Expansion and contraction of the chloroplast inverted repeat in Apiaceae subfamily Apioideae

Chloroplast DNA (cpDNA) restriction site maps for 113 species of Apiaceae (Umbelliferae) and the allied families Araliaceae and Pittosporaceae were constructed for two enzymes and examined for variation in position of J(LB), the junction between the large single copy and inverted repeat regions that is typically contained within the ribosomal protein S10 operon. With the exception of one large clade in Apiaceae subfamily Apioideae, all species possess a J(LB) indistinguishable from that found in the vast majority of angiosperms. Within this large clade, however, at least one expansion and seven different contractions of the IR relative to the tobacco J(LB) were detected, each ranging in size from similar to1-16 kb. Five of the junction shifts are parsimony informative and three support major clades delimited in earlier phylogenetic studies. In light of cladograms based on previous studies of restriction site and DNA sequencing data, the IR appears to have expanded and contracted a minimum of ten times during the evolution of Apioideae, with several presumably identical size variants occurring in parallel. The frequency and large size of J(LB) shifts in Apioideae cpDNAs are unprecedented among angiosperms, indicating that the subfamily represents a model system to study the mechanisms leading to large-scale expansions and contractions of the IR.