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A survey of transcriptome complexity using full-length isoform sequencing in the tea plant Camellia sinensis

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Abstract

Tea is one of the most popular beverages and its leaves are rich in catechins, contributing to the diverse flavor as well as beneficial for human health. However, the study of the post-transcriptional regulatory mechanism affecting the synthesis of catechins remains insufficient. Here, we sequenced the transcriptome using PacBio sequencing technology and obtained 63,111 full-length high-quality isoforms, including 1302 potential novel genes and 583 highly reliable fusion transcripts. We also identified 1204 lncRNAs with high quality, containing 188 known and 1016 novel lncRNAs. In addition, 311 mis-annotated genes were corrected based on the high-quality Isoseq reads. A large number of alternative splicing (AS) events (3784) and alternative polyadenylation (APA) genes (18,714) were analyzed, accounting for 8.84% and 43.7% of the total annotated genes, respectively. We also found that 2884 genes containing AS and APA features exhibited higher expression levels than other genes. These genes are mainly involved in amino acid biosynthesis, carbon fixation in photosynthetic organisms, phenylalanine, tyrosine, tryptophan biosynthesis, and pyruvate metabolism, suggesting that they play an essential role in the catechins content of tea polyphenols. Our results further improved the level of genome annotation and indicated that post-transcriptional regulation plays a crucial part in synthesizing catechins.

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Acknowledgements

This work was supported by Key-Area Research And Development Program of Guangdong Province (2020B020220004), the Natural Science Foundation of Fujian Province, China (Grant Number 2019J05066), and Key Projects of Science and Technology Bureau of Fuzhou, Fujian, China (Grant Number 2021-N-119). We appreciate anonymous reviewers and editor for the insightful comments and valuable suggestions.

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Authors and Affiliations

  1. Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China

    Dongna Ma & Xingtan Zhang

  2. Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China

    Dongna Ma, Qiansu Ding & Liufeng Wei

  3. College of Life Sciences, Fujian Normal University, Fuzhou, China

    Jingping Fang

  4. College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China

    Yiying Li & Liwen Zhang

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  1. Dongna Ma
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Contributions

XZ designed and performed the entire project together. DM was involved in the analysis of the entire study. DM and JF drafted the manuscript. YL and LZ participated in the creation of the results picture. XZ, QD and LW participated in manuscript revision. All authors read and approved the final manuscript.

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Correspondence to Xingtan Zhang.

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Ma, D., Fang, J., Ding, Q. et al. A survey of transcriptome complexity using full-length isoform sequencing in the tea plant Camellia sinensis. Mol Genet Genomics 297, 1243–1255 (2022). https://doi.org/10.1007/s00438-022-01913-2

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