BackgroundDespite considerable progress in our understanding of land plant phylogeny, several nodes in the green tree of life remain poorly resolved. Furthermore, the bulk of currently available data come from only a subset of major land plant clades. Here we examine early land plant evolution using complete plastome sequences including two previously unexamined and phylogenetically critical lineages. To better understand the evolution of land plants and their plastomes, we examined aligned nucleotide sequences, indels, gene and nucleotide composition, inversions, and gene order at the boundaries of the inverted repeats.ResultsWe present the plastome sequences of Equisetum arvense, a horsetail, and of Isoetes flaccida, a heterosporous lycophyte. Phylogenetic analysis of aligned nucleotides from 49 plastome genes from 43 taxa supported monophyly for the following clades: embryophytes (land plants), lycophytes, monilophytes (leptosporangiate ferns + Angiopteris evecta + Psilotum nudum + Equisetum arvense), and seed plants. Resolution among the four monilophyte lineages remained moderate, although nucleotide analyses suggested that P. nudum and E. arvense form a clade sister to A. evecta + leptosporangiate ferns. Results from phylogenetic analyses of nucleotides were consistent with the distribution of plastome gene rearrangements and with analysis of sequence gaps resulting from insertions and deletions (indels). We found one new indel and an inversion of a block of genes that unites the monilophytes.ConclusionsMonophyly of monilophytes has been disputed on the basis of morphological and fossil evidence. In the context of a broad sampling of land plant data we find several new pieces of evidence for monilophyte monophyly. Results from this study demonstrate resolution among the four monilophytes lineages, albeit with moderate support; we posit a clade consisting of Equisetaceae and Psilotaceae that is sister to the "true ferns," including Marattiaceae.

Most of the publicly available data on chloroplast (plastid) genes and genomes come from seed plants, with relatively little information from their sister group, the ferns. Here we describe several broad evolutionary patterns and processes in fern plastid genomes (plastomes), and we include some new plastome sequence data. We review what we know about the evolutionary history of plastome structure across the fern phylogeny and we compare plastome organization and patterns of evolution in ferns to those in seed plants. A large clade of ferns is characterized by a plastome that has been reorganized with respect to the ancestral gene order (a similar order that is ancestral in seed plants). We review the sequence of inversions that gave rise to this organization. We also explore global nucleotide substitution patterns in ferns versus those found in seed plants across plastid genes, and we review the high levels of RNA editing observed in fern plastomes.

Abstract:The plastid genome (plastome) is a rich source of phylogenetic and other comparative data in plants. Most land plants possess a plastome of similar structure. However, in a major group of plants, the ferns, a unique plastome structure has evolved. The gene order in ferns has been explained by a series of genomic inversions relative to the plastome organization of seed plants. Here, we examine for the first time the structure of the plastome across fern phylogeny. We used a PCR-based strategy to map and partially sequence plastomes. We found that a pair of partially overlapping inversions in the region of the inverted repeat occurred in the common ancestor of most ferns. However, the ancestral (seed plant) structure is still found in early diverging branches leading to the osmundoid and filmy fern lineages. We found that a second pair of overlapping inversions occurred on a branch leading to the core leptosporangiates. We also found that the unique placement of the gene matK in ferns (lacking a flanking intron) is not a result of a large-scale inversion, as previously thought. This is because the intron loss maps to an earlier point on the phylogeny than the nearby inversion. We speculate on why inversions may occur in pairs and what this may mean for the dynamics of plastome evolution.Key words: Osmunda, Gleichenia, Lygodium, Vandenboschia, Dicksonia, Marsilea, Adiantum, genome evolution, inversion.Résumé : Le génome plastidique (plastome) est une riche source de données phylogénétiques et autres chez les plantes. La plupart des plantes terrestres possèdent un plastome de structure semblable. Cependant, au sein d'un groupe majeur de plantes, les fougères, a évolué un plastome à la structure unique. L'ordre des gènes chez les fougères a été expliqué par une série d'inversions génomiques par rapport à l'organisation du plastome rencontré chez les plantes à graines. Dans ce travail, les auteurs examinent pour la première fois la structure du plastome à travers tout le groupe des fougères. Les auteurs emploient une stratégie PCR pour cartographier et partiellement séquencer les plastomes. Les auteurs ont observé qu'une paire d'inversions se chevauchant partiellement dans la région inversée répétée était présente chez l'ancêtre commun à la majorité des fougères. Cependant, la structure ancestrale (des plantes à graines) est encore observée chez les premières branches à diverger du tronc, lesquelles mènent aux osmundacées et aux hymenophyllacées. Une seconde paire d'inversions chevauchantes est présente dans l'embranchement qui mène aux principales fougères leptosporangiées. Les auteurs ont également trouvé que la position unique du gène matK chez les fougères (dépourvu d'un intron flanquant) n'est pas le résultat d'une inversion de grande taille comme cela a été suggéré antérieurement. Elle découle plutôt du fait que la perte de l'intron serait survenue plus tôt dans la phylogénie que l'inversion voisine. Les auteurs spéculent sur les causes possibles de l'occurrence des inversions en paires et ce que cela s...

BackgroundTortula ruralis, a widely distributed species in the moss family Pottiaceae, is increasingly used as a model organism for the study of desiccation tolerance and mechanisms of cellular repair. In this paper, we present the chloroplast genome sequence of T. ruralis, only the second published chloroplast genome for a moss, and the first for a vegetatively desiccation-tolerant plant.ResultsThe Tortula chloroplast genome is ~123,500 bp, and differs in a number of ways from that of Physcomitrella patens, the first published moss chloroplast genome. For example, Tortula lacks the ~71 kb inversion found in the large single copy region of the Physcomitrella genome and other members of the Funariales. Also, the Tortula chloroplast genome lacks petN, a gene found in all known land plant plastid genomes. In addition, an unusual case of nucleotide polymorphism was discovered.ConclusionsAlthough the chloroplast genome of Tortula ruralis differs from that of the only other sequenced moss, Physcomitrella patens, we have yet to determine the biological significance of the differences. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for mosses) of the generation of DNA markers for fine-level phylogenetic studies, or to investigate individual variation within populations.

The Gesneriaceae is a family known for convergent evolution of complex floral forms. As a result, defining genera and resolving evolutionary relationships among such genera using morphological data alone has been challenging and often does not accurately reflect monophyletic lineages. The tribe Episcieae is the most diverse within Neotropical Gesneriaceae in terms of its number of species and morphological diversity. As a result, defining genera using floral characters has been historically troublesome. Here we investigate relationships among genera of the tribe using an array of chloroplast DNA, nuclear ribosomal genes, and low-copy nuclear genes to provide resolution for the monophyly of the genera and relationships among the monophyletic groups. All known genera in the tribe (with the exception of the monospecific Lampadaria) have been sampled, and most have been sampled to provide an assessment to determine their monophyly. Of the 17 genera in the tribe that comprise more than a single species, we have sampled 15 with at least two species. The following six genera are identified as para-or polyphyletic: Neomortonia, Episcia, Paradrymonia, Nautilocalyx, Codonanthe, and Nematanthus. Our results strongly support at least three independent origins of fleshy fruits, which are defined here as fleshy display capsules or indehiscent berries.