Comprehensive identification of the full-length transcripts and alternative splicing related to the secondary metabolism pathways in the tea plant (Camellia sinensis)

Dahe Qiao,Chun Yang,Kemei Cao,Zhengwu Chen,Juan Chen,Suzhen Niu,Yan Guo,Yan Li

doi:10.1038/s41598-019-39286-z

Dahe Qiao, Chun Yang + Show 6 more

Open Access

https://doi.org/10.1038/s41598-019-39286-z

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Abstract

Flavonoids, theanine and caffeine are the main secondary metabolites of the tea plant (Camellia sinensis), which account for the tea’s unique flavor quality and health benefits. The biosynthesis pathways of these metabolites have been extensively studied at the transcriptional level, but the regulatory mechanisms are still unclear. In this study, to explore the transcriptome diversity and complexity of tea plant, PacBio Iso-Seq and RNA-seq analysis were combined to obtain full-length transcripts and to profile the changes in gene expression during the leaf development. A total of 1,388,066 reads of insert (ROI) were generated with an average length of 1,762 bp, and more than 54% (755,716) of the ROIs were full-length non-chimeric (FLNC) reads. The Benchmarking Universal Single-Copy Orthologue (BUSCO) completeness was 92.7%. A total of 93,883 non-redundant transcripts were obtained, and 87,395 (93.1%) were new alternatively spliced isoforms. Meanwhile, 7,650 differential expression transcripts (DETs) were identified. A total of 28,980 alternative splicing (AS) events were predicted, including 1,297 differential AS (DAS) events. The transcript isoforms of the key genes involved in the flavonoid, theanine and caffeine biosynthesis pathways were characterized. Additionally, 5,777 fusion transcripts and 9,052 long non-coding RNAs (lncRNAs) were also predicted. Our results revealed that AS potentially plays a crucial role in the regulation of the secondary metabolism of the tea plant. These findings enhanced our understanding of the complexity of the secondary metabolic regulation of tea plants and provided a basis for the subsequent exploration of the regulatory mechanisms of flavonoid, theanine and caffeine biosynthesis in tea plants.

Highlights

The tea plant [Camellia sinensis (L.) O
In this study, RNA-seq and full-length transcriptome techniques were used to explore the regulation of alternative splicing events in the secondary metabolism pathways in tea plants
1,297 differential alternative splicing (AS) events were detected between the apical bud and the second leaf under the apical bud, suggesting that AS events occer extensively in tea plants but are tissue-specific

Summary

Introduction

The tea plant [Camellia sinensis (L.) O. The types and contents of the secondary metabolites vary depending on the tissue type and in different periods as well as in different environments[6,31,32], which is similar to the expression patterns of alternatively spliced isoforms. This phenomenon suggests that the AS events of related genes may regulate the secondary metabolism of tea plant and may affect the tea quality. Our results provide a foundation for future studies and insight into the role of AS in flavonoid, theanine and caffeine metabolism in tea plants

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