De novo transcriptome analysis to identify flavonoid biosynthesis genes in Stellera chamaejasme

Abstract

Stellera chamaejasme L. is a well-recognized traditional medicine in China and can synthesizes various secondary metabolites including a group of flavonoids. However, little is known about the molecular mechanisms underlying flavonoid biosynthesis. In this study, large-scale RNA sequencing on flower of S. chamaejasme produced a de novo transcriptome consisting of 32,216 unigenes with a N50 length of 1745 bp. Among all unigenes, 21,355 unigenes were identified as putative homologs of annotated sequences in the public protein databases. Further functional classification revealed that the active genes in flower are predominately involved in metabolic process and biosynthesis of secondary metabolite pathways. A total of 19 candidate genes encoding 11 structural enzymes involved in flavonoid biosynthesis were identified in the unigene dataset by targeted searches of their annotations. In addition, a number of regulatory genes including MYB, basic helix-loop-helix (bHLH), and WD40 repeat proteins were discovered based on transcriptome dataset. Therefore, this study presents the first survey of transcriptome on the flower of S. chamaejasme to discover the major candidate genes involved in flavonoid biosynthesis pathway. These results will promote an understanding of the genetic mechanism of flavonoid biosynthesis in S. chamaejasme. At the same time, this transcriptome dataset can serve as an important public information platform for gene expression, genomic and functional genomic studies in this species.

Genome-scale transcriptional study of hybrid effects and regulatory divergence in an F1 hybrid Ruellia (Wild Petunias: Acanthaceae) and its parents

“…6), including two chalcone synthase (CHS), two chalcone isomerase (CHI), two flavanone 3-hydroxylase (F3H), five flavonoid 3'-hydroxylase (F3'H), two flavonoid 3',5'-hydroxylase (F3’5’H), four dihydroflavonol 4-reductase (DFR), four anthocyanidin synthase (ANS) and seven UDP-glucose flavonoid glucosyl transferase (UFGT). Aspects of the above ratios corroborate prior studies that have found comparatively high copy numbers for DFR ( Lotus japonicus [43]; cherries [44]; red leaf lettuce [45]), UFGT (columbines [46]; cherries [44]; Stellera chamaejasme [47]), F3H (peonies [48]), and ANS ( Zoysia [49]). Similarly, our finding of a low copy number for F3'5'H corroborates data from the above studies (one prominent exception is grapevines, which have been found to have exceptionally high copy variants of this enzyme [50]).…”

De novo sequencing and transcriptome assembly of Arisaema heterophyllum Blume and identification of genes involved in isoflavonoid biosynthesis

“…Before assembly, the raw reads with low quality (above 50% of bases with Q-value ≤ 20), ambiguous reads, adaptor sequences and duplication sequences were removed. A process of transcriptome assembly was described previously 37 . The transcriptome assembler, Trinity 38 , was performed by default parameters (K-mer = 25, group pairs distance = 400) with the following command: Trinity.pl–seqTypefq–left reads_1.fq–right reads_2.fq–max_memory 50 G–CPU 8.…”

Transcriptome-Wide Identification and Prediction of miRNAs and Their Targets in Paris polyphylla var. yunnanensis by High-Throughput Sequencing Analysis

“…Before RNA sequencing, the quality and quantity of total RNA were examined using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The mRNA sequencing was constructed using previously described methods [ 32 ]. Briefly, total RNA were extracted and subsequently prepared for mRNA-Seq on the Illumina Genome Analyzer II following the manufacturer’s instructions (Illumina Inc., San Diego, CA, USA) and cDNA libraries were constructed using random hexamer primers and samples were sequenced using an Illumina HiSeq™ 2000 platform (Illumina Inc.).…”