SOME SUGGESTION ON PHYLOGENETIC ANALYSIS OF A PLASTIDIAL GENE??????
Plastidial genes primarily play a great role in the plant photosynthetic evolution. Remembering the endosymbiotic theory where the chloroplast was traced is a great way to venture for researches. Now as the prokaryote is evolving, their photosynthetic metabolism is also changing which is dependent on the current atmospheric status of the earth billion years ago.
If we start with the chloroplasts, we can venture on the pigments that have evolved to the latest sets of plants. You can trace at what point in time when pigments have evolve OR was it already present in the first photosynthetic organism? Looking at that point, you can also see which pigment came out first.
Since there are lots of plastids in plants, you can look at the possibilities of the characteristics of each. For example Chloroplasts, chromoplasts, etioplasts, and leucoplasts have different characteristics and have a wide research interest to venture in.
Hope this helps.