A proposal for identifying the short ID sequence which addresses the plastid subtype of higher plants

Abstract

Recent complete sequence data of the cyanobacteria genome and the plastid genome of algae and land plants clearly show that plastids originated from the endosymbiotic integration of a photosynthetic prokaryote into eukaryotic host cells. One indication of this event is that the organization of ribosomal protein genes has been conserved from bacteria to plastids of land plants. We are interested in the rpl16 and rpl14 genes, which are interrupted by the rpl29 and rps17 genes in both the cyanobacteria genome and the plastid genome of red alga, but are adjacent in liverwort to higher plants. This suggests that a linker between rpl16 and rpl14 was made by deletion of the rpl29 and rps17 genes at the appearance of land plants, and therefore the rpl16-rpl14 linkers of land plants have diverged from a common ancestral sequence. The rpl16 and rpl14 genes are highly conserved (more than 84 % homology) among rice, spinach and tobacco, whereas their linkers show low homology (28 %). The plastid rpl16-rp114 linker sequences of higher plants, such as barnyard grass, gentian and oak tree could be amplified and sequenced using a pair of common primers, even if their sequences are unknown. We propose short DNA sequence in the 3' noncoding region from the stop codon of the rpl16 gene as plastid subtype ID sequence (PS-ID). PS-IDs of ca. 50 bp are thought to be long enough to address plastid subtypes of higher plants and the establishment of a PS-ID database could contribute to plant phylogeny.