Comparative transcriptomics of seed nourishing tissues: uncovering conserved and divergent pathways in seed plants.

The evolutionary and ecological success of spermatophytes is intrinsically linked to the seed habit, which provides a protective environment for the initial development of the new generation. This environment includes an ephemeral nourishing tissue that supports embryo growth. In gymnosperms this tissue originates from the asexual proliferation of the maternal megagametophyte, while in angiosperms it is a product of fertilization, and is called the endosperm. The emergence of these nourishing tissues is of profound evolutionary value, and they are also food staples for most of the world's population. Here, using Orthofinder to infer orthologue genes among newly generated and previously published datasets, we provide a comparative transcriptomic analysis of seed nourishing tissues from species of several angiosperm clades, including those of early diverging lineages, as well as of one gymnosperm. Our results show that, although the structure and composition of seed nourishing tissues has seen significant divergence along evolution, there are signatures that are conserved throughout the phylogeny. Conversely, we identified processes that are specific to species within the clades studied, and thus illustrate their functional divergence. With this, we aimed to provide a foundation for future studies on the evolutionary history of seed nourishing structures, as well as a resource for gene discovery in future functional studies.

Integration of large and diverse angiosperm DNA fragments into Asian Gnetum mitogenomes.

BACKGROUND: Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus. RESULTS: We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots-mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT. CONCLUSIONS: Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages.

Different photorespiratory mechanisms in conifer leaves, where peroxisomes have intrinsically low catalase activity.

Photorespiration is an essential metabolic mechanism associated with photosynthesis; however, little is known about the photorespiratory pathway of conifer gymnosperms. Metabolite analyses of the leaves of 27 tree species showed that the mean glycerate content in conifer leaves was lower than that in angiosperm leaves. We performed experiments where [13 C]-serine was fed to detached shoots of a conifer (Cryptomeria japonica), via the transpiration stream, and compared the labeling patterns of photorespiratory metabolites with those of an angiosperm tree (Populus nigra), because glycerate is produced from serine via hydroxypyruvate in peroxisomes. In P. nigra, hydroxypyruvate, glycerate and glycine were labeled with 13 C, whereas in C. japonica, glycolate and a non-canonical photorespiratory metabolite, formate, were also labeled, suggesting that an H2 O2 -mediated non-enzymatic decarboxylation (NED) reaction occurs in C. japonica. We analyzed changes in the metabolite contents of leaves kept in the dark and leaves exposed to illuminated photorespiration-promoting conditions: a positive relationship between formate and serine levels in C. japonica implied that the active C1 -metabolism pathway synthesizes serine from formate. Leaf gas exchange analyses revealed that CO2 produced through NED was recaptured by chloroplasts. Database analysis of the peroxisomal targeting signal motifs of an H2 O2 -scavenging enzyme, catalase, derived from various species, including nine coniferous species, as well as analyses of peroxisomal fractions isolated from C. japonica and P. nigra leaves indicated that conifer peroxisomes had less catalase activity. These results suggest that NED and the subsequent C1 metabolism are involved in the photorespiratory pathway of conifer leaves, where peroxisomes have intrinsically low catalase activity.

Development of pollinated and unpollinated ovules in Ginkgo biloba: unravelling the role of pollen in ovule tissue maturation.

In gymnosperms such as Ginkgo biloba, the arrival of pollen plays a key role in ovule development, before fertilization occurs. Accordingly, G. biloba female plants geographically isolated from male plants abort all their ovules after the pollination drop emission, which is the event that allows the ovule to capture pollen grains. To decipher the mechanism induced by pollination required to avoid ovule senescence and then abortion, we compared the transcriptomes of pollinated and unpollinated ovules at three time points after the end of the emission of pollination drop. Transcriptomic and in situ expression analyses revealed that several key genes involved in programmed cell death such as senescence and apoptosis, DNA replication, and cell cycle regulation were differentially expressed in unpollinated ovules compared to pollinated ovules. We provide evidence that the pollen captured by the pollination drop affects auxin local accumulation and might cause deregulation of key genes required for the ovule's programmed cell death, activating both the cell cycle regulation and DNA replication genes.

