Chloroplast phylogeny indicates that bryophytes are monophyletic

Control of sporophyte secondary cell wall development in Marchantia by a Class II KNOX gene

Land plants evolved from an ancestral alga around 470 mya, evolving complex multicellularity in both haploid gametophyte and diploid sporophyte generations. The evolution of water-conducting tissues in the sporophyte generation was crucial for the success of land plants, paving the way for the colonization of a variety of terrestrial habitats. Class II KNOX (KNOX2) genes are major regulators of secondary cell wall formation and seed mucilage (pectin) deposition in flowering plants. Here, we show that, in the liverwort Marchantia polymorpha, loss-of-function alleles of the KNOX2 ortholog, MpKNOX2, or its dimerization partner, MpBELL1, have defects in capsule wall secondary cell wall and spore pectin biosynthesis. Both genes are expressed in the gametophytic calyptra surrounding the sporophyte and exert maternal effects, suggesting intergenerational regulation from the maternal gametophyte to the sporophytic embryo. These findings also suggest the presence of a secondary wall genetic program in the non-vascular liverwort capsule wall, with attributes of secondary walls in vascular tissues.

Dynamic Membrane Lipid Changes in Physcomitrium patens Reveal Developmental and Environmental Adaptations

Membrane lipid composition is critical for an organism's growth, adaptation, and functionality. Mosses, as early non-vascular land colonizers, show significant adaptations and changes, but their dynamic membrane lipid alterations remain unexplored. Here, we investigated the temporal changes in membrane lipid composition of the moss Physcomitrium patens during five developmental stages and analyzed the acyl content and composition of the lipids. We observed a gradual decrease in total lipid content from the filamentous protonema stage to the reproductive sporophytes. Notably, we found significant levels of very long-chain polyunsaturated fatty acids, particularly arachidonic acid (C20:4), which are not reported in vascular plants and may aid mosses in cold and abiotic stress adaptation. During vegetative stages, we noted high levels of galactolipids, especially monogalactosyldiacylglycerol, associated with chloroplast biogenesis. In contrast, sporophytes displayed reduced galactolipids and elevated phosphatidylcholine and phosphatidic acid, which are linked to membrane integrity and environmental stress protection. Additionally, we observed a gradual decline in the average double bond index across all lipid classes from the protonema stage to the gametophyte stage. Overall, our findings highlight the dynamic nature of membrane lipid composition during moss development, which might contribute to its adaptation to diverse growth conditions, reproductive processes, and environmental challenges.

The Shoot Apical Meristem: An Evolutionary Molding of Higher Plants

The shoot apical meristem (SAM) gives rise to the aerial structure of plants by producing lateral organs and other meristems. The SAM is responsible for plant developmental patterns, thus determining plant morphology and, consequently, many agronomic traits such as the number and size of fruits and flowers and kernel yield. Our current understanding of SAM morphology and regulation is based on studies conducted mainly on some angiosperms, including economically important crops such as maize (Zea mays) and rice (Oryza sativa), and the model species Arabidopsis (Arabidopsis thaliana). However, studies in other plant species from the gymnosperms are scant, making difficult comparative analyses that help us understand SAM regulation in diverse plant species. This limitation prevents deciphering the mechanisms by which evolution gave rise to the multiple plant structures within the plant kingdom and determines the conserved mechanisms involved in SAM maintenance and operation. This review aims to integrate and analyze the current knowledge of SAM evolution by combining the morphological and molecular information recently reported from the plant kingdom.

Chloroplast genome evolution and phylogeny of the early-diverging charophycean green algae with a focus on the Klebsormidiophyceae and Streptofilum

The Klebsormidiophyceae are a class of green microalgae observed globally in both freshwater and terrestrial habitats. Morphology-based classification schemes of this class have been shown to be inadequate due to the simple morphology of these algae, the tendency of morphology to vary in culture versus field conditions, and rampant morphological homoplasy. Molecular studies revealing cryptic diversity have renewed interest in this group. We sequenced the complete chloroplast genomes of a broad series of taxa spanning the known taxonomic breadth of this class. We also sequenced the chloroplast genomes of three strains of Streptofilum, a recently discovered green algal lineage with close affinity to the Klebsormidiophyceae. Our results affirm the previously hypothesized polyphyly of the genus Klebsormidium as well as the polyphyly of the nominal species in this genus, K. flaccidum. Furthermore, plastome sequences strongly support the status of Streptofilum as a distinct, early-diverging lineage of charophytic algae sister to a clade comprising Klebsormidiophyceae plus Phragmoplastophyta. We also uncovered major structural alterations in the chloroplast genomes of species in Klebsormidium that have broad implications regarding the underlying mechanisms of chloroplast genome evolution.

Meristem dormancy in Marchantia polymorpha is regulated by a liverwort-specific miRNA and a clade III SPL gene

The shape of modular organisms depends on the branching architecture, which in plants is determined by the fates of generative centers called meristems. The branches of the liverwort Marchantia polymorpha are derived from two adjacent meristems that develop at thallus apices. These meristems may be active and develop branches or may be dormant and do not form branches. The relative number and position of active and dormant meristems define the overall shape and form of the thallus. We show that the clade III SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor MpSPL1 is required for meristem dormancy. The activity of MpSPL1 is regulated by the liverwort-specific Mpo-MR13 miRNA, which, in turn, is regulated by PIF-mediated signaling. An unrelated PIF-regulated miRNA, MIR156, represses a different SPL gene (belonging to clade IV) that inhibits branching during the shade avoidance response in Arabidopsis thaliana. This suggests that a conserved light signaling mechanism modulates branching architecture in liverworts and angiosperms and therefore is likely operated in the last common ancestor. However, PIF-mediated signaling represses the expression of different miRNA genes with different SPL targets during dichotomous, apical branching in liverworts and during lateral, subapical branching in angiosperms. We speculate that the mechanism that acts downstream of light and regulates meristem dormancy evolved independently in liverworts and angiosperms.

