Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense

Zhonghua Tu; Yufang Shen; Shaoying Wen; Yaxian Zong; Huogen Li

doi:10.3389/fpls.2020.578100

Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense

Front Plant Sci. 2020 Sep 23:11:578100. doi: 10.3389/fpls.2020.578100. eCollection 2020.

Authors

Zhonghua Tu^{1

2}, Yufang Shen^{1

2}, Shaoying Wen^{1

2}, Yaxian Zong^{1

2}, Huogen Li^{1

2}

Affiliations

¹ Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China.
² Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.

Abstract

Alternative splicing (AS) plays pivotal roles in regulating plant growth and development, flowering, biological rhythms, signal transduction, and stress responses. However, no studies on AS have been performed in Liriodendron chinense, a deciduous tree species that has high economic and ecological value. In this study, we used multiple tools and algorithms to analyze transcriptome data derived from seven tissues via hybrid sequencing. Although only 17.56% (8,503/48,408) of genes in L. chinense were alternatively spliced, these AS genes occurred in 37,844 AS events. Among these events, intron retention was the most frequent AS event, producing 1,656 PTC-containing and 3,310 non-PTC-containing transcripts. Moreover, 183 long noncoding RNAs (lncRNAs) also underwent AS events. Furthermore, weighted gene coexpression network analysis (WGCNA) revealed that there were great differences in the activities of transcription and post-transcriptional regulation between pistils and leaves, and AS had an impact on many physiological and biochemical processes in L. chinense, such as photosynthesis, sphingolipid metabolism, fatty acid biosynthesis and metabolism. Moreover, our analysis showed that the features of genes may affect AS, as AS genes and non-AS genes had differences in the exon/intron length, transcript length, and number of exons/introns. In addition, the structure of AS genes may impact the frequencies and types of AS because AS genes with more exons or introns tended to exhibit more AS events, and shorter introns tended to be retained, whereas shorter exons tended to be skipped. Furthermore, eight AS genes were verified, and the results were consistent with our analysis. Overall, this study reveals that AS and gene interaction are mutual-on one hand, AS can affect gene expression and translation, while on the other hand, the structural characteristics of the gene can also affect AS. This work is the first to comprehensively report on AS in L. chinense, and it can provide a reference for further research on AS in L. chinense.

Keywords: L. chinense; alternative splicing; heterogeneous nuclear ribonucleoprotein genes; hybrid sequencing; long noncoding RNAs; premature termination codon; serine/arginine-rich genes; weighted gene coexpression network analysis.