Evolutionary trends of reproductive phenotype in Cycadales: an analysis of morphological evolution in Ceratozamia.

BACKGROUND AND AIMS: The size and shape of reproductive structures is especially relevant in evolution because these characters are directly related to the capacity of pollination and seed dispersal, a process that plays a basic role in evolutionary patterns. The evolutionary trajectories of reproductive phenotypes in gymnosperms have received special attention in terms of pollination and innovations related to the emergence of the Spermatophytes. However, variability of reproductive structures, evolutionary trends and the role of environment in the evolution of cycad species have not been well documented and explored. This study considered this topic under an explicitly phylogenetic and evolutionary approach that included a broad sampling of reproductive structures in the genus Ceratozamia. METHODS: We sampled 1400 individuals of 36 Ceratozamia species to explore evolutionary pattern and identify and evaluate factors that potentially drove their evolution. We analyzed characters for both pollen and ovulate strobili within a phylogenetic framework using different methods and characters (i. e., molecular and both quantitative and qualitative morphological) to infer phylogenetic relationships. Using this phylogenetic framework, evolutionary models of trait evolution for strobilar size were evaluated. In addition, quantitative morphological variation and its relation to environmental variables across species were analyzed. KEY RESULTS: We found contrasting phylogenetic signals between characters of pollen and ovulate strobili. These structures exhibited high morphological disparity in several characters related to size. Results of analyses of evolutionary trajectories suggested a stabilizing selection model. In regards to phenotype-environment, the analysis produced mixed results and differences for groups in the vegetation type where the species occur; however, a positive relationship with climatic variables was found. CONCLUSIONS: The integrated approach synthesized reproductive phenotypic variation with current phylogenetic hypotheses and provided explicit statements of character evolution. The characters of volume for ovulate strobili were the most informative, which could provide a reference for further study of the evolutionary complexity in Ceratozamia. Finally, heterogeneous environments, which are under changing weather conditions, promote variability of reproductive structures.

The D14 and KAI2 Orthologs of Gymnosperms Sense Strigolactones and KL Mimics, Respectively, and the Signals Are Transduced to Control Downstream Genes.

Strigolactones (SLs), lactone-containing carotenoid derivatives, function as signaling molecules in the rhizosphere, inducing symbiosis with arbuscular mycorrhizal. In addition, as a class of plant hormones, SLs control plant growth and development in flowering plants (angiosperms). Recent studies show that the ancestral function of SLs, which precede terrestrialization of plants, is as rhizosphere signaling molecules. SLs were then recruited as a class of plant hormones through the step-by-step acquisition of signaling components. The D14 gene encoding the SL receptor arose by gene duplication of KARRIKIN INSENSITIVE2 (KAI2), the receptor of karrikins and KAI2 ligand (KL), an unknown ligand, in the common ancestor of seed plants. KL signaling targets SMAX1, a repressor protein. On the other hand, the SL signaling targets SMXL78 subclade repressors, which arose by duplication of SMAX1 in angiosperms. Thus, gymnosperms contain the SL receptor D14 but not SMXL78, the SL signaling-specific repressor proteins. We studied two gymnosperm species, ginkgo (Ginkgo biloba) and Japanese umbrella pine (Sciadopitys verticillata), to clarify whether SLs are perceived and the signals are transduced in gymnosperms. We show that D14 and KAI2 of ginkgo and Japanese umbrella pine specifically perceive an SL analog and KL mimic, respectively. Furthermore, our results suggest that both SL signaling and KL signaling target SMAX1, and the specific localization of the receptor may result in the specificity of the signaling in gymnosperms.