The origin of a land flora

The origin of a land flora fundamentally shifted the course of evolution of life on earth, facilitating terrestrialization of other eukaryotic lineages and altering the planet's geology, from changing atmospheric and hydrological cycles to transforming continental erosion processes. Despite algal lineages inhabiting the terrestrial environment for a considerable preceding period, they failed to evolve complex multicellularity necessary to conquer the land. About 470 million years ago, one lineage of charophycean alga evolved complex multicellularity via developmental innovations in both haploid and diploid generations and became land plants (embryophytes), which rapidly diversified to dominate most terrestrial habitats. Genome sequences have provided unprecedented insights into the genetic and genomic bases for embryophyte origins, with some embryophyte-specific genes being associated with the evolution of key developmental or physiological attributes, such as meristems, rhizoids and the ability to form mycorrhizal associations. However, based on the fossil record, the evolution of the defining feature of embryophytes, the embryo, and consequently the sporangium that provided a reproductive advantage, may have been most critical in their rise to dominance. The long timeframe and singularity of a land flora were perhaps due to the stepwise assembly of a large constellation of genetic innovations required to conquer the terrestrial environment.

The cell wall of hornworts and liverworts: innovations in early land plant evolution?

An important step for plant diversification was the transition from freshwater to terrestrial habitats. The bryophytes and all vascular plants share a common ancestor that was probably the first to adapt to life on land. A polysaccharide-rich cell wall was necessary to cope with newly faced environmental conditions. Therefore, some pre-requisites for terrestrial life have to be shared in the lineages of modern bryophytes and vascular plants. This review focuses on hornwort and liverwort cell walls and aims to provide an overview on shared and divergent polysaccharide features between these two groups of bryophytes and vascular plants. Analytical, immunocytochemical, and bioinformatic data were analysed. The major classes of polysaccharides-cellulose, hemicelluloses, and pectins-seem to be present but have diversified structurally during evolution. Some polysaccharide groups show structural characteristics which separate hornworts from the other bryophytes or are too poorly studied in detail to be able to draw absolute conclusions. Hydroxyproline-rich glycoprotein backbones are found in hornworts and liverworts, and show differences in, for example, the occurrence of glycosylphosphatidylinositol (GPI)-anchored arabinogalactan-proteins, while glycosylation is practically unstudied. Overall, the data are an appeal to researchers in the field to gain more knowledge on cell wall structures in order to understand the changes with regard to bryophyte evolution.

Evolution of meristem zonation by CLE gene duplication in land plants

In angiosperms, a negative feedback pathway involving CLAVATA3 (CLV3) peptide and WUSCHEL transcription factor maintains the stem-cell population in the shoot apical meristem and is central for continued shoot growth and organogenesis. An intriguing question is how this cell-signalling system was established during the evolution of land plants. On the basis of two recent studies on CLV3/ESR-related (CLE) genes, this paper proposes a model for the evolution of meristem zonation. The model suggests that a stem-cell-limiting CLV3 pathway is derived from stem-cell-promoting CLE pathways conserved in land pants by gene duplication in the angiosperm lineage. The model can be examined in the future by genomic and developmental studies on diverse plant species.

The liverwort Marchantia polymorpha, a model for all ages

The liverwort Marchantia polymorpha has been known to man for millennia due to its inclusion Greek herbals. Perhaps due to its familiarity and association with growth in, often, man-made disturbed habitats, it was readily used to address fundamental biological questions of the day, including elucidation of land plant life cycles in the late 18th century, the formulation of cell theory early in the 19th century and the discovery of the alternation of generations in land plants in the mid-19th century. Subsequently, Marchantia was used as model in botany classes. With the arrival of the molecular era, its organellar genomes, the chloroplast and mitochondrial, were some of the first to be sequenced from any plant. In the past two decades, molecular genetic tools have been applied such that genes may be manipulated seemingly at will. Here, are past, present, and some views to the future of Marchantia as a model.

Origins and evolution of the dual functions of strigolactones as rhizosphere signaling molecules and plant hormones

Strigolactones (SLs) play roles as a class of plant hormones and rhizosphere signaling chemicals that induce hyphal branching of arbuscular mycorrhizal fungi and seed germination of parasitic plants. Therefore, SLs have dual functions. Recent progress in genome sequencing and genetic studies of bryophytes and algae has begun to shed light on the origin and evolution of these two functions of SLs.

Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants

The plastid organelle is essential for many vital cellular processes and the growth and development of plants. The availability of a large number of complete plastid genomes could be effectively utilized to understand the evolution of the plastid genomes and phylogenetic relationships among plants. We comprehensively analyzed the plastid genomes of Viridiplantae comprising 3,654 taxa from 298 families and 111 orders and compared the genomic organizations in their plastid genomic DNA among major clades, which include gene gain/loss, gene copy number, GC content, and gene blocks. We discovered that some important genes that exhibit similar functions likely formed gene blocks, such as the psb family presumably showing co-occurrence and forming gene blocks in Viridiplantae. The inverted repeats (IRs) in plastid genomes have doubled in size across land plants, and their GC content is substantially higher than non-IR genes. By employing three different data sets [all nucleotide positions (nt123), only the first and second codon positions (nt12), and amino acids (AA)], our phylogenomic analyses revealed Chlorokybales + Mesostigmatales as the earliest-branching lineage of streptophytes. Hornworts, mosses, and liverworts forming a monophylum were identified as the sister lineage of tracheophytes. Based on nt12 and AA data sets, monocots, Chloranthales and magnoliids are successive sister lineages to the eudicots + Ceratophyllales clade. The comprehensive taxon sampling and analysis of different data sets from plastid genomes recovered well-supported relationships of green plants, thereby contributing to resolving some long-standing uncertainties in the plant phylogeny.

