment.
Figure 4
Figure 4
GO analysis of DEGs of A. pseudosieboldianum under freezing stress at different temperatures. The Y and X axes correspond to GO terminology and the number of DEGs. The (A) figure shows the comparison of −10 °C treatment and 4 °C treatment; the (B) diagram shows the comparison of −20 °C treatment and 4 °C treatment; the (C) diagram shows the comparison of −30 °C treatment and 4 °C treatment; and the (D) diagram shows the comparison of −40 °C treatment and 4 °C treatment.
Figure 5
Figure 5
KEGG enrichment analysis of DEGs in A. pseudosieboldianum under freezing stress at different temperatures. KEGG pathway classification of DEGs of A. pseudosieboldianum under low-temperature stress at different temperatures and CK group control, respectively. The y-axis corresponds to the KEGG pathway, the x-axis indicates the number of DEGs enriched in a pathway between the enrichment rate. The color of the dot represents the q-value and the size of the dot represents the number of DEGs mapped to the reference pathway. A larger rich factor indicates a greater enrichment. A smaller q-value indicates a more significant enrichment. (A) is the KEGG enrichment analysis of DEGs between APCK (4 °C) and APA (−10 °C), (B) is the KEGG enrichment analysis of DEGs between APCK (4 °C) and APB (−20 °C), (C) is the KEGG enrichment analysis of DEGs between APCK (4 °C) and APC (−30 °C), (D) is the KEGG enrichment analysis of DEGs between APCK (4 °C) and APD (−40 °C).
Figure 6
Figure 6
Expression of DEGs on MAPK pathway in A. pseudosieboldianum under freezing stress at different temperatures. The heatmap expression shows the differential gene expression of A. pseudosieboldianum under freezing stress at different temperatures compared to CK (4 °C).
Figure 7
Figure 7
Expression of DEGs in the gluconeogenic pathway of A. pseudosieboldianum under freezing stress at different temperatures. The heat map shows the differential gene expression of A. pseudosieboldianum under freezing stress at different temperatures compared to CK (4 °C).
Figure 8
Figure 8
Transfer factors of A. pseudosieboldianum under freezing stress at different temperatures.
Figure 9
Figure 9
Expression of MYB, AP2/ERF, and WRKY genes. APCK: A. pseudosieboldianum treated at 4 °C; APA: A. pseudosieboldianum treated at −10 °C; APB: A. pseudosieboldianum treated at −20 °C; APC: A. pseudosieboldianum treated at −30 °C; APD: A. pseudosieboldianum treated at −40 °C.
Figure 9
Figure 9
Expression of MYB, AP2/ERF, and WRKY genes. APCK: A. pseudosieboldianum treated at 4 °C; APA: A. pseudosieboldianum treated at −10 °C; APB: A. pseudosieboldianum treated at −20 °C; APC: A. pseudosieboldianum treated at −30 °C; APD: A. pseudosieboldianum treated at −40 °C.
Figure 10
Figure 10
A. pseudosieboldianum freezing stress summary figure.
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