Transcriptome technology

Genomic and transcriptomic technologies have been used to rapidly identify biosynthetic steps. There are currently over 40,000 expressed enzyme tags (ESTs) generated fi om alkaloid-producing plants that have been used to isolate genes involved in the alkaloid pathway [7]. Some alkaloid biosynthetic steps occur as spontaneous chemical reactions without the use of enzymes, for example, conversion of the intermediate neopine into codeinone in the morphine biosynthetic pathway. Also, some enzymes may catalyze two or more separate reactions in the pathway, for example, hyoscyamine 6-hydroxylase, which carries out two consecutive steps in the scopolamine biosynthetic pathway. Alkaloid biosynthesis also involves compartmentalization. Tissue-specific localization studies have shown that sequential biosynthetic enzymes can occur in distinct cell types [8, 9]. During the biosynthesis of the indole alkaloids vinblastine and vincristine in Catharanthus roseus, different enzymatic steps are carried out in different cellular compartments (Fig. 8.5) [10]. Various steps in the pathway are carried out in different types of cell. This requires the intercellular transport of metabolic intermediates. Similarly, scopolamine biosynthesis also involves two different cell types. 

Transcriptomic studies, which analyze gene expression, have improved the understanding of the complex interaction between genetic and environmental factors, such as lifestyle and nutrition. Transcriptomic technologies have arguably... 

Use of a systems approach to study efficiency, including nse of transcriptomic technologies... 

In summary, the technology and methodology of transcriptional profiling continues to improve. It is foreseeable that transcriptomics will eventually join... 

Most recent studies in the area of transcriptomics have focused on the utility of microarray technologies which consist of pre-syn-thesized probes (cDNA or oligonucleotides) bound to an appara-... 

As a general trend, de novo transcriptome assembly studies reveal greater transcriptome complexity than expected and provide a blueprint for further studies. De novo transcriptome assembly of black pepper is a representative example of the application of SOLiD RNA-Seq technology in nonmodel species (29). In that study, 71 million short reads, representing a sequencing coverage per base (depth) of 62X, were used to assemble a total of 22,363 transcripts in root samples. Transcript and functional annotation was performed based on the sequence homology with other species. 

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