Abstract
BackgroundAlternative splicing (AS) regulates mRNA at the post-transcriptional level to change gene function in organisms. However, little is known about the AS and its roles in tea plant (Camellia sinensis), widely cultivated for making a popular beverage tea.ResultsIn our study, the AS landscape and dynamics were characterized in eight tissues (bud, young leaf, summer mature leaf, winter old leaf, stem, root, flower, fruit) of tea plant by Illumina RNA-Seq and confirmed by Iso-Seq. The most abundant AS (~ 20%) was intron retention and involved in RNA processes. The some alternative splicings were found to be tissue specific in stem and root etc. Thirteen co-expressed modules of AS transcripts were identified, which revealed a similar pattern between the bud and young leaves as well as a distinct pattern between seasons. AS events of structural genes including anthocyanidin reductase and MYB transcription factors were involved in biosynthesis of flavonoid, especially in vegetative tissues. The AS isoforms rather than the full-length ones were the major transcripts involved in flavonoid synthesis pathway, and is positively correlated with the catechins content conferring the tea taste. We propose that the AS is an important functional mechanism in regulating flavonoid metabolites.ConclusionOur study provides the insight into the AS events underlying tea plant’s uniquely different developmental process and highlights the important contribution and efficacy of alternative splicing regulatory function to biosynthesis of flavonoids.
Highlights
Alternative splicing (AS) regulates mRNA at the post-transcriptional level to change gene function in organisms
Approximately 81.9% of AS transcripts were uniquely identified by Illumina sequencing;the lower number of AS transcripts detected from SMRT data may have resulted from the low coverage of the SMRT sequencing reads generated here
Detection and characterization of AS in genes involved in the flavonoid pathway To better understand the putative influence of alternative splicing on secondary metabolism, we investigated AS transcripts of genes which are directly or indirectly involved in characteristic secondary metabolism pathways including the flavonoid, theanine and caffeine (Additional file 1: Figures S2, S3 and S4) [2, 3, 30, 31]
Summary
Alternative splicing (AS) regulates mRNA at the post-transcriptional level to change gene function in organisms. Little is known about the AS and its roles in tea plant (Camellia sinensis), widely cultivated for making a popular beverage tea. Flavonoids are major secondary metabolites present in tea Alternative splicing (AS) is alternative splice site selection, which results in the generation of multiple isoforms from precursor-mRNA (pre-mRNA) transcripts [6, 7]; these AS transcripts are universally present in plants and animals [8]. Analyses of comprehensive transcriptomes from different tissues indicate that almost every intron-containing gene generates multiple tissue-specific splice variants [15, 16]. Despite some studies having explored AS-mediated regulation of flavonoid biosynthesis [21, 22], very little is known of how and by which isoforms modulation occurs in the expression of related structural genes and transcription factors in the flavonoid biosynthesis pathway
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