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Background and Aims The size and shape of reproductive structures is especially relevant in evolution because these characters are directly related to the capacity for 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 the evolutionary pattern and identify and evaluate factors that potentially drove their evolution. We analysed 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 analysed. 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. With regard 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, and 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. [ABSTRACT FROM AUTHOR]

SUMMARY: 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. Significance Statement: Within seeds a specialized structure is responsible for nourishing the embryo during its development. These nourishing tissues are also important sources of staple foods and feed. Here, we provide gene expression datasets of nourishing tissues of early diverging angiosperms, and use this information for a meta‐analysis to identify pathways conserved, or divergent, throughout evolution. Thus, we aim to provide a resource for gene discovery for seed biology studies. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Cycads have a unique phylogenetic position within the gymnosperms which is most typically recognized by the production of motile sperm. The formation of sperm in Cycas revoluta was discovered in 1896 by Seiichiro Ikeno. This discovery and that of Ginkgo biloba by Sakugoro Hirase represent the first great scientific achievements in Japan after the Meiji Restoration. The role of Seiichiro Ikeno in these achievements is highlighted in this review. Later, he became a pioneer in the introduction of genetics and genetic studies in Japan. Throughout his life, he devoted himself to scientific studies. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Gymnosperms encompass a diverse group of mostly woody plants with high ecological and economic value, yet little is known about the scope and organization of fine‐root trait diversity among gymnosperms due to the undersampling of most gymnosperm families and the dominance of angiosperm groups in recent syntheses.New and existing data were compiled for morphological traits (root diameter, length, tissue density, specific root length [SRL] and specific root area [SRA]), the architectural trait branching ratio, root nitrogen content [N] and mycorrhizal colonization. We used phylogenetic least squares regression and principal component analysis to determine trait–trait relationships and coordination across 66 species, representing 11 of the 12 extant gymnosperm families from boreal, temperate, subtropical and tropical biomes. Finally, we compared the relationship between family divergence time and mean trait values to determine whether evolutionary history structured variation in fine‐root traits within the gymnosperm phylogeny.Wide variation in gymnosperm root traits could be largely captured by two primary axes of variation defined by SRL and diameter, and root tissue density and root nitrogen, respectively. However, individual root length and SRA each had significant correlations with traits defining both main axes of variation. Neither mycorrhizal colonization nor root branching ratio were closely related to other traits. We did not observe a directional evolution of mean trait values from older to more recently diverged gymnosperm families.Synthesis. Despite their unique evolutionary history, gymnosperms display a root economic space similar to that identified in angiosperms, likely reflecting common constraints on plants adapting to diverse environments in both groups. These findings provide greater confidence that patterns observed in broad syntheses justly capture patterns of trait diversity among multiple, distinct lineages. Additionally, independence between root architecture and other traits may support greater diversity in below‐ground resource acquisition strategies. Unlike angiosperms, there were no clear trends towards increasingly thin roots over evolutionary time, possibly because of lower diversification rates or unique biogeographic history among gymnosperms, though additional observations are needed to more richly test evolutionary trends among gymnosperms. [ABSTRACT FROM AUTHOR]

Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in the Western contiguous United States and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short reads of haploid megagametophyte tissue and Oxford Nanopore long reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gb of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gb). Approximately 87.2% (24.0 Gb) of total sequence was placed on the 12 WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the 3 subclasses of NLRs. Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo-assembled transcriptomes. [ABSTRACT FROM AUTHOR]

