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

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.

Analysis of Terpene Synthase Family Genes in Camellia sinensis with an Emphasis on Abiotic Stress Conditions

“…Putatively functional TPS genes. For assessment of the tea TPS gene functions, full-length transcriptome sequencing data 37,38 were employed to verify the putative functional TPS genes obtained from tea genome. Sequence similarity comparison between the full-length transcripts of TPS and genome assembly were conducted using BLAST with a threshold E-value < 1e-5 and identity >98%.…”

“…These genes have been identified in vivo or vitro 13,33,34,39 . c The predicted protein depend on the transcriptome data 37,38 .…”

Transcriptional regulation of amino acid metabolism in response to nitrogen deficiency and nitrogen forms in tea plant root (Camellia sinensis L.)

“…It is important to achieve a comprehensive understanding of the underlying molecular basis of www.nature.com/scientificreports www.nature.com/scientificreports/ how amino acid biosynthesis and catabolism are regulated at molecular level by N forms in tea plant root. Several studies have explored amino acid contents and corresponding molecular changes that occur in tea plants in response to nutritional and environmental conditions 26,27,30,43,[54][55][56][57] .…”

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus

“…RNA alternative splicing (AS) is another important post-transcriptional regulation mechanism, producing diverse transcript isoforms encoded by the same genes [18]. With the widespread application of fulllength transcriptome sequencing technology, plenty of isoforms produced by alternative splicing events were identi ed in plants [19][20][21]. The structure variation in transcript isoforms can often result in proteins with altered physical characteristics and molecular functions [22].…”

“…These studies focused on the regulation of miRNA on target gene expression, but the in uence of miRNAs on the co-expression network of different splicing isoforms calls for further investigation in the plant. Besides, our understanding of expression and functional divergence of isoforms in response to different developmental and growth factors is impeded by the paucity of relevant case studies in plants [19][20][21][22].…”