Cold Response Transcriptome Analysis of the Alternative Splicing Events Induced by the Cold Stress in D. catenatum.

Yan Zheng,Xiangxiang Kong,Danni Yang,Qian Chen,Yongping Yang,Yuhua Wang,Ya Yang,Xiangshi Qin,Landi Luo,Yuqiang Gong

doi:10.3390/ijms23020981

Abstract

Dendrobium catenatum Lindl is a valuable medicinal herb and gardening plant due to its ornamental value and special medical value. Low temperature is a major bottleneck restricting D. catenatum expansion towards the north, which influences the quality and yield of D. catenatum. In this study, we analysed the cold response of D. catenatum by RNA-Seq. A total of 4302 differentially expressed genes were detected under cold stress, which were mainly linked to protein kinase activity, membrane transport and the glycan biosynthesis and metabolism pathway. We also identified 4005 differential alternative events in 2319 genes significantly regulated by cold stress. Exon skipping and intron retention were the most common alternative splicing isoforms. Numerous genes were identified that differentially modulated under cold stress, including cold-induced transcription factors and splicing factors mediated by AS (alternative splicing). GO enrichment analysis found that differentially alternatively spliced genes without differential expression levels were related to RNA/mRNA processing and spliceosomes. DAS (differentially alternative splicing) genes with different expression levels were mainly enriched in protein kinase activity, plasma membrane and cellular response to stimulus. We further identified and cloned DcCBP20 in D. catenatum; we found that DcCBP20 promotes the generation of alternative splicing variants in cold-induced genes under cold stress via genetic experiments and RT–PCR. Taken together, our results identify the main cold-response pathways and alternative splicing events in D. catenatum responding to cold treatment and that DcCBP20 of D. catenatum get involved in regulating the AS and gene expression of cold-induced genes during this process. Our study will contribute to understanding the role of AS genes in regulating the cold stress response in D. catenatum.

Highlights

Cold stress is a significant environmental factor that has an adverse impact on plant growth and development, as well as plant spatial distribution and crop productivity [1]
The foliage became desiccated; plant sections died (Figure 1A). Consistent with these significant cold injury symptoms, we found that the Chl fluorescence in chilled D. catenatum plants was repressed after chilling treatment, with a lower Fv/Fm level compared to the control plants
The abundance and variants of Alternative splicing (AS) in DcCBP20 transgenic plants were altered after cold treatment, and the AS isoforms changes were much similar among three independent transgenic lines. These genes include the gene encoding a pentatricopeptide repeat-containing protein (At4G19440, homologous gene of 110098492 in D. catenatum), which is involved in the transferase activity pathway; we found that the expression level of this gene increased in DcCBP20-OE plants compared to Col-0 Arabidopsis under control condition, and a newly shorter AS product with higher expression level was generated in DcCBP20-OE plants after cold stress compared to Col-0 Arabidopsis

Summary

Introduction

Cold stress is a significant environmental factor that has an adverse impact on plant growth and development, as well as plant spatial distribution and crop productivity [1]. Many crops, including rice, tomato, soybean and cotton, are susceptible to cold stress and lack of cold acclimation mechanisms, causing them to grow exclusively in tropical or subtropical regions [2,3]. At both the physiological and molecular levels, plants have developed a series of mechanisms to acclimatize to cold stress. When plants are exposed to nonfatal low temperatures for a period, they establish an enhanced ability to resist subsequent cold stress, which is termed cold acclimation [4,5]. Cold signaling changes the fluidity of cellular membranes and calcium (Ca2+) influx, which is a critical process to trigger downstream cold-response gene expression [6,7]

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Results

Conclusion