SOG1, a plant-specific master regulator of DNA damage responses, originated from nonvascular land plants

The suppressor of gamma response 1 (SOG1), a NAM, ATAF1, 2, and CUC2 (NAC)-type transcription factor found in seed plants, is a master regulator of DNA damage responses (DDRs). Upon DNA damage, SOG1 regulates the expression of downstream DDR genes. To know the origin of the DDR network in land plants, we searched for a homolog(s) of SOG1 in a moss Physcomitrium (Physcomitrella) patens and identified PpSOG1a and PpSOG1b. To assess if either or both of them function(s) in DDR, we knocked out the PpSOG1s using CRISPR/Cas9-mediated gene editing and analyzed the responses to DNA-damaging treatments. The double-knockout (KO) sog1a sog1b plants showed resistance to γ-rays, bleomycin, and ultraviolet B (UVB) treatments similarly seen in Arabidopsis sog1 plants. Next, we irradiated wild-type (WT) and KO plants with γ-rays and analyzed the whole transcriptome to examine the effect on the expression of DDR genes. The results revealed that many P. patens genes involved in the checkpoint, DNA repair, replication, and cell cycle-related genes were upregulated after γ-irradiation, which was not seen in sog1a sog1b plant. These results suggest that PpSOG1a and PpSOG1b work redundantly on DDR response in P. patens; in addition, plant-specific DDR systems had been established before the emergence of vascular plants.

Large-Scale Phylogenomic Analyses Reveal the Monophyly of Bryophytes and Neoproterozoic Origin of Land Plants

The relationships among the four major embryophyte lineages (mosses, liverworts, hornworts, vascular plants) and the timing of the origin of land plants are enigmatic problems in plant evolution. Here, we resolve the monophyly of bryophytes by improving taxon sampling of hornworts and eliminating the effect of synonymous substitutions. We then estimate the divergence time of crown embryophytes based on three fossil calibration strategies, and reveal that maximum calibration constraints have a major effect on estimating the time of origin of land plants. Moreover, comparison of priors and posteriors provides a guide for evaluating the optimal calibration strategy. By considering the reliability of fossil calibrations and the influences of molecular data, we estimate that land plants originated in the Precambrian (980–682 Ma), much older than widely recognized. Our study highlights the important contribution of molecular data when faced with contentious fossil evidence, and that fossil calibrations used in estimating the timescale of plant evolution require critical scrutiny.

Auxin Biology in Bryophyta: A Simple Platform with Versatile Functions

Bryophytes, including liverworts, mosses, and hornworts, are gametophyte-dominant land plants that are derived from a common ancestor and underwent independent evolution from the sporophyte-dominant vascular plants since their divergence. The plant hormone auxin has been shown to play pleiotropic roles in the haploid bodies of bryophytes. Pharmacological and chemical studies identified conserved auxin molecules, their inactivated forms, and auxin transport in bryophyte tissues. Recent genomic and molecular biological studies show deep conservation of components and their functions in auxin biosynthesis, inactivation, transport, and signaling in land plants. Low genetic redundancy in model bryophytes enable unique assays, which are elucidating the design principles of the auxin signaling pathway. In this article, the physiological roles of auxin and regulatory mechanisms of gene expression and development by auxin in Bryophyta are reviewed.

The hornworts: morphology, evolution and development

Extant land plants consist of two deeply divergent groups, tracheophytes and bryophytes, which shared a common ancestor some 500 million years ago. While information about vascular plants and the two of the three lineages of bryophytes, the mosses and liverworts, is steadily accumulating, the biology of hornworts remains poorly explored. Yet, as the sister group to liverworts and mosses, hornworts are critical in understanding the evolution of key land plant traits. Until recently, there was no hornwort model species amenable to systematic experimental investigation, which hampered detailed insight into the molecular biology and genetics of this unique group of land plants. The emerging hornwort model species, Anthoceros agrestis, is instrumental in our efforts to better understand not only hornwort biology but also fundamental questions of land plant evolution. To this end, here we provide an overview of hornwort biology and current research on the model plant A. agrestis to highlight its potential in answering key questions of land plant biology and evolution.

Cryogenian Glacial Habitats as a Plant Terrestrialisation Cradle - The Origin of the Anydrophytes and Zygnematophyceae Split

For tens of millions of years (Ma), the terrestrial habitats of Snowball Earth during the Cryogenian period (between 720 and 635 Ma before present-Neoproterozoic Era) were possibly dominated by global snow and ice cover up to the equatorial sublimative desert. The most recent time-calibrated phylogenies calibrated not only on plants but on a comprehensive set of eukaryotes indicate that within the Streptophyta, multicellular charophytes (Phragmoplastophyta) evolved in the Mesoproterozoic to the early Neoproterozoic. At the same time, Cryogenian is the time of the likely origin of the common ancestor of Zygnematophyceae and Embryophyta and later, also of the Zygnematophyceae-Embryophyta split. This common ancestor is proposed to be called Anydrophyta; here, we use anydrophytes. Based on the combination of published phylogenomic studies and estimated diversification time comparisons, we deem it highly likely that anydrophytes evolved in response to Cryogenian cooling. Also, later in the Cryogenian, secondary simplification of multicellular anydrophytes and loss of flagella resulted in Zygnematophyceae diversification as an adaptation to the extended cold glacial environment. We propose that the Marinoan geochemically documented expansion of first terrestrial flora has been represented not only by Chlorophyta but also by Streptophyta, including the anydrophytes, and later by Zygnematophyceae, thriving on glacial surfaces until today. It is possible that multicellular early Embryophyta survived in less abundant (possibly relatively warmer) refugia, relying more on mineral substrates, allowing the retention of flagella-based sexuality. The loss of flagella and sexual reproduction by conjugation evolved in Zygnematophyceae and zygomycetous fungi during the Cryogenian in a remarkably convergent way. Thus, we support the concept that the important basal cellular adaptations to terrestrial environments were exapted in streptophyte algae for terrestrialization and propose that this was stimulated by the adaptation to glacial habitats dominating the Cryogenian Snowball Earth. Including the glacial lifestyle when considering the rise of land plants increases the parsimony of connecting different ecological, phylogenetic, and physiological puzzles of the journey from aquatic algae to terrestrial floras.

