The earliest diversifications of land plants in Ordovician and Silurian times are unclear, mainly due to a lack of macrofossils. The increasing wealth of molecular data, however, converges on the view that bryophytes are paraphyletic with only one of its classes being sister to all other land plants and another bryophyte clade being sister to the tracheophytes. We continue to explore mitochondrial gene regions with respect to their unique modes of gene expression such as RNA editing and trans-splicing and their phylogenetic information potential. Plant mitochondrial genes drift slowly in sequence and mitochondrial introns are mostly stable in position, yet vary in occurrence between clades. These two features make mitochondrial DNA an attractive reservoir of old phylogenetic information. On the other hand, there is striking structural plasticity of mitochondrial DNA (the chondriome) in embryophytes, which grossly contrasts with the conservative evolution of chloroplast DNA (the plastome) in the land plant lineage. We find that mitochondrial intron occurrence strongly adds to the view of the deepest dichotomy separating liverworts and all non-liverwort embryophytes. Other intron occurrences, including the presence of ancestors of trans-splicing group II introns, tend to place hornworts as a sister group to tracheophytes, a grouping that we find corroborated by most multi-gene analyses. Furthermore, conserved intron sequences add phylogenetic resolution within clades. The use of gene spacers for phylogenetic analysis, as commonly investigated in chloroplast DNA, has so far been precluded in plant mitochondria due to rampant recombination of the chondriome, at least in tracheophytes. To investigate whether at least some ancestral gene orders are still conserved among bryophytes and provide useful phylogenetic information, we have recently explored the nad5-nad4-nad2 gene arrangement. We find it conserved, yet with strikingly different modes of evolution in the two spacers.
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