Key message: In Araucaria angustifolia, the seed scale is part of the ovule, the female gametophyte presents a monosporic origin and arises from a coenocytic tetrad, and the pollen tube presents a single axis. The seed cone of conifers has many informative features, and its ontogenetic data may help interpret relationships among function, development patterns, and homology among seed plants. We reported the seed cone development, from pollination to pre-fertilization, including seed scale, ovule ontogeny, and pollen tube growth in Araucaria angustifolia. The study was performed using light microscopy, scanning electron microscopy, and X-ray microcomputed tomography (μCT). During the pollination period, the ovule arises right after the seed scale has emerged. From that event to the pre-fertilization period takes about 14 months. Megasporogenesis occurs three weeks after ovule formation, producing a coenocytic tetrad. At the same time as the female gametophyte's first nuclear division begins, the pollen tube grows through the seed scale adaxial face. Until maturity, the megagametophyte goes through the free nuclei stage, cellularization stage, and cellular growth stage. Along its development, many pollen tubes develop in the nucellar tissue extending straight toward the female gametophyte. Our observations show that the seed scale came out of the same primordia of the ovule, agreeing with past studies that this structure is part of the ovule itself. The formation of a female gametophyte with a monosporic origin that arises from a coenocytic tetrad was described for the first time in conifers, and the three-dimensional reconstruction of the ovule revealed the presence of pollen tubes with only one axis and no branches, highlighting a new pattern of pollen tube growth in Araucariaceae. [ABSTRACT FROM AUTHOR]

Plants can improve their resistance to feeding damage by insects if they have perceived insect egg deposition prior to larval feeding. Molecular analyses of these egg-mediated defence mechanisms have until now focused on angiosperm species. It is unknown how the transcriptome of a gymnosperm species responds to insect eggs and subsequent larval feeding. Scots pine (Pinus sylvestris L.) is known to improve its defences against larvae of the herbivorous sawfly Diprion pini L. if it has previously received sawfly eggs. Here, we analysed the transcriptomic and phytohormonal responses of Scots pine needles to D. pini eggs (E-pine), larval feeding (F-pine) and to both eggs and larval feeding (EF-pine). Pine showed strong transcriptomic responses to sawfly eggs and—as expected—to larval feeding. Many egg-responsive genes were also differentially expressed in response to feeding damage, and these genes play an important role in biological processes related to cell wall modification, cell death and jasmonic acid signalling. EF-pine showed fewer transcriptomic changes than F-pine, whereas EF-treated angiosperm species studied so far showed more transcriptional changes to the initial phase of larval feeding than only feeding-damaged F-angiosperms. However, as with responses of EF-angiosperms, EF-pine showed higher salicylic acid concentrations than F-pine. Based on the considerable overlap of the transcriptomes of E- and F-pine, we suggest that the weaker transcriptomic response of EF-pine than F-pine to larval feeding damage is compensated by the strong, egg-induced response, which might result in maintained pine defences against larval feeding. [ABSTRACT FROM AUTHOR]