Exploring the Seasonal Dynamics and Molecular Mechanism of Wood Formation in Gymnosperm Trees.

Forests, comprising 31% of the Earth's surface, play pivotal roles in regulating the carbon, water, and energy cycles. Despite being far less diverse than angiosperms, gymnosperms account for over 50% of the global woody biomass production. To sustain growth and development, gymnosperms have evolved the capacity to sense and respond to cyclical environmental signals, such as changes in photoperiod and seasonal temperature, which initiate growth (spring and summer) and dormancy (fall and winter). Cambium, the lateral meristem responsible for wood formation, is reactivated through a complex interplay among hormonal, genetic, and epigenetic factors. Temperature signals perceived in early spring induce the synthesis of several phytohormones, including auxins, cytokinins, and gibberellins, which in turn reactivate cambium cells. Additionally, microRNA-mediated genetic and epigenetic pathways modulate cambial function. As a result, the cambium becomes active during the summer, resulting in active secondary xylem (i.e., wood) production, and starts to become inactive in autumn. This review summarizes and discusses recent findings regarding the climatic, hormonal, genetic, and epigenetic regulation of wood formation in gymnosperm trees (i.e., conifers) in response to seasonal changes.

Independent recruitment of glycosyltransferase family 61 members for xylan substitutions in conifers.

MAIN CONCLUSION: Several pine members of the gymnosperm-specific GT61 clades were demonstrated to be arabinosyltransferases and xylosyltransferases catalyzing the transfer of 2-O-Araf, 3-O-Araf and 2-O-Xyl side chains onto xylooligomer acceptors, indicating their possible involvement in Araf and Xyl substitutions of xylan in pine. Xylan in conifer wood is substituted at O-2 with methylglucuronic acid (MeGlcA) as well as at O-3 with arabinofuranose (Araf), which differs from xylan in dicot wood that is typically decorated with MeGlcA but not Araf. Currently, glycosyltransferases responsible for conifer xylan arabinosylation have not been identified. Here, we investigated the roles of pine glycosyltransferase family 61 (GT61) members in xylan substitutions. Biochemical characterization of four pine wood-associated GT61 members showed that they exhibited three distinct glycosyltransferase activities involved in xylan substitutions. Two of them catalyzed the addition of 2-O-α-Araf or 3-O-α-Araf side chains onto xylooligomer acceptors and thus were named Pinus taeda xylan 2-O-arabinosyltransferase 1 (PtX2AT1) and 3-O-arabinosyltransferase 1 (PtX3AT1), respectively. Two other pine GT61 members were found to be xylan 2-O-xylosyltransferases (PtXYXTs) adding 2-O-ß-Xyl side chains onto xylooligomer acceptors. Furthermore, sequential reactions with PtX3AT1 and the PtGUX1 xylan glucuronyltransferase demonstrated that PtX3AT1 could efficiently arabinosylate glucuronic acid (GlcA)-substituted xylooligomers and likewise, PtGUX1 was able to add GlcA side chains onto 3-O-Araf-substituted xylooligomers. Phylogenetic analysis revealed that PtX2AT1, PtX3AT1 and PtXYXTs resided in three gymnosperm-specific GT61 clades that are separated from the grass-expanded GT61 clade harboring xylan 3-O-arabinosyltransferases and 2-O-xylosyltransferases, suggesting that they might have been recruited independently for xylan substitutions in gymnosperms. Together, our findings have established several pine GT61 members as xylan 2-O- and 3-O-arabinosyltransferases and 2-O-xylosyltransferases and they indicate that pine xylan might also be substituted with 2-O-Araf and 2-O-Xyl side chains.

Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway.

Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.

Both Conifer II and Gnetales are characterized by a high frequency of ancient mitochondrial gene transfer to the nuclear genome.

