Phylogenetic relationships among the four major lineages of land plants (liverworts, mosses, hornworts, and vascular plants) remain vigorously contested; their resolution is essential to our understanding of the origin and early evolution of land plants. We analyzed three different complementary data sets: a multigene supermatrix, a genomic structural character matrix, and a chloroplast genome sequence matrix, using maximum likelihood, maximum parsimony, and compatibility methods. Analyses of all three data sets strongly supported liverworts as the sister to all other land plants, and analyses of the multigene and chloroplast genome matrices provided moderate to strong support for hornworts as the sister to vascular plants. These results highlight the important roles of liverworts and hornworts in two major events of plant evolution: the water-to-land transition and the change from a haploid gametophyte generation-dominant life cycle in bryophytes to a diploid sporophyte generation-dominant life cycle in vascular plants. This study also demonstrates the importance of using a multifaceted approach to resolve difficult nodes in the tree of life. In particular, it is shown here that densely sampled taxon trees built with multiple genes provide an indispensable test of taxon-sparse trees inferred from genome sequences.alternation of generations ͉ hornworts ͉ liverworts ͉ phylogeny ͉ taxon sampling T he origin and early evolution of land plants (embryophytes) during the mid-Ordovician to lower Silurian (480-430 million years ago) initiated the establishment of the modern terrestrial ecosystems and fundamentally altered the course of evolution of life on earth. Two important events marked this period of unprecedented innovation in plant evolution: the massive colonization of the land by plants descended from charophyte algae and the change of the dominant generation in the plant life cycle from a haploid gametophyte to a diploid sporophyte (1-5). The first event opened a vastly underexplored niche of high-intensity solar radiation and abundant CO 2 to photosynthetic life. The second event conferred on plants two abilities to adapt to a life in a water-deficient and UV-abundant terrestrial environment. One is the ability to produce a large number of genetically diverse gametes to ensure fertilization on land where sperm locomotion is hindered, and the other is the ability to mask deleterious mutations through the dominantrecessive interaction of alleles, thus allowing a large number of alleles to persist in the gene pool (2-4). Our understanding of these events hinges on our knowledge of relationships between the organisms involved in these major evolutionary transitions. Despite numerous studies using diverse approaches analyzing morphological and͞or molecular characters, relationships among early land plants remain controversial (5-19). Fossil evidence, although increasingly improved, has not helped to resolve the issues decisively (20,21).A multitude of phenomena characterizing diversification of many major clades o...

Mitochondrial genomes (mitogenomes) of flowering plants are well known for their extreme diversity in size, structure, gene content, and rates of sequence evolution and recombination. In contrast, little is known about mitogenomic diversity and evolution within gymnosperms. Only a single complete genome sequence is available, from the cycad Cycas taitungensis, while limited information is available for the one draft sequence, from Norway spruce (Picea abies). To examine mitogenomic evolution in gymnosperms, we generated complete genome sequences for the ginkgo tree (Ginkgo biloba) and a gnetophyte (Welwitschia mirabilis). There is great disparity in size, sequence conservation, levels of shared DNA, and functional content among gymnosperm mitogenomes. The Cycas and Ginkgo mitogenomes are relatively small, have low substitution rates, and possess numerous genes, introns, and edit sites; we infer that these properties were present in the ancestral seed plant. By contrast, the Welwitschia mitogenome has an expanded size coupled with accelerated substitution rates and extensive loss of these functional features. The Picea genome has expanded further, to more than 4 Mb. With regard to structural evolution, the Cycas and Ginkgo mitogenomes share a remarkable amount of intergenic DNA, which may be related to the limited recombinational activity detected at repeats in Ginkgo Conversely, the Welwitschia mitogenome shares almost no intergenic DNA with any other seed plant. By conducting the first measurements of rates of DNA turnover in seed plant mitogenomes, we discovered that turnover rates vary by orders of magnitude among species.

RNA editing in plant organelles is an enigmatic process leading to conversion of cytidines into uridines. Editing specificity is determined by proteins; both those known so far are pentatricopeptide repeat (PPR) proteins. The enzyme catalysing RNA editing in plants is still totally unknown. We propose that the DYW domain found in many higher plant PPR proteins is the missing catalytic domain. This hypothesis is based on two compelling observations: (i) the DYW domain contains invariant residues that match the active site of cytidine deaminases; (ii) the phylogenetic distribution of the DYW domain is strictly correlated with RNA editing.

Using an independent fosmid cloning approach and comprehensive transcriptome analysis to complement data from the Selaginella moellendorffii genome project, we determined the complete mitochondrial genome structure of this spikemoss. Numerous recombination events mediated mainly via long sequence repeats extending up to 7kbp result in a complex mtDNA network structure. Peculiar features associated with the repeat sequences are more than 80 different microsatellite sites (predominantly trinucleotide motifs). The S. moellendorffii mtDNA encodes a plant-typical core set of a twin-arginine translocase (tatC), 17 respiratory chain subunits, and 2 rRNAs but lacks atp4 and any tRNA genes. As a further novelty among plant chondromes, the nad4L gene is encoded within an intron of the nad1 gene. A total of 37 introns occupying the 20 mitochondrial genes (four of which are disrupted into trans-splicing arrangements including two novel instances of trans-splicing introns) make the S. moellendorffii chondrome the intron-richest and gene-poorest plant mtDNA known. Our parallel transcriptome analyses demonstrates functional splicing of all 37 introns and reveals a new record amount of plant organelle RNA editing with a total of 2,139 sites in mRNAs and 13 sites in the two rRNAs, all of which are exclusively of the C-to-U type.

Land plants exhibit a significant evolutionary plasticity in their mitochondrial DNA (mtDNA), which contrasts with the more conservative evolution of their chloroplast genomes. Frequent genomic rearrangements, the incorporation of foreign DNA from the nuclear and chloroplast genomes, an ongoing transfer of genes to the nucleus in recent evolutionary times and the disruption of gene continuity in introns or exons are the hallmarks of plant mtDNA, at least in flowering plants. Peculiarities of gene expression, most notably RNA editing and trans-splicing, are significantly more pronounced in land plant mitochondria than in chloroplasts. At the same time, mtDNA is generally the most slowly evolving of the three plant cell genomes on the sequence level, with unique exceptions in only some plant lineages. The slow sequence evolution and a variable occurrence of introns in plant mtDNA provide an attractive reservoir of phylogenetic information to trace the phylogeny of older land plant clades, which is as yet not fully resolved. This review attempts to summarize the unique aspects of land plant mitochondrial evolution from a phylogenetic perspective.