An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis

Discovery of putative capsaicin biosynthetic genes by RNA-Seq and digital gene expression analysis of pepper

The Indian pepper 'Guijiangwang' (Capsicum frutescens L.), one of the world's hottest chili peppers, is rich in capsaicinoids. The accumulation of the alkaloid capsaicin and its analogs in the epidermal cells of the placenta contribute to the pungency of Capsicum fruits. To identify putative genes involved in capsaicin biosynthesis, RNA-Seq was used to analyze the pepper's expression profiles o...

Cloning and expression of SgCYP450-4 from Siraitia grosvenorii

CYP450 plays an essential role in the development and growth of the fruits of Siraitia grosvenorii. However, little is known about the SgCYP450-4 gene in S. grosvenorii. Here, based on transcriptome data, a full-length cDNA sequence of SgCYP450-4 was cloned by reverse transcriptase-polymerase chain reaction (RT-PCR) and rapid-amplification of cDNA ends (RACE) strategies. SgCYP450-4 is 1677 bp i...

Npr1 Gene Transformation as Assessed by Germ Cell in Situ Transformation Pathway into Siraitia Grosvenorii

NPR1 gene was transformed into Siraitia grosvenorii (Swingle) C. Jeffrey ex. A.M. Lu and Zhi Y. Zhang by germ cell in situ transformation. Ovary injection, cutting chapiter, and chapiter spreading treatments were applied in this study. The transgenic plants were selected using hygromycin screening and confirmed by PCR testing, genome integrated with NPR1 gene in transgenic plants was analyzed b...

Introduction to differential gene expression analysis using RNA-seq

RNA-Seq workflow: gene-level exploratory analysis and differential expression

Here we walk through an end-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were aligned to the reference genome, and prepare a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample. We will perform exploratory data analysis (EDA) for quality assessment and to e...