Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense

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 PTCcontaining 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.

A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense

“…Through in-depth analysis, we detected 7,527 lncRNAs, much more than the 183 AS lncRNAs. Compared with protein-coding genes, the effect of AS in lncRNAs was much weaker (Tu et al, 2020). Among these lncRNAs, lincRNA accounted for the largest proportion, a finding that was consistent with reports in poplar and hickory (Carya cathayensis) (Liu et al, 2018;Fan et al, 2020;Guo et al, 2020).…”

“…lncRNAs are essential regulators involved in plant growth and development, the stress response, disease resistance, the immune response, and the vernalization response (Wu et al, 2020). In our previous study, we identified only 183 lncRNAs affected by AS (Tu et al, 2020). However, in other studies, the number of lncRNAs was much more than 183.…”

“…Total RNA isolation, library construction, sequencing, and row data processing were fully described in our previous study (Tu et al, 2020). In total, 21 Illumina sequencing libraries and 1 mixed SMRT library were constructed, sequenced, and analyzed.…”

“…In our previous study, we identified 8,503 AS genes (Tu et al, 2020). Actually, 310 tissue-specific genes had undergone AS; stamen-specific genes accounted for most of these (171), followed by leaf-specific genes (65), shoot-apex-specific genes (35), bractspecific genes (21), pistil-specific genes (15), petal-specific genes (2), and a sepal-specific gene (1) (Figure 6C).…”

“…These lncRNAs participate in multiple biological processes, including plant growth and development, the stress response, disease resistance, the immune response, and vernalization response (Liu et al, 2020;Wu et al, 2020); for example, ASCO and COLDAIR participate in Arabidopsis thaliana root development and the vernalization response, respectively (Heo and Sung, 2011;Bardou et al, 2014), ALEX1 enhances rice (Oryza sativa) disease resistance (Yu et al, 2020), and PILNCR1 improves the tolerance of maize (Zea mays) under phosphate deficiency conditions (Du et al, 2018). In our previous study, we identified only 183 lncRNAs that had undergone alternative splicing (AS), and this value was far lower than the number of lncRNAs found in other species (Liu et al, 2018;Guo et al, 2020;Tu et al, 2020). Therefore, it is necessary to comprehensively study lncRNAs in L. chinense.…”