Wood is the most important renewable resource not only for numerous practical utilizations but also for mitigating the global climate crisis by sequestering atmospheric carbon dioxide. The compressed wood (CW) of gymnosperms, such as conifers, plays a pivotal role in determining the structure of the tree through the reorientation of stems displaced by environmental forces and is characterized by a high content of lignin. Despite extensive studies on many genes involved in wood formation, the molecular mechanisms underlying seasonal and, particularly, CW formation remain unclear. This study examined the seasonal dynamics of two wood tissue types in Pinus densiflora: CW and opposite wood (OW). RNA sequencing of developing xylem for two consecutive years revealed comprehensive transcriptome changes and unique differences in CW and OW across seasons. During growth periods, such as spring and summer, we identified 2255 transcripts with differential expression in CW, with an upregulation in lignin biosynthesis genes and significant downregulation in stress response genes. Notably, among the laccases critical for monolignol polymerization, PdeLAC17 was found to be specifically expressed in CW, suggesting its vital role in CW formation. PdeERF4, an ERF transcription factor preferentially expressed in CW, seems to regulate PdeLAC17 activity. This research provides an initial insight into the transcriptional regulation of seasonal CW development in P. densiflora, forming a foundation for future studies to enhance our comprehension of wood formation in gymnosperms. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Zamia integrifolia L.f. (Cycadales), a threatened cycad native to Florida, depends on 2 native beetle species for pollination: Rhopalotria slossoni (Chevrolat; Coleoptera: Belidae) and Pharaxanotha floridana (Casey; Coleoptera: Erotylidae). Both insects are brood-site pollination mutualists, known to live and feed within the pollen (male) cone. However, for pollination to occur, beetles must also visit ovulate (female) cones, which have been assumed to offer no benefits to them as food or nurseries. We tested the potential for beetle pollinator use of ovulate cones by performing no-choice behavior and feeding trials for adults of both beetle species on both ovulate cones and pollen cones of Z. integrifolia. Rhopalotria slossoni beetles showed greater survival on ovulate cone tissues despite showing no significant difference in total tissue mass consumed between cone sexes. Conversely, P. floridana consumed more tissue mass from ovulate cone scales yet showed no difference in survivorship on ovulate vs. pollen cone scales. Although neither beetle species is found in large numbers on ovulate cones in the field, our laboratory study suggests that both species could potentially benefit from feeding on ovulate cone tissues, questioning the standing hypothesis that Z. integrifolia pollination occurs by deceit. Zamia integrifolia L. f. (Cycadales), una cicadácea nativa amenazada en la Florida, depende de 2 especies nativas de escarabajos para la polinización: Rhopalotria slossoni (Chevrolat; Coleoptera: Belidae) y Pharaxanotha floridana (Casey; Coleoptera: Erotylidae). Ambos insectos son mutualistas de la polinización del sitio de cría, y se sabe que viven y se alimentan dentro del cono de polen (macho). Sin embargo, para que ocurra la polinización, los escarabajos también deben visitar conos de ovulación (femeninos), que se supone que no les ofrecen ningún beneficio como alimento o vivero. Probamos el potencial para el uso de conos de ovulación por parte de escarabajos polinizadores, esto mediante la realización de pruebas de alimentación y comportamiento de no elección para adultos de ambas especies de escarabajos tanto en conos de ovulación como en conos de polen de Z. integrifolia. Los escarabajos Rhopalotria slossoni mostraron una mayor sobrevivencia en los tejidos del cono ovulado a pesar de no mostrar diferencias significativas en la masa total de tejido consumido entre los sexos del cono. Por el contrario, P. floridana consumió más masa de tejido de las escamas de los conos de ovulación, pero no mostró diferencias en la sobrevivencia en las escamas de los conos de ovulación frente a las de los conos de polen. Aunque ninguna de las especies de escarabajos se encuentra en grandes cantidades en los conos de ovulación en el campo, nuestro estudio de laboratorio sugiere que ambas especies podrían beneficiarse potencialmente al alimentarse de los tejidos de los conos de ovulación, lo que cuestiona la hipótesis actual de que la polinización de Z. integrifolia se produce por engaño. [ABSTRACT FROM AUTHOR]

SUMMARY: 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 [13C]‐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 13C, whereas in C. japonica, glycolate and a non‐canonical photorespiratory metabolite, formate, were also labeled, suggesting that an H2O2‐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 H2O2‐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. Significance Statement: Photorespiration is a crucial metabolism that has a significant impact on the net CO2 fixation rates and energy‐use efficiencies of plants. It is thought that the photorespiratory pathway is identical among tree species; however, this study demonstrates that conifer gymnosperms have a different photorespiratory mechanism than that of angiosperm trees. [ABSTRACT FROM AUTHOR]

