Multiple Independent Losses of Two Genes and One Intron from Legume Chloroplast Genomes

Abstract

The losses of genes or introns from the chloroplast genome are of potential utility as phylogenetic characters. Previous broad surveys of angiosperms, along with sequencing studies in Pisum sativum, uncovered several instances of variation for such characters within the Legumi- nosae. Using a slot blot hybridization method that did not require high molecular weight DNA, probes for six genes and three introns typically found in angiosperm chloroplast genomes were used to screen 392 legume genera, representing all three subfamilies and 50 out of 51 tribes, and 48 genera from 26 other families of dicots. Few cases of chloroplast gene or intron loss from chloroplast genomes were observed among nonlegumes or within the legume subfamilies Mimo- soideae and Caesalpinioideae, but numerous apparent losses were observed in the large subfamily Papilionoideae. Certain cases of suspected losses were tested by polymerase chain reaction. The genes rpl2 and rbcL appear to be present in all taxa surveyed, and virtually all possess accD. In contrast, ORF184 and rpsl6 each appear to have been lost multiple, independent times within Leguminosae, while all members of the family appear to lack rp122. The intron of rpl2 has likely been lost at least four times within the family, and its absence is a synapomorphy for a core group of the papilionoid tribe Desmodieae. No convincing evidence of loss was observed among legumes for the introns of trnI and rpll6. These results indicate that gene or intron loss characters may often be homoplastic. Intron losses are a more reliable and valuable class of phylogenetic characters than are gene losses.