Phylogenetic significance of the rpoA loss in the chloroplast genome of mosses

Abstract

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 determine 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.

20,000 species and five key markers: The status of molecular bryophyte phylogenetics

“…A subsequent study (Sugita et al 2004) confirmed the absence for four other 'true' mosses (compare Tortula ruralis, Oliver et al 2010), whereas in the basalmost lineages (Sphagnophytina, Takakiophytina) it was present, situated between rps11 and petD in the LSC. Goffinet et al (2005) again expanded the survey of presence/absence of rpoA in mosses, and concluded that the absence of rpoA is characteristic for all peristomate-arthrodontous mosses (Bryopsida), except Buxbaumiidae, as well as the nematodontous Tetraphidopsida.…”

Deep sequencing of Ptilidium (Ptilidiaceae) suggests evolutionary stasis in liverwort plastid genome structure

“…Gene loss can be a powerful phylogenetic marker, as has been shown in mosses, where transfer of the rpoA gene to the nuclear genome denotes a clade comprising nearly 90% of moss species (Sugita et al 2004, Goffinet et al 2005). However, a wider taxonomic survey for presence/loss of the cysA and cysT genes shows that these have most likely been lost multiple times in hepatics (Wickett et al, unpubl.…”

“…changes in gene order, gene duplication and loss) are thought to be relatively rare. Plastid genome rearrangements have proved informative in many groups including embryophytes (Kelch et al 2004, Mishler & Kelch 2009), vascular plants (Raubeson & Jansen 1992), ferns (Stein et al 1992), Asteraceae (Jansen & Palmer 1987) and recently in mosses (Goffinet et al 2005(Goffinet et al , 2007; rearrangements in mitochondrial gene order have also provided supporting information for liverwort relationships inferred from DNA sequence data (e.g. Wahrmund et al 2008, Knoop 2010.…”

Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

“…The rpoA gene seems to have been lost in Polytrichaceae. The absence of this gene had been reported in T. pellucida as well as in all arthrodontous groups [53,54]. Goffinet et al [55] showed that rpoA does not seem to have been lost in Polytrichum pallidisetum Funck.…”