Mapping Plastid Transcript Population by Circular Reverse Transcription Polymerase Chain Reaction.

During evolution of photosynthetic organisms, the genetic information provided by the internalized cyanobacteria has been transferred to the nucleus. The small genome kept by the chloroplast, the so-called plastome, displays a complex organization, comprising operons under the control of multiples promoters. In addition, polycistronic transcripts undergo multiple processing events, thus generating a complex population of mRNAs from a single gene. This chapter describes a method to investigate the diversity of the mRNA population from a single gene by circular RT-PCR. The protocol provided here allows for the simultaneous mapping of both 5' and 3' ends of the same RNA molecule.