## 8 Comprehensive Gene Expression and Transcriptome Analysis Solution in Medicinal Plants  
There are many gene mining approaches employed for the elucidation of the biosynthetic pathway regulation that occurs in plants; they involve several -omics studies such as transcriptomics, proteomics, metabolomics and bioinformatics approaches. The transcriptome is the complete set of all RNA available in a particular cell, including noncoding RNAs [104]. Transcriptome analysis is a molecular genetic strategy that enables scientists to describe and quantify the transcriptome of a particular organism with the intention of deciphering the complex genetic regulation at the transcriptional level. The develop ment of biotechnology has enabled the utilization of a variety of high-throughput DNA sequencing and identification methods for mining and quantifying transcriptomes, including PCR amplification, microarray analysis and next-generation sequence (NGS)-based RNA-seq [105]. In the field of functional genomics, the transcriptome analysis approach has played a crucial role in decoding the complexity of gene regulation in plants. Numerous transcriptomes have been sequenced in plants using a variety of technological approaches that allowed considerable identification and quantification of the transcriptome, including hybridization- or sequencing-based methods [106; 107; 108]. Hybridization-based technologies, such as DNA microarrays, are used in a powerful technique that requires a preselected RNs library for the fulfillment of a simultaneous hybridization with a fluorescence agent. The intensity levels of the hybridization signify and indicate the expression levels of the genes [109; 110]. On the other hand, sequencing-based methods, such as expressed sequence tag (EST), serial analysis of gene expression (SAGE) and massively parallel signature sequencing (MPSS), use sequencing strategies that do not require the involvement of a preselected RNA library for obtaining results. The MPSS is also known as deep sequencing or next-generation sequencing (NGS) [111]. NGS has become the revolutionary approach in biology due to its remarkable ability to collect and obtain valuable data in a short time, and it has been considered a very useful technique for studying the transcriptome of plants and other organisms. NGS could be coupled with other techniques such as the RNA-seq approach. RNA-seq is a high-throughput sequencing technique that provides a comprehensive gene expression profile of each sample with the potential to quantify and annotate all genes and isoforms [112]. RNA-seq is a sequencing-based approach that is coupled with next-generation sequencing tools for the fulfillment of a variety of objectives. Using RNA-seq technology enabled scientists to perform several experiments such as measuring gene expression levels, obtaining differential expression profiles (DEG), identifying gene structural properties (transcription start site, exon-exon junctions, etc. ), identifying novel transcripts, identifying transcript isoforms and determining allele-specific expression [113]. A transcriptome analysis study conducted by [PERSON] et al. [90] provided large-scale transcriptome profile data for understanding the specialized metabolism of _C. roseus_ that includes the metabolic pathways for the pharmaceutically useful secondary metabolites. The medicinal plant _Catharantthus roseus_ accumulates a wide range of terpenoid indole alkaloids, which are well documented for their medicinal purposes and include the well-known drugs vinblastine and vincitaine, which are widely used in anticancer chemotherapies. The plant is known to treat diabetes also, due to the hypoglycemic properties in its tissue extracts [114]. In general, the natural product of this plant is known to be of significant value medicinally. Using the RNA-seq technique, scientists were able to present a great body of valuable knowledge regarding the gene regulation of the plant [115].