The Chloroplast Land Plant Phylogeny: Analyses Employing Better-Fitting Tree- and Site-Heterogeneous Composition Models

The colonization of land by descendants of charophyte green algae marked a turning point in Earth history that enabled the development of the diverse terrestrial ecosystems we see today. Early land plants diversified into three gametophyte-dominant lineages, namely the hornworts, liverworts, and mosses, collectively known as bryophytes, and a sporophyte-dominant lineage, the vascular plants, or tracheophytes. In recent decades, the prevailing view of evolutionary relationships among these four lineages has been that the tracheophytes were derived from a bryophyte ancestor. However, recent phylogenetic evidence has suggested that bryophytes are monophyletic, and thus that the first split among land plants gave rise to the lineages that today we recognize as the bryophytes and tracheophytes. We present a phylogenetic analysis of chloroplast protein-coding data that also supports the monophyly of bryophytes. This newly compiled data set consists of 83 chloroplast genes sampled across 30 taxa that include chlorophytes and charophytes, including four members of the Zygnematophyceae, and land plants, that were sampled following a balanced representation of the main bryophyte and tracheophyte lineages. Analyses of non-synonymous site nucleotide data and amino acid translation data result in congruent phylogenetic trees showing the monophyly of bryophytes, with the Zygnematophyceae as the charophyte group most closely related to land plants. Analyses showing that bryophytes and tracheophytes evolved separately from a common terrestrial ancestor have profound implications for the way we understand the evolution of plant life cycles on land and how we interpret the early land plant fossil record.

The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models

Congruence among analyses of plant genomic data partitions (nuclear, chloroplast and mitochondrial) is a strong indicator of accuracy in plant molecular phylogenetics. Recent analyses of both nuclear and chloroplast genome data of land plants (embryophytes) have, controversially, been shown to support monophyly of both bryophytes (mosses, liverworts, and hornworts) and tracheophytes (lycopods, ferns, and seed plants), with mosses and liverworts forming the clade Setaphyta. However, relationships inferred from mitochondria are incongruent with these results, and typically indicate paraphyly of bryophytes with liverworts alone resolved as the earliest-branching land plant group. Here, we reconstruct the mitochondrial land plant phylogeny from a newly compiled data set. When among-lineage composition heterogeneity is accounted for in analyses of codon-degenerate nucleotide and amino acid data, the clade Setaphyta is recovered with high support, and hornworts are supported as the earliest-branching lineage of land plants. These new mitochondrial analyses demonstrate partial congruence with current hypotheses based on nuclear and chloroplast genome data, and provide further incentive for revision of how plants arose on land.

Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.

Accounting for Uncertainty in the Evolutionary Timescale of Green Plants Through Clock-Partitioning and Fossil Calibration Strategies

Establishing an accurate evolutionary timescale for green plants (Viridiplantae) is essential to understanding their interaction and coevolution with the Earth's climate and the many organisms that rely on green plants. Despite being the focus of numerous studies, the timing of the origin of green plants and the divergence of major clades within this group remain highly controversial. Here, we infer the evolutionary timescale of green plants by analyzing 81 protein-coding genes from 99 chloroplast genomes, using a core set of 21 fossil calibrations. We test the sensitivity of our divergence-time estimates to various components of Bayesian molecular dating, including the tree topology, clock models, clock-partitioning schemes, rate priors, and fossil calibrations. We find that the choice of clock model affects date estimation and that the independent-rates model provides a better fit to the data than the autocorrelated-rates model. Varying the rate prior and tree topology had little impact on age estimates, with far greater differences observed among calibration choices and clock-partitioning schemes. Our analyses yield date estimates ranging from the Paleoproterozoic to Mesoproterozoic for crown-group green plants, and from the Ediacaran to Middle Ordovician for crown-group land plants. We present divergence-time estimates of the major groups of green plants that take into account various sources of uncertainty. Our proposed timeline lays the foundation for further investigations into how green plants shaped the global climate and ecosystems, and how embryophytes became dominant in terrestrial environments.

Evolutionary History of the Marchantia polymorpha Complex

The potential role of introgression in evolution has gained increased interest in recent years. Although some fascinating examples have been reported, more information is needed to generalize the importance of hybridization and introgression for adaptive divergence. As limited data exist on haploid dominant species, we analyzed genomes of three subspecies of the liverwort Marchantia polymorpha. We used available genomic data for subsp. ruderalis and carried out whole-genome (PacBio) sequencing for one individual each of subsp. montivagans and subsp. polymorpha as well as Illumina resequencing of additional genomes for all three subspecies. The three subspecies were compared against M. paleacea as outgroup. Our analyses revealed separation of the three taxa, but all three possible topologies were richly represented across the genomes, and the underlying divergence order less obvious. This uncertainty could be the result of the divergence of the three subspecies close in time, or that introgression has been frequent since divergence. In particular, we found that pseudo-chromosome 2 in subsp. montivagans was much more diverged than other parts of the genomes. This could either be explained by specific capture of chromosome 2 from an unknown related species through hybridization or by conservation of chromosome 2 despite intermittent or ongoing introgression affecting more permeable parts of the genomes. A higher degree of chromosomal rearrangements on pseudo-chromosome 2 support the second hypothesis. Species tree analyses recovered an overall topology where subsp. montivagans diverged first and subsp. ruderalis and subsp. polymorpha appeared as sister lineages. Each subspecies was associated with its own chloroplast and mitochondrial haplotype group. Our data suggest introgression but refute a previous hypothesis that subsp. ruderalis is a new stabilized hybrid between the other two subspecies.

Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution

PREMISE

Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution.

METHODS

We employed diverse likelihood-based analyses to infer large-scale bryophyte phylogeny for mitochondrial and plastid data sets. We tested for changes in purifying selection in plastid genes of a mycoheterotrophic liverwort (Aneura mirabilis) and a putatively mycoheterotrophic moss (Buxbaumia), and compared 15 bryophyte plastomes for major structural rearrangements.

RESULTS

Overall land-plant relationships conflict across analyses, generally weakly. However, an underlying (unrooted) four-taxon tree is consistent across most analyses and published studies. Despite gene coverage patchiness, relationships within mosses, liverworts, and hornworts are largely congruent with previous studies, with plastid results generally better supported. Exclusion of RNA edit sites restores cases of unexpected non-monophyly to monophyly for Takakia and two hornwort genera. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophic Aneura but not Buxbaumia. Plastid genome structure is nearly invariant across bryophytes, but the tufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses.