BACKGROUND: Mitochondrial gene transfer/loss is common in land plants, and therefore the fate of missing mitochondrial genes has attracted more and more attention. The gene content of gymnosperm mitochondria varies greatly, supplying a system for studying the evolutionary fate of missing mitochondrial genes. RESULTS: Here, we studied the tempo and pattern of mitochondrial gene transfer/loss in gymnosperms represented by all 13 families, using high-throughput sequencing of both DNA and cDNA. All 41 mitochondrial protein-coding genes were found in cycads, Ginkgo and Pinaceae, whereas multiple mitochondrial genes were absent in Conifer II and Gnetales. In Conifer II, gene transfer from mitochondria to the nucleus followed by loss of the mitochondrial copy was common, but complete loss of a gene in both mitochondrial and nuclear genomes was rare. In contrast, both gene transfer and loss were commonly found in Gnetales. Notably, in Conifer II and Gnetales, the same five mitochondrial genes were transferred to the nuclear genome, and these gene transfer events occurred, respectively, in ancestors of the two lineages. A two-step transfer mechanism (retroprocessing and subsequent DNA-mediated gene transfer) may be responsible for mitochondrial gene transfer in Conifer II and Gnetales. Moreover, the mitochondrial gene content variation is correlated with gene length, GC content, hydrophobicity, and nucleotide substitution rates in land plants. CONCLUSIONS: This study reveals a complete evolutionary scenario for variations of mitochondrial gene transferring in gymnosperms, and the factors responsible for mitochondrial gene content variation in land plants.

Study of the Pollen Grain Metabolome under Deposition of Nitrogen and Phosphorus in Taxus baccata L. and Juniperus communis L.

Nitrogen plays an important role in both quantitative and qualitative aspects of plant reproduction, including pollen grain compounds and seed production. Recent studies have pointed out that pollen grains produced by male plants of T. baccata and J. communis subjected to a long period of fertilizer supplementation have lower in vitro germination ability and higher nitrogen content. To gain molecular insights into these observations, we conducted GC-MS analysis of both species to characterize the metabolomes of dry, mature pollen grains, which allowed for the identification and quantification of more than 200 metabolites. The results demonstrated that fertilizer supplementation impacts the relative content of 14 metabolites in J. communis (9 downregulated and 5 upregulated) and 21 in T. baccata (6 downregulated and 15 upregulated). Although plants showed little similarity in patterns, in metabolite profiles, both up and down fold-changes were observed. This is the first report on the gymnosperm pollen grain metabolomic profile and changes induced by long-term nitrogen and phosphorus supplementation. Pollen grains produced by fertilizer-supplemented male individuals had significantly lower relative content of linolenic acid, 5,6-dihydrouracil, maltotriose, galactonic acid, D-xylulose, and glycerol-α-phosphate but higher content of sorbitol, glucosamine, and 1,5-anhydro-D-glucitol as well as n-acetyl-d-hexosamine, dimethyl phthalate, glycine, galactose-6-phosphate, D-fructose-6-phosphate, pyroglutamic acid, and 3-(3-hydroxyphenyl)-3-hydroxypropionic acid. Thus, in pollen grain samples earlier shown to have different germination abilities, the presence of different metabolites indicates a significant environmental impact on the quality of gymnosperm pollen grains.

The genomic architecture of the sex-determining region and sex-related metabolic variation in Ginkgobiloba.

Sex differences and evolutionary differences are critical biological issues. Ginkgo is an ancient lineage of dioecious gymnosperms with special value for studying the mechanism of sex determination in plants. However, the major genetic basic underlying sex chromosomes remains to be uncovered. In this study, we identify the sex-determining region of Ginkgo and locate it to the area from megabases 48 to 75 on chromosome 2. We find that the male sex-determining region of Ginkgo contains more than 200 genes, including four MADS-box genes, demonstrating that the Ginkgo sex determination system is of the XY type. We also find that genetic sex differences result in specialized flavonoid metabolism and regulation in each sex. These findings establish a foundation for revealing the molecular mechanism of sexual dimorphism and promoting the development of the Ginkgo industry.

Comparative Gene Expression Analysis Reveals Mechanism of Pinus contorta Response to the Fungal Pathogen Dothistroma septosporum.

Many conifers have distributions that span wide ranges in both biotic and abiotic conditions, but the basis of response to biotic stress has received much less attention than response to abiotic stress. In this study, we investigated the gene expression response of lodgepole pine (Pinus contorta) to attack by the fungal pathogen Dothistroma septosporum, which causes Dothistroma needle blight, a disease that has caused severe climate-related outbreaks in northwestern British Columbia. We inoculated tolerant and susceptible pines with two D. septosporum isolates and analyzed the differentially expressed genes (DEGs), differential exon usage, and coexpressed gene modules using RNA-sequencing data. We found a rapid and strong transcriptomic response in tolerant lodgepole pine samples inoculated with one D. septosporum isolate, and a late and weak response in susceptible samples inoculated with another isolate. We mapped 43 of the DEG- or gene module-identified genes to the reference plant-pathogen interaction pathway deposited in the Kyoto Encyclopedia of Genes and Genomes database. These genes are present in PAMP-triggered and effector-triggered immunity pathways. Genes comprising pathways and gene modules had signatures of strong selective constraint, while the highly expressed genes in tolerant samples appear to have been favored by selection to counterattack the pathogen. We identified candidate resistance genes that may respond to D. septosporum effectors. Taken together, our results show that gene expression response to D. septosporum infection in lodgepole pine varies both among tree genotypes and pathogen strains and involves both known candidate genes and a number of genes with previously unknown functions.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Full-length transcriptomic identification of R2R3-MYB family genes related to secondary cell wall development in Cunninghamia lanceolata (Chinese fir).

BACKGROUND: R2R3-MYB is a class of transcription factor crucial in regulating secondary cell wall development during wood formation. The regulation of wood formation in gymnosperm has been understudied due to its large genome size. Using Single-Molecule Real-Time sequencing, we obtained full-length transcriptomic libraries from the developmental stem of Cunninghamia lanceolata, a perennial conifer known as Chinese fir. The R2R3-MYB of C. lanceolata (hereafter named as ClMYB) associated with secondary wall development were identified based on phylogenetic analysis, expression studies and functional study on transgenic line. RESULTS: The evolutionary relationship of 52 ClMYBs with those from Arabidopsis thaliana, Eucalyptus grandis, Populus trichocarpa, Oryza sativa, two gymnosperm species, Pinus taeda, and Picea glauca were established by neighbour-joining phylogenetic analysis. A large number of ClMYBs resided in the woody-expanded subgroups that predominated with the members from woody dicots. In contrast, the woody-preferential subgroup strictly carrying the members of woody dicots contained only one candidate. The results suggest that the woody-expanded subgroup emerges before the gymnosperm/angiosperm split, while most of the woody-preferential subgroups are likely lineage-specific to woody dicots. Nine candidates shared the same subgroups with the A. thaliana orthologs, with known function in regulating secondary wall development. Gene expression analysis inferred that ClMYB1/2/3/4/5/26/27/49/51 might participate in secondary wall development, among which ClMYB1/2/5/26/27/49 were significantly upregulated in the highly lignified compression wood region, reinforcing their regulatory role associated with secondary wall development. ClMYB1 was experimentally proven a transcriptional activator that localised in the nucleus. The overexpression of ClMYB1 in Nicotiana benthamiana resulted in an increased lignin deposition in the stems. The members of subgroup S4, ClMYB3/4/5 shared the ERF-associated amphiphilic repression motif with AtMYB4, which is known to repress the metabolism of phenylpropanoid derived compounds. They also carried a core motif specific to gymnosperm lineage, suggesting divergence of the regulatory process compared to the angiosperms. CONCLUSIONS: This work will enrich the collection of full-length gymnosperm-specific R2R3-MYBs related to stem development and contribute to understanding their evolutionary relationship with angiosperm species.

Reconstructing development of the earliest seed integuments raises a new hypothesis for the evolution of ancestral seed-bearing structures.

How plant seeds originated remains unresolved, in part due to disconnects between fossil intermediates and developmental genetics in extant species. The Carboniferous fossil Genomosperma is considered among the most primitive known seeds, with highly lobed integument and exposed nucellus. We have used this key fossil taxon to investigate the evolutionary origins of seed development. We examined sectioned Genomosperma specimens using modern digital 3D reconstruction techniques and established population-level measurements of Genomosperma ovules for quantitative analysis. Genomosperma ovules show significant variation in integumentary lobe fusion and curvature. Our analysis suggests that this variation represents a single species with significant variations in lobe number and fusion, reminiscent of floral development in extant species. We conclude that changes in lobe flexure occurred late in development, consistent with a previously hypothesized function in pollen guidance/retention. We also identify seeds of Genomosperma within cupules for the first time. The presence of a cupule adds evidence towards the plesiomorphy of cupules within seed plants. Together with the similarities identified between the Genomosperma lobed integument and floral organs, we propose that the cupule, integument and nucellus together developed in a shoot-like fashion, potentially ancestral to extant seed plant reproductive shoots.

Plastome phylogenomics of Cephalotaxus (Cephalotaxaceae) and allied genera.

BACKGROUND AND AIMS: Cephalotaxus is a paleo-endemic genus in East Asia that consists of about 7-9 conifer species. Despite its great economic and ecological importance, the relationships between Cephalotaxus and related genera, as well as the interspecific relationships within Cephalotaxus, have long been controversial, resulting in contrasting taxonomic proposals in delimitation of Cephalotaxaceae and Taxaceae. Based on plastome data, this study aims to reconstruct a robust phylogeny to infer the systematic placement and the evolutionary history of Cephalotaxus. METHODS: A total of 11 plastomes, representing all species currently recognized in Cephalotaxus and two Torreya species, were sequenced and assembled. Combining these with previously published plastomes, we reconstructed a phylogeny of Cephalotaxaceae and Taxaceae with nearly full taxonomic sampling. Under a phylogenetic framework and molecular dating, the diversification history of Cephalotaxus and allied genera was explored. KEY RESULTS: Phylogenetic analyses of 81 plastid protein-coding genes recovered robust relationships between Cephalotaxus and related genera, as well as providing a well-supported resolution of interspecific relationships within Cephalotaxus, Taxus, Torreya and Amentotaxus. Divergence time estimation indicated that most extant species of these genera are relatively young, although fossil and other molecular evidence consistently show that these genera are ancient plant lineages. CONCLUSIONS: Our results justify the taxonomic proposal that recognizes Cephalotaxaceae as a monotypic family, and contribute to a clear-cut delineation between Cephalotaxaceae and Taxaceae. Given that extant species of Cephalotaxus are derived from recent divergence events associated with the establishment of monsoonal climates in East Asia and Pleistocene climatic fluctuations, they are not evolutionary relics.

Extending the fossil record for foliicolous Dothideomycetes: Bleximothyrium ostiolatum gen. et sp. nov., a unique fly-speck fungus from the Lower Cretaceous of Virginia, USA.

PREMISE: Fossils can reveal long-vanished characters that inform inferences about the timing and patterns of diversification of living fungi. Through analyzing well-preserved fossil scutella, shield-like covers of fungal sporocarps, we describe a new taxon of early Dothideomycetes with a combination of characters unknown among extant taxa. METHODS: Macerated clays from the Potomac Group, lower Zone 1, from the Lower Cretaceous (Aptian, 125-113 Ma) of Virginia USA yielded one gymnospermous leaf cuticle colonized by 21 sporocarps of a single fungal morphotype. We inferred a tree from nuclear ribosomal DNA of extant species, and coded morphological characters to evaluate alternative, equally parsimonious placements of the fossil in a molecular constraint tree of extant species. RESULTS: Bleximothyrium ostiolatum gen. et sp. nov. has an ostiolate scutellum of radiate, dichotomizing hyphae. Unlike otherwise similar extant and fossil taxa, B. ostiolatum has tangled hyphae at its scutellum margin. Scutella of B. ostiolatum are connected to superficial mycelium, to intercalary and lateral appressoria, and to extensive subcuticular "mycélium en palmettes". The gymnospermous host has characters consistent with identity as a non-papillate ginkgophyte or cycad. CONCLUSIONS: Bleximothyrium ostiolatum is the oldest known fossil fly-speck fungus that occurs on plant cuticles and has the radiate, ostiolate scutellum known only from Dothideomycetes. Its combination of characters, its scutellum margin, and mycélium en palmettes are unknown in other extant and fossil species, and Bleximothyrium ostiolatum likely represents a new group of fly-speck fungi that may now be extinct.

Natural Phytochemicals Derived from Gymnosperms in the Prevention and Treatment of Cancers.

The incidence of various types of cancer is increasing globally. To reduce the critical side effects of cancer chemotherapy, naturally derived compounds have been considered for cancer treatment. Gymnosperms are a group of plants found worldwide that have traditionally been used for therapeutic applications. Paclitaxel is a commercially available anticancer drug derived from gymnosperms. Other natural compounds with anticancer activities, such as pinostrobin and pinocembrin, are extracted from pine heartwood, and pycnogenol and enzogenol from pine bark. Gymnosperms have great potential for further study for the discovery of new anticancer compounds. This review aims to provide a rational understanding and the latest developments in potential anticancer compounds derived from gymnosperms.

Light- and hormone-mediated development in non-flowering plants: An overview.

MAIN CONCLUSION: Light, hormones and their interaction regulate different aspects of development in non-flowering plants. They might have played a role in the evolution of different plant groups by conferring specific adaptive evolutionary changes. Plants are sessile organisms. Unlike animals, they lack the opportunity to abandon their habitat in unfavorable conditions. They respond to different environmental cues and adapt accordingly to control their growth and developmental pattern. While phytohormones are known to be internal regulators of plant development, light is a major environmental signal that shapes plant processes. It is plausible that light-hormone crosstalk might have played an important role in plant evolution. But how the crosstalk between light and phytohormone signaling pathways might have shaped the plant evolution is unclear. One of the possible reasons is that flowering plants have been studied extensively in context of plant development, which cannot serve the purpose of evolutionary comparisons. In order to elucidate the role of light, hormone and their crosstalk in the evolutionary adaptation in plant kingdom, one needs to understand various light- and hormone-mediated processes in diverse non-flowering plants. This review is an attempt to outline major light- and phytohormone-mediated responses in non-flowering plant groups such as algae, bryophytes, pteridophytes and gymnosperms.

Darwin's second 'abominable mystery': trait flexibility as the innovation leading to angiosperm diversity.

The fact that angiosperms are so species-rich and ecologically diverse - Darwin's second abominable mystery - could be explained by their ability to 'reinvent' themselves by evolving functional traits repeatedly over time, space and taxonomic clades. These trait innovations may facilitate adaptation and increase diversification rates. In this article, I quantify this 'trait flexibility' by reviewing the literature on trait transition rates and trait-dependent diversification rates in angiosperms and their extant sister clade, acrogymnosperms. I show that angiosperms indeed evolved elevated trait transition and trait-dependent diversification rates compared to gymnosperms, and rates are highest within species-rich angiosperm orders (e.g. Fabales, Lamiales). The (genetic) ability of certain angiosperm lineages to repeatedly evolve adaptive traits may have facilitated sustained high net diversification resulting from numerous episodic radiations.