Novel evolutionary variation in transcription and location of two chloroplast genes

We have found major evolutionary changes in the types of transcripts produced by specific chloroplast genes, in particular those encoding the large subunit (LS) of ribulose-1,5-bisphosphate carboxylase and a photosystem II polypeptide (PII). Two distinct patterns of LS gene transcripts are revealed by hybridizing an LS gene probe to electrophoretically separated RNA from 19 angiosperms. Most species, including pea, contain the single transcript of approximately 1.6 kb previously observed in corn, spinach and mustard. However, in mung bean and other members of the legume genera Vigna and Phaseolus, the 1.6 kb transcript represents only a minor fraction of LS transcripts, and instead, two larger LS transcripts of approximately 2.4 and 2.6 kb predominate. The PII gene produces a single transcript in pea and most other species examined, while members of the related legume genera Vigna, Phaseolus and Glycine contain two additional transcripts which are smaller in size and probably represent specific RNA breakdown products. A single species, sweet pea (Lathyrus odoratus), contains a second PII transcript which is 0.2 kb larger than the approximately 1.2 kb transcript found in all species. The LS and PII genes map to the same 5 kb region in both pea and mung bean and are transcribed off the same DNA strand. In contrast, published studies indicate that the two genes are approximately 50 kb apart and are transcribed off opposite DNA strands in five other chloroplast genomes. These differences are probably the consequence of an approximately 50 kb inversion which distinguishes the pea and mung bean genomes from those of most other angiosperms (1).