CONCLUSIONS

A common unrooted tree underlies embryophyte phylogeny, [(liverworts, mosses), (hornworts, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups. Analyses combining genomic and transcriptomic data may be misled locally for heavily RNA-edited taxa. The Buxbaumia plastome lacks hallmarks of relaxed selection found in mycoheterotrophic Aneura. Autotrophic bryophyte plastomes, including Buxbaumia, hardly vary in overall structure.

Complete Chloroplast Genome of Pinus densiflora Siebold & Zucc. and Comparative Analysis with Five Pine Trees

Pinus densiflora (Korean red pine) is widely distributed in East Asia and considered one of the most important species in Korea. In this study, the complete chloroplast genome of P. densiflora was sequenced by combining the advantages of Oxford Nanopore MinION and Illumina MiSeq. The sequenced genome was then compared with that of a previously published conifer plastome. The chloroplast genome was found to be circular and comprised of a quadripartite structure, including 113 genes encoding 73 proteins, 36 tRNAs and 4 rRNAs. It had short inverted repeat regions and lacked ndh gene family genes, which is consistent with other Pinaceae species. The gene content of P. densiflora was found to be most similar to that of P. sylvestris. The newly attempted sequencing method could be considered an alternative method for obtaining accurate genetic information, and the chloroplast genome sequence of P. densiflora revealed in this study can be used in the phylogenetic analysis of Pinus species.

Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.)

Unraveling the phylogenetic relationships between the four major lineages of terrestrial plants (mosses, liverworts, hornworts, and vascular plants) is essential for an understanding of the evolution of traits specific to land plants, such as their complex life cycles, and the evolutionary development of stomata and vascular tissue. Well supported phylogenetic hypotheses resulting from different data and methods are often incongruent due to processes of nucleotide evolution that are difficult to model, for example substitutional saturation and composition heterogeneity. We reanalysed a large published dataset of nuclear data and modelled these processes using degenerate-codon recoding and tree-heterogeneous composition substitution models. Our analyses resolved bryophytes as a monophyletic group and showed that the nonnonmonophyly of the clade that is supported by the analysis of nuclear nucleotide data is due solely to fast-evolving synonymous substitutions. The current congruence among phylogenies of both nuclear and chloroplast analyses lent considerable support to the conclusion that the bryophytes are a monophyletic group. An initial split between bryophytes and vascular plants implies that the bryophyte life cycle (with a dominant gametophyte nurturing an unbranched sporophyte) may not be ancestral to all land plants and that stomata are likely to be a symplesiomorphy among embryophytes.

Evolution and co-option of developmental regulatory networks in early land plants

Land plants evolved from an ancestral alga from which they inherited developmental and physiological characters. A key innovation of land plants is a life cycle with an alternation of generations, with both haploid gametophyte and diploid sporophyte generations having complex multicellular bodies. The origins of the developmental genetic programs patterning these bodies, whether inherited from an algal ancestor or evolved de novo, and whether programs were co-opted between generations, are largely open questions. We first provide a framework for land plant evolution and co-option of developmental regulatory pathways and then examine two cases in more detail.

The timescale of early land plant evolution

Establishing the timescale of early land plant evolution is essential for testing hypotheses on the coevolution of land plants and Earth's System. The sparseness of early land plant megafossils and stratigraphic controls on their distribution make the fossil record an unreliable guide, leaving only the molecular clock. However, the application of molecular clock methodology is challenged by the current impasse in attempts to resolve the evolutionary relationships among the living bryophytes and tracheophytes. Here, we establish a timescale for early land plant evolution that integrates over topological uncertainty by exploring the impact of competing hypotheses on bryophyte-tracheophyte relationships, among other variables, on divergence time estimation. We codify 37 fossil calibrations for Viridiplantae following best practice. We apply these calibrations in a Bayesian relaxed molecular clock analysis of a phylogenomic dataset encompassing the diversity of Embryophyta and their relatives within Viridiplantae. Topology and dataset sizes have little impact on age estimates, with greater differences among alternative clock models and calibration strategies. For all analyses, a Cambrian origin of Embryophyta is recovered with highest probability. The estimated ages for crown tracheophytes range from Late Ordovician to late Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider the implications of a much earlier, middle Cambrian-Early Ordovician, origin.

Plastid phylogenomic analysis of green plants: A billion years of evolutionary history

PREMISE OF THE STUDY

For the past one billion years, green plants (Viridiplantae) have dominated global ecosystems, yet many key branches in their evolutionary history remain poorly resolved. Using the largest analysis of Viridiplantae based on plastid genome sequences to date, we examined the phylogeny and implications for morphological evolution at key nodes.

METHODS

We analyzed amino acid sequences from protein-coding genes from complete (or nearly complete) plastomes for 1879 taxa, including representatives across all major clades of Viridiplantae. Much of the data used was derived from transcriptomes from the One Thousand Plants Project (1KP); other data were taken from GenBank.

KEY RESULTS

Our results largely agree with previous plastid-based analyses. Noteworthy results include (1) the position of Zygnematophyceae as sister to land plants (Embryophyta), (2) a bryophyte clade (hornworts, mosses + liverworts), (3) Equisetum + Psilotaceae as sister to Marattiales + leptosporangiate ferns, (4) cycads + Ginkgo as sister to the remaining extant gymnosperms, within which Gnetophyta are placed within conifers as sister to non-Pinaceae (Gne-Cup hypothesis), and (5) Amborella, followed by water lilies (Nymphaeales), as successive sisters to all other extant angiosperms. Within angiosperms, there is support for Mesangiospermae, a clade that comprises magnoliids, Chloranthales, monocots, Ceratophyllum, and eudicots. The placements of Ceratophyllum and Dilleniaceae remain problematic. Within Pentapetalae, two major clades (superasterids and superrosids) are recovered.

CONCLUSIONS

This plastid data set provides an important resource for elucidating morphological evolution, dating divergence times in Viridiplantae, comparisons with emerging nuclear phylogenies, and analyses of molecular evolutionary patterns and dynamics of the plastid genome.

The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte

The evolutionary emergence of land plant body plans transformed the planet. However, our understanding of this formative episode is mired in the uncertainty associated with the phylogenetic relationships among bryophytes (hornworts, liverworts, and mosses) and tracheophytes (vascular plants). Here we attempt to clarify this problem by analyzing a large transcriptomic dataset with models that allow for compositional heterogeneity between sites. Zygnematophyceae is resolved as sister to land plants, but we obtain several distinct relationships between bryophytes and tracheophytes. Concatenated sequence analyses that can explicitly accommodate site-specific compositional heterogeneity give more support for a mosses-liverworts clade, "Setaphyta," as the sister to all other land plants, and weak support for hornworts as the sister to all other land plants. Bryophyte monophyly is supported by gene concatenation analyses using models explicitly accommodating lineage-specific compositional heterogeneity and analyses of gene trees. Both maximum-likelihood analyses that compare the fit of each gene tree to proposed species trees and Bayesian supertree estimation based on gene trees support bryophyte monophyly. Of the 15 distinct rooted relationships for embryophytes, we reject all but three hypotheses, which differ only in the position of hornworts. Our results imply that the ancestral embryophyte was more complex than has been envisaged based on topologies recognizing liverworts as the sister lineage to all other embryophytes. This requires many phenotypic character losses and transformations in the liverwort lineage, diminishes inconsistency between phylogeny and the fossil record, and prompts re-evaluation of the phylogenetic affinity of early land plant fossils, the majority of which are considered stem tracheophytes.

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome

The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.

The Exceptional Preservation of Plant Fossils: A Review of Taphonomic Pathways and Biases in the Fossil Record

The exceptional preservation of plant fossils falls into two categories: whole plant preservation and anatomical detail. Whole plant preservation is controlled primarily by transport and event preservation (e.g., ash falls), whereas anatomical preservation can occur through one of several taphonomic pathways: compression-impression, silicification, coal-ball formation, pyritization, and charcoalification. This review focuses on these taphonomic pathways, highlighting important factors and controls on the exceptional preservation of plants. Special emphasis is given to data garnered from experimental and actualistic approaches.

Development and genetics in the evolution of land plant body plans

The colonization of land by plants shaped the terrestrial biosphere, the geosphere and global climates. The nature of morphological and molecular innovation driving land plant evolution has been an enigma for over 200 years. Recent phylogenetic and palaeobotanical advances jointly demonstrate that land plants evolved from freshwater algae and pinpoint key morphological innovations in plant evolution. In the haploid gametophyte phase of the plant life cycle, these include the innovation of mulitcellular forms with apical growth and multiple growth axes. In the diploid phase of the life cycle, multicellular axial sporophytes were an early innovation priming subsequent diversification of indeterminate branched forms with leaves and roots. Reverse and forward genetic approaches in newly emerging model systems are starting to identify the genetic basis of such innovations. The data place plant evo-devo research at the cusp of discovering the developmental and genetic changes driving the radiation of land plant body plans.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.

Molecular and Morphological Evidence Challenges the Records of the Extant Liverwort Ptilidium pulcherrimum in Eocene Baltic Amber

Preservation of liverworts in amber, a fossilized tree resin, is often exquisite. Twenty-three fossil species of liverworts have been described to date from Eocene (35–50 Ma) Baltic amber. In addition, two inclusions have been assigned to the extant species Ptilidium pulcherrimum (Ptilidiales or Porellales). However, the presence of the boreal P. pulcherrimum in the subtropical or warm-temperate Baltic amber forest challenges the phytogeographical interpretation of the Eocene flora. A re-investigation of one of the fossils believed to be P. pulcherrimum reveals that this specimen in fact represents the first fossil evidence of the genus Tetralophozia, and thus is re-described here as Tetralophozia groehnii sp. nov. A second fossil initially assigned to P. pulcherrimum is apparently lost, and can be reassessed only based on the original description and illustrations. This fossil is morphologically similar to the extant North Pacific endemic Ptilidium californicum, rather than P. pulcherrimum. Divergence time estimates based on chloroplast DNA sequences provide evidence of a Miocene origin of P. pulcherrimum, and thus also argue against the presence of this taxon in the Eocene. Ptilidium californicum originated 25–43 Ma ago. As a result, we cannot rule out that the Eocene fossil belongs to P. californicum. Alternatively, the fossil might represent a stem lineage element of Ptilidium or an early crown group species with morphological similarities to P. californicum.

Organelle Simple Sequence Repeat Markers Help to Distinguish Carpelloid Stamen and Normal Cytoplasmic Male Sterile Sources in Broccoli

We previously discovered carpelloid stamens when breeding cytoplasmic male sterile lines in broccoli (Brassica oleracea var. italica). In this study, hybrids and multiple backcrosses were produced from different cytoplasmic male sterile carpelloid stamen sources and maintainer lines. Carpelloid stamens caused dysplasia of the flower structure and led to hooked or coiled siliques with poor seed setting, which were inherited in a maternal fashion. Using four distinct carpelloid stamens and twelve distinct normal stamens from cytoplasmic male sterile sources and one maintainer, we used 21 mitochondrial simple sequence repeat (mtSSR) primers and 32 chloroplast SSR primers to identify a mitochondrial marker, mtSSR2, that can differentiate between the cytoplasm of carpelloid and normal stamens. Thereafter, mtSSR2 was used to identify another 34 broccoli accessions, with an accuracy rate of 100%. Analysis of the polymorphic sequences revealed that the mtSSR2 open reading frame of carpelloid stamen sterile sources had a deletion of 51 bases (encoding 18 amino acids) compared with normal stamen materials. The open reading frame is located in the coding region of orf125 and orf108 of the mitochondrial genomes in Brassica crops and had the highest similarity with Raphanus sativus and Brassica carinata. The current study has not only identified a useful molecular marker to detect the cytoplasm of carpelloid stamens during broccoli breeding, but it also provides evidence that the mitochondrial genome is maternally inherited and provides a basis for studying the effect of the cytoplasm on flower organ development in plants.

