INTRODUCTION The genomes of the chloroplast and the mitochon- drion have undergone severe reduction in size since their acquisition as endosymbionts by a protoeukaryotic cell (Dyall & al., 2004; Knoop, 2004; Timmis & al., 2004). In plants, genes lacking from these genomes have either been completely lost (such as genes required for a free- living existence) or have been transferred to the nucleus (Korpelainen, 2004). In fact, many of the proteins occur- ring in the mitochondrion and the chloroplast are synthe- sized in the cytosol and subsequently imported into the organelles. Analyses of the nuclear genome of Arabidopsis suggest that possibly as much as 18% of its genes have a cyanobacterial, and hence a plastid origin (Martin & al., 2002). By contrast, translocations between the cytoplasmic genomes seem very rare. The chloroplast genome of the angiosperm Calycanthus contains a gene of mitochondrial origin (Goremykin & al., 2003), and the mitochondrial genomes of maize and rice comprise vari- ous sequences of chloroplast origin (Nakazano & Hirai, 1993; Zheng & al., 1997). Transfers from the cytoplas- mic to the nuclear genome characterize particular lineag- es of land plants (e.g., Turmel & al., 1999; Adams & al., 2002, 2003; Martin & al., 2002; Hackett & al., 2004), but their phylogenetic significance is often ambiguous, as organellar genomes have only been sequenced for few taxa, from the major lineages of green plants (see Timmis & al., 2004). One exception is the presence in the nucle- us of two mitochondrial genes (i.e., rps14 and rpl15) in maize and rice, and hence potentially in many or all grasses (Sandoval & al., 2003). However, the process of gene transfer is ongoing (Timmis & al., 2004), and the rate of transfer estimated from the progeny of artificial crosses (Huang & al., 2002) suggests that losses from the cytoplasmic genomes are not rare events (Richly & Leister, 2004a, b). These observations are not surprising considering that a single locus may be lost repeatedly during the evolution of a lineage, such as infA during the diversification of angiosperms (Millen & al., 2003). To date the chloroplast genome has been completely sequenced for three bryophytes: Marchantia polymorpha L. (Ohyama & al., 1986), Anthoceros formosae Steph. (Kugita & al., 2003), and Physcomitrella patens (Hedw.) Bruch & W.P. Schimp. (Sugiura & al., 2003). The rps16 gene is lacking from the Marchantia genome, and has been lost from the plastid at least four times in the evo- lution of green plants (Martin & al., 2002). The genome of Anthoceros formosae is characterized by the presence of pseudogenes for matK and rps15 (Kugita & al., 2003). The structure of its inverted repeat is similar to that of vascular plants since it includes the rps12 gene (or only the 3' exon, according to Kugita & al. [2003]) in the inverted repeat (Kelch & al., 2004). The reconstruction of the genome of Physcomitrella patens by Sugiura & al. (2003) revealed (1) that a fragment encompassing much of the large single copy of the genome is inverted, and (2) that the rpoA gene, which codes for the alpha subunit of the RNA polymerase, an enzyme essential for catalyzing the transcription of DNA into RNA, is lacking. 353 Goffinet & al.  Evolution of the rpoA region 54 (2)  May 2005: 353–360 Phylogenetic significance of the rpoA loss in the chloroplast genome of mosses Bernard Goffinet 1 , Norman J. Wickett 1 , A. Jonathan Shaw 2 & Cymon J. Cox 2 1 Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs 06269, Connecticut, U.S.A. goffinet@uconn.edu (author for correspiondence); norman.wickett@uconn.edu 2 Department of Biology, Duke University, Durham 27708, North Carolina, U.S.A. shaw@duke.edu; cymon@duke.edu A recent survey of arthrodontous mosses revealed that their chloroplast genome lacks the gene encoding the alpha subunit of the RNA polymerase (i.e., rpoA), and that at least in Physcomitrella patens the gene has been transferred to the nuclear genome. Subsequently the gene was recorded from the cytoplasmic genome in Takakia and Sphagnum. Here we extend the survey to representatives of all major lineages of mosses to deter- mine when in the evolutionary history of the Bryophyta the loss took place. Amplifications using primers annealing to the flanking regions of the rpoA gene yield a product that contains the gene in Takakia, Sphagnum, Andreaea, Oedipodium, Polytrichaceae, and Buxbaumia. The gene is lacking in all arthrodontous mosses, including Diphyscium but also in both species of Tetraphis. Reconstruction of the transfer on the phylogeny of mosses suggests (a) that the rpoA gene was lost twice and (b) that the gene was lost after the divergence of Buxbaumiidae and prior to the divergence of Diphyscium from the remaining Bryopsida. KEYWORDS: Bryophyta, chloroplast genome, gene transfer, phylogeny, rpoA.