Universal primers for amplification and sequencing a noncoding spacer between the atpB and rbcL genes of chloroplast DNA

Universal primers for amplifying and sequencing a noncoding spacer between the atpB and rbcL genes of the chloroplast DNA were constructed from the published sequences of Marchantia (a liverwort), tobacco, and rice. Our results indicate an evolutionary trend of increasing spacer size from liverworts, through mosses, to vascular plants. This atpB-rbcL spacer is AT-rich, consistent with other chloroplast noncoding spacers. Due to weak functional constraints, the spacer is evolving rapidly. A sequence identity of 92.2% was observed between spacers of two closely related moss species, Rhytidiadelphus loreus and R. triquestrus. Insertion/deletion events are common in the evolution of this spacer. A 23 bp deletion occurs in R. loreus. Variation is found between two populations of Amorphophallus henryi (Araceae) and between individuals in a populations of Pasania formosana (Fagaceae). We suggest that this spacer will be useful for molecular systematics at the subspecific, specific, and generic levels and, in some species, for population genetics studies.