Establishment of Anthoceros agrestis as a model species for studying the biology of hornworts

BACKGROUND

Plants colonized terrestrial environments approximately 480 million years ago and have contributed significantly to the diversification of life on Earth. Phylogenetic analyses position a subset of charophyte algae as the sister group to land plants, and distinguish two land plant groups that diverged around 450 million years ago - the bryophytes and the vascular plants. Relationships between liverworts, mosses hornworts and vascular plants have proven difficult to resolve, and as such it is not clear which bryophyte lineage is the sister group to all other land plants and which is the sister to vascular plants. The lack of comparative molecular studies in representatives of all three lineages exacerbates this uncertainty. Such comparisons can be made between mosses and liverworts because representative model organisms are well established in these two bryophyte lineages. To date, however, a model hornwort species has not been available.

RESULTS

Here we report the establishment of Anthoceros agrestis as a model hornwort species for laboratory experiments. Axenic culture conditions for maintenance and vegetative propagation have been determined, and treatments for the induction of sexual reproduction and sporophyte development have been established. In addition, protocols have been developed for the extraction of DNA and RNA that is of a quality suitable for molecular analyses. Analysis of haploid-derived genome sequence data of two A. agrestis isolates revealed single nucleotide polymorphisms at multiple loci, and thus these two strains are suitable starting material for classical genetic and mapping experiments.

CONCLUSIONS

Methods and resources have been developed to enable A. agrestis to be used as a model species for developmental, molecular, genomic, and genetic studies. This advance provides an unprecedented opportunity to investigate the biology of hornworts.

Evolution. Response to Comment on "A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity"

Brunkard et al. propose that the identification of novel LEAFY sequences contradicts our model of evolution through promiscuous intermediates. Based on the debate surrounding land plant phylogeny and on our analysis of these interesting novel sequences, we explain why there is no solid evidence to disprove our model.

Phylotranscriptomic analysis of the origin and early diversification of land plants

Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.

Transcriptomic evidence for the evolution of shoot meristem function in sporophyte-dominant land plants through concerted selection of ancestral gametophytic and sporophytic genetic programs

Alternation of generations, in which the haploid and diploid stages of the life cycle are each represented by multicellular forms that differ in their morphology, is a defining feature of the land plants (embryophytes). Anciently derived lineages of embryophytes grow predominately in the haploid gametophytic generation from apical cells that give rise to the photosynthetic body of the plant. More recently evolved plant lineages have multicellular shoot apical meristems (SAMs), and photosynthetic shoot development is restricted to the sporophyte generation. The molecular genetic basis for this evolutionary shift from gametophyte-dominant to sporophyte-dominant life cycles remains a major question in the study of land plant evolution. We used laser microdissection and next generation RNA sequencing to address whether angiosperm meristem patterning genes expressed in the sporophytic SAM of Zea mays are expressed in the gametophytic apical cells, or in the determinate sporophytes, of the model bryophytes Marchantia polymorpha and Physcomitrella patens. A wealth of upregulated genes involved in stem cell maintenance and organogenesis are identified in the maize SAM and in both the gametophytic apical cell and sporophyte of moss, but not in Marchantia. Significantly, meiosis-specific genetic programs are expressed in bryophyte sporophytes, long before the onset of sporogenesis. Our data suggest that this upregulated accumulation of meiotic gene transcripts suppresses indeterminate cell fate in the Physcomitrella sporophyte, and overrides the observed accumulation of meristem patterning genes. A model for the evolution of indeterminate growth in the sporophytic generation through the concerted selection of ancestral meristem gene programs from gametophyte-dominant lineages is proposed.

Overly simplistic substitution models obscure green plant phylogeny

Phylogenetic analysis is an increasingly common and valuable component of plant science. Knowledge of the phylogenetic relationships between plant groups is a prerequisite for understanding the origin and evolution of important plant features, and phylogenetic analysis of individual genes and gene families provides fundamental insights into how those genes and their functions evolved. However, despite an active research community exploring and improving phylogenetic methods, the analytical methods commonly used, and the phylogenetic results they produce, are accorded far more confidence than they warrant. In this opinion article, I emphasise that important parts of the green plant phylogeny are inconsistently resolved and I argue that the lack of consistency arises due to inadequate modelling of changes in the substitution process.

Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias

Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea for resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to the, perhaps cumulative, effects of saturation, among-taxa compositional (GC content) heterogeneity, or codon-usage bias plaguing the individual nucleotide loci that are concatenated. Here, we provide an example of how these factors affect the inferences of the phylogeny of early land plants based on mitochondrial genomic data. Mitochondrial sequences evolve slowly in plants and hence are thought to be suitable for resolving deep relationships. We newly assembled mitochondrial genomes from 20 bryophytes, complemented these with 40 other streptophytes (land plants plus algal outgroups), compiling a data matrix of 60 taxa and 41 mitochondrial genes. Homogeneous analyses of the concatenated nucleotide data resolve mosses as sister-group to the remaining land plants. However, the corresponding translated amino acid data support the liverwort lineage in this position. Both results receive weak to moderate support in maximum-likelihood analyses, but strong support in Bayesian inferences. Tests of alternative hypotheses using either nucleotide or amino acid data provide implicit support for their respective optimal topologies, and clearly reject the hypotheses that bryophytes are monophyletic, liverworts and mosses share a unique common ancestor, or hornworts are sister to the remaining land plants. We determined that land plant lineages differ in their nucleotide composition, and in their usage of synonymous codon variants. Composition heterogeneous Bayesian analyses employing a nonstationary model that accounts for variation in among-lineage composition, and inferences from degenerated nucleotide data that avoid the effects of synonymous substitutions that underlie codon-usage bias, again recovered liverworts being sister to the remaining land plants but without support. These analyses indicate that the inference of an early-branching moss lineage based on the nucleotide data is caused by convergent compositional biases. Accommodating among-site amino acid compositional heterogeneity (CAT-model) yields no support for the optimal resolution of liverwort as sister to the rest of land plants, suggesting that the robust inference of the liverwort position in homogeneous analyses may be due in part to compositional biases among sites. All analyses support a paraphyletic bryophytes with hornworts composing the sister-group to tracheophytes. We conclude that while genomic data may generate highly supported phylogenetic trees, these inferences may be artifacts. We suggest that phylogenomic analyses should assess the possible impact of potential biases through comparisons of protein-coding gene data and their amino acid translations by evaluating the impact of substitutional saturation, synonymous substitutions, and compositional biases through data deletion strategies and by analyzing the data using heterogeneous composition models. We caution against relying on any one presentation of the data (nucleotide or amino acid) or any one type of analysis even when analyzing large-scale data sets, no matter how well-supported, without fully exploring the effects of substitution models.

