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

Scientific Reports
Dahe QiaoZhengwu Chen

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...Continue Reading

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Citations

Nov 30, 2019·International Journal of Molecular Sciences·Lin LinMingjie Chen
Jul 7, 2020·Advanced Materials·Lishuai JinKatia Bertoldi
Aug 10, 2019·Frontiers in Genetics·Nam V HoangRobert J Henry

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Methods Mentioned

BETA
RNA-seq
ICE
PCR
reverse transcription PCR

Software Mentioned

Perl scripts
KOBAS
rMATS
TransDecoder
Primer Premier
Iso
- ToFU
CNCI
SMRT
Quiver

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