Transcriptome profiling of Hibiscus sabdariffa L. at two maturation stages of calyx tissue
Roselle (Hibiscus sabdariffa L.) is a non-model plant species whose calyces have been studied progressively in science for their metabolite composition and pharmacological potentials in the treatment of hypertension, diabetes, cancer, hyperlipidemia and hyperglycemia. The genetic mechanism that g...
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| Main Author: | |
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| Format: | Thesis |
| Language: | English |
| Published: |
2020
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| Subjects: | |
| Online Access: | http://psasir.upm.edu.my/id/eprint/99212/1/FS%202020%2046%20IR.pdf |
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| Summary: | Roselle (Hibiscus sabdariffa L.) is a non-model plant species whose calyces have been
studied progressively in science for their metabolite composition and pharmacological
potentials in the treatment of hypertension, diabetes, cancer, hyperlipidemia and
hyperglycemia. The genetic mechanism that governs the production of potent
phytochemicals found in roselle calyx tissues such as anthocyanin are yet to be
deciphered and understood. The purpose of this study is to construct a transcriptome
dataset for H. sabdariffa calyx tissues during the last two stages of maturation (stages
three and four) using next-generation sequencing (NGS) technologies. These two
maturation stages are critical as they may affect the quality of the calyx produced. A
series of wet lab experiments were conducted prior to sequencing which included RNAextractions,
rRNA-depletion and cDNA sequencing library constructions. The Illumina
NextSeq 500 sequencer platform was employed for sequencing; while data analysis was
orchestrated using a number of software that included Trinity version 2.2.0 and CLC
Genomic Workbench version 10.1.0. A combined total of more than 200 million good
quality paired-end reads were generated from sequencing that resulted in a de novo
assembled reference transcriptome consisting of 221,334 transcripts, of which 92,974
transcripts (42%) were successfully annotated. Twelve anthocyanin-related genes were
effectually annotated; chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase,
flavanoid 3’-monoxygenase, flavonoid 3’,5’-hydroxylase, dihydroflavonol 4-reductase,
leucoanthocyanidin dioxygenase, flavonoid 3-O-glucosyltransferase, anthocyanidin 3-
O-glucoside 2''-O-glucosyltransferase, coumaroyl-CoA:anthocyanidin 3-O-glucoside-
6''-O-coumaroyltransferase, malonyl-CoA:anthocyanidin 5-O-glucoside-6''-Omalonyltransferase
and flavonoid 3',5'-methyltransferase in this dataset. Differential
expression analysis had identified a total of 504 significant differentially expressed genes
(SDEGs) that were effectively mapped onto 193 KEGG pathway maps. The secondary
metabolites biosynthesis category had attained a relatively high number of SDEGs (40)
mappings. To name a few: the phenylalanine biosynthesis pathway, isoquinoline
alkaloid biosynthesis pathway, diterpenoid biosynthesis pathway, and stilbenoid, diarylheptanoid and gingerol biosynthesis pathway. This study represents the first time
the transcriptome of H. sabdariffa calyx tissues were sequenced using NGS
technologies. The novel transcriptomic data produced in this research provides an
expansion of information on the genetics alongside their dynamics in the calyx tissues
of H. sabdariffa throughout the third and fourth maturation stages, which is useful for
future studies on functional analysis and marker development. |
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