From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

BACKGROUND

Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data.

RESULTS

We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa.

CONCLUSIONS

Analyses of the plastid sequence data recovered a strongly supported framework of relationships for green plants. This framework includes: i) the placement of Zygnematophyceace as sister to land plants (Embryophyta), ii) a clade of extant gymnosperms (Acrogymnospermae) with cycads + Ginkgo sister to remaining extant gymnosperms and with gnetophytes (Gnetophyta) sister to non-Pinaceae conifers (Gnecup trees), and iii) within the monilophyte clade (Monilophyta), Equisetales + Psilotales are sister to Marattiales + leptosporangiate ferns. Our analyses also highlight the challenges of using plastid genome sequences in deep-level phylogenomic analyses, and we provide suggestions for future analyses that will likely incorporate plastid genome sequence data for thousands of species. We particularly emphasize the importance of exploring the effects of different partitioning and character coding strategies.

A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity

Transcription factors (TFs) are key players in evolution. Changes affecting their function can yield novel life forms but may also have deleterious effects. Consequently, gene duplication events that release one gene copy from selective pressure are thought to be the common mechanism by which TFs acquire new activities. Here, we show that LEAFY, a major regulator of flower development and cell division in land plants, underwent changes to its DNA binding specificity, even though plant genomes generally contain a single copy of the LEAFY gene. We examined how these changes occurred at the structural level and identify an intermediate LEAFY form in hornworts that appears to adopt all different specificities. This promiscuous intermediate could have smoothed the evolutionary transitions, thereby allowing LEAFY to evolve new binding specificities while remaining a single-copy gene.

Chloroplast subspecies-specific SNP detection and its maternal inheritance in Brassica oleracea L. by using a dCAPS marker

Chloroplast simple sequence repeats amplicons in 5 subspecies of Brassica oleracea were sequenced, and one chloroplast SNP was detected in amplicon ACP43. Through the introduction of an RsaI recognition site by adding one mismatch in the forward primer, combined with the increased primer length and raised annealing temperature, the dCAPS (derived cleaved amplified polymorphic sequences) marker ACP43-93 RsaI was successfully developed. By using the dCAPS marker, the subspecies-specific SNP was assayed in 206 materials representing the wide distribution of B. oleracea. This is the first report of chloroplast DNA (cpDNA) variation in cultivated subspecies of B. oleracea, which showed that chloroplast diversity existed at the intersubspecies level. Unlike other subspecies, most of the broccoli and all of the cauliflower materials sharing the same haplotype showed closer relationships in cpDNA level. Furthermore, the dCAPS haplotype of the offspring from 7 male sterile backcross populations was the same as the female parents, indicating maternal inheritance.

Bryophyte diversity and evolution: windows into the early evolution of land plants

The "bryophytes" comprise three phyla of plants united by a similar haploid-dominant life cycle and unbranched sporophytes bearing one sporangium: the liverworts (Marchantiophyta), mosses (Bryophyta), and hornworts (Anthocerophyta). Combined, these groups include some 20000 species. As descendents of embryophytes that diverged before tracheophytes appeared, bryophytes offer unique windows into the early evolution of land plants. We review insights into the evolution of plant life cycles, in particular the elaboration of the sporophyte generation, the major lineages within bryophyte phyla, and reproductive processes that shape patterns of bryophyte evolution. Recent transcriptomic work suggests extensive overlap in gene expression in bryophyte sporophytes vs. gametophytes, but also novel patterns in the sporophyte, supporting Bower's antithetic hypothesis for origin of alternation of generations. Major lineages of liverworts, mosses, and hornworts have been resolved and general patterns of morphological evolution can now be inferred. The life cycles of bryophytes, arguably more similar to those of early embryophytes than are those in any other living plant group, provide unique insights into gametophyte mating patterns, sexual conflicts, and the efficacy and effects of spore dispersal during early land plant evolution.

Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages

Background

Despite 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.

Results

We 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.

Conclusions

Monophyly 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.

Newly resolved relationships in an early land plant lineage: Bryophyta class Sphagnopsida (peat mosses)

PREMISE OF THE STUDY

The Sphagnopsida, an early-diverging lineage of mosses (phylum Bryophyta), are morphologically and ecologically unique and have profound impacts on global climate. The Sphagnopsida are currently classified in two genera, Sphagnum (peat mosses) with some 350-500 species and Ambuchanania with one species. An analysis of phylogenetic relationships among species and genera in the Sphagnopsida were conducted to resolve major lineages and relationships among species within the Sphagnopsida. •

METHODS

Phylogenetic analyses of nucleotide sequences from the nuclear, plastid, and mitochondrial genomes (11 704 nucleotides total) were conducted and analyzed using maximum likelihood and Bayesian inference employing seven different substitution models of varying complexity. •

KEY RESULTS

Phylogenetic analyses resolved three lineages within the Sphagnopsida: (1) Sphagnum sericeum, (2) S. inretortum plus Ambuchanania leucobryoides, and (3) all remaining species of Sphagnum. Sister group relationships among these three clades could not be resolved, but the phylogenetic results indicate that the highly divergent morphology of A. leucobryoides is derived within the Sphagnopsida rather than plesiomorphic. A new classification is proposed for class Sphagnopsida, with one order (Sphagnales), three families, and four genera. •

CONCLUSIONS

The Sphagnopsida are an old lineage within the phylum Bryophyta, but the extant species of Sphagnum represent a relatively recent radiation. It is likely that additional species critical to understanding the evolution of peat mosses await discovery, especially in the southern hemisphere.