Multidisciplinary taxonomic studies have enhanced the delimitation of species within complex taxonomic groups. In the cycad genus Ceratozamia, the taxonomy is still not fully resolved for the several species complexes that have been proposed. Five Ceratozamia species occur in geographic proximity in the Soconusco region of southwestern Mexico. Because of similarity and variable morphology across these species, their taxonomy is a source of confusion. Based on integrative taxonomy, including morphological (qualitative and quantitative), ecological, and molecular data, we aimed to diagnose the species from the Soconusco region. We carried out extensive field sampling, collecting 225 individuals from a total of 12 populations, and reviewed one hundred herbarium specimens to evaluate whether the species are diagnosable. We carried out morphometric analyses at the population level on vegetative and reproductive characters and present the first analyses of phenotypic variability of pollen and ovulate strobili in neotropical cycads. Additionally, we evaluated the influence of climatic factors on morphological variation. Morphological characters of ovulate strobili were correlated with climatic conditions. In contrast, there was no significant correlation between the morphology of pollen strobili and the environment. In the pollen strobili, we found fixed characters that allow for the identification of the species. The haplotype networks displayed several groups of related haplotypes, which in some species corresponded to mixed population clusters. We detected a discordance between phenotypic and genetic evidence. The integration of evidence offers grounded views for clarifying species boundaries and outlining the differences among species, which we incorporated into a taxonomic key. In general, the mixed relations within this group of species may be due to historical hybridization events favored by common phenology and sharing of biotic pollination vectors. Finally, based on our results, we discuss the use of morphology for species delimitation and inference of evolutionary relationships in cycads. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Spring leaf phenology is an important event for trees to determine carbon fixation during the growing season. However, less is understood about the intraspecific variation in spring leaf phenology and its relationship with the spring temperature requirements of conifers, which is problematic for accurately predicting the influence of spring climate warming on conifers. I monitored bud burst timing and the degree days required for bud burst for seedlings and large individuals of Abies sachalinensis (fir) and Larix kaempferi (larch) over two seasons in northern Japan. Contrary to my expectation, the degree days required for the bud burst of small individuals were similar to or larger than those of the large individuals for fir and larch. Consequently, the bud burst timing of small individuals was similar to or later than that of large individuals for fir and larch. Even when conifer species are in their early stage, the spring temperature requirement for bud burst is not necessarily less than that for large individuals, which is not the case for many broad-leaved species. These results indicate that for these two coniferous species, ontogenetic differences in temperature requirements are not necessary to be considered for the response of communities to spring climate change. [ABSTRACT FROM AUTHOR]

Chamaecyparis obtusa var. formosana is significant as a precious and endemic plant in Taiwan. The trunk, renowned for its excellent texture and color, is ideal for construction materials and furniture. Moreover, the entire plant is rich in aroma, which can be made into essential oils, fragrances, and a series of related products. Volatile terpenoids are the major compounds in the composition of essential oils, many of which can only be found in C. obtusa var. formosana. In this study, we successfully identified 12 volatile terpene synthases from C. obtusa var. formosan a. Most of the selected TPSs displayed the ability to catalyze precursors into cyclic terpenoids, except for CovfTPS8, which also exhibited the capability to react with FPP and GPP. CovfTPS10 is particularly noteworthy for its multi-product characteristics and the ability to synthesize acoradiene. Moreover, it produces a novel compound, cis-isoduacene. Through the investigation of these volatile-terpenoid synthases, we can gain a better understanding of the cyclization process for terpenoids. • Sesquiterpene synthases for 1,6 cyclization, 1,10 cyclization, and 1,11 cyclization sesquiterpene were found in C. obtusa var. formosan a. [ABSTRACT FROM AUTHOR]

Mixing tree species can lead to more productive forests, but how belowground productivity is affected by mixtures of trees of diverse phylogenetic and eco‐evolutionary histories is unclear. Here, we examine how species origin and phylogeny affect belowground productivity in tree communities of varied richness and functional diversity. We measured standing fine‐root biomass and annual fine‐root production across 41 assemblages of 12 tree species, representing both angiosperms and gymnosperms originating from North America and Europe. Increasing functional diversity of mixtures stimulated overyielding of annual production but did not affect standing biomass. In general, annual productivity of mixtures of species that were less productive in monoculture had neutral (angiosperms) to positive (North American species: +16%) responses to mixing, whereas annual productivity of mixtures of species that were more productive in monoculture had neutral (European species) to negative (gymnosperms: −6%) responses to mixing. These differences translated into angiosperm mixtures overyielding in standing biomass by 16% but no effects of mixing on gymnosperm mixtures. The trends we observed between North American and European species annual production were reversed when considering standing biomass. European mixtures had 14% more standing biomass and North American mixtures had 10% less standing biomass than expected from monocultures. Our study offers a rare examination of the combined roles of origin and phylogeny in forest fine‐root productivity, and suggests varied consequences of biodiversity change for forest belowground productivity based on composition. In North America, belowground productivity of young forests composed of angiosperms and native tree species may be more tightly linked to diversity than that of forests dominated by gymnosperms or European species. This suggests that increased diversity may lead to the greatest enhancement of belowground productivity in native, North American forests dominated by angiosperms, but also that declines in diversity may be felt most strongly in these forests as well. [ABSTRACT FROM AUTHOR]

Summary: 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. [ABSTRACT FROM AUTHOR]

The type of Cycas debaoensis Y.C.Zhong & C.J.Chen (Y.C.Zhong 8762) consists of nine duplicates in PE. Our new investigation of the type collection suggests that the type includes at least two different gatherings which should be considered as syntypes. For nomenclatural purposes, we lectotypify the name Cycas debaoensis with the herbarium sheet PE00047578 and consider other duplicates in PE and GXMI as isolectotypes. The seeds in the capsule (Y.C.Zhong s.n. collected in Oct 1998) are considered as a syntype. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Little is known about the competition between and niche differentiation of water and nutrients between angiosperm and gymnosperm tree species under prolonged drought stress, especially in fragile environments. We imposed 21 d drought and competition treatments on Broussonetia papyrifera and Platycladus orientalis and measured water, N, and P contents, the isotopic composition of N and C, the activity of P assimilation enzymes, and stomatal conductance under solo planting and mixed planting to characterize resource diversity and competition in response to treatments. The N content, δ13C, δ15N, phosphomonoesterase, phosphodiesterase, gs, and foliage water content were significantly affected by the soil water content. The δ15N content in young leaves showed that N competition between these two plants could be alleviated through niche differentiation, but the changes in the PDE: PME ratio for these two plants indicated that they lost the niche differentiation of the P source under drought stress. Additionally, it was observed that foliage water content, WUE, N contents, and N and P sources were significantly affected by interspecific competition, and Broussonetia papyrifera benefited from water competition under moderate drought. Our results indicate that plants have different competition and niche differentiation modes to different nutrients under drought stress, and the effect of interspecific water competition should be seriously considered in mixed forests in semiarid areas. [ABSTRACT FROM AUTHOR]

Torreya dapanshanica X.F.Jin, Y.F.Lu & Zi L.Chen, a new species endemic to central Zhejiang, East China, is described and illustrated. This new species is most similar to T. jiulongshanensis (Z.Y.Li, Z.C.Tang & N.Kang) C.C.Pan, J.L.Liu & X.F.Jin, but differs in having leaves with an acuminate apex (vs. leaves with an acute apex), broadly ovoid-globose or globose seeds (vs. obovoid to narrowly obovoid seeds), slightly emarginate at the apex and obtuse-rounded at the base (vs. both acute at the apex and base), testa with irregular shallow grooves (vs. testa smooth or sometimes slightly concave). The diagnostic characters are critically compared and an IUCN assessment for the risk to the new species is estimated. [ABSTRACT FROM AUTHOR]

Plastid genomes (plastomes) have a quadripartite structure, but some species have drastically reduced or lost inverted repeat (IR) regions. IR regions are important for genome stability and the evolution rate. In the evolutionary process of gymnosperms, the typical IRs of conifers were lost, possibly affecting the evolutionary rate and selection pressure of genomic protein‐coding genes. In this study, we selected 78 gymnosperm species (51 genera, 13 families) for evolutionary analysis. The selection pressure analