The plastid (chloroplast) genome

The higher plant chloroplast genome is roughly 150,000 bps.  It contains genes for the obvious, photosynthesis and gene expression (transcription and translation), and the less obvious, such as one subunit of an enzyme involved in lipid synthesis.  Because of cytoplasmic segregation (a random process where regions of plant tissue end up with identical chloroplast genomes – IF there were any variants to start), you can isolate DNA from plant tissue and assume, with some confidence, that all the molecules are the same.  As such, you rarely find multiple alleles in a sample of chloroplast DNAs.  Therefore, most workers use techniques such as the polymerase chain reaction to amplify a region of interest and sequence the amplified product without need of cloning (needed to separate alleles/loci).  The diagram below shows a chloroplast genome with the typical structural features: a large single-copy region (LSC), a small single copy region (SSC) and two inverted repeats (IR).  Because of their capacity to recombine with each other, gene sequences in the IRs match each other and are more conserved on average than sequences in either of the single-copy regions.

http://www.orchidstudium.com/Estrangeiras/Phalaenopsis%20aphrodite.html

Four regions were chosen for your research project:  the accD-psaI spacer, the atpF intron, the petB intron and the rpoB-trnC spacer.  Since the goal is to identify chloroplast sequences evolving at a sufficiently rapid pace to differentiate closely related genera, spacers and introns were chosen over coding sequences (exons).

The image below represents the recently sequenced chloroplast genome of Phalaenopsis aphrodite Rchb.f, a member of the subtribe Aeridinae from Taiwan to the Philippines, that has been frequently used as a parent in making the showy Phalaenopsis hybrids for sale in box stores.  The placement of boxes/lines inside or outside the circle indicates what strand of DNA is used as the template for gene expression.  Orkdorks, try to find your region and those other teams are working with on this map.

Chang, C.C., Lin, H.C., Lin, I.P., Chow, T.Y., Chen, H.H., Chen, W.H., Cheng, C.H., Lin, C.Y., Liu, S.M. and Chaw, S.M. 2006. The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Mol. Biol. Evol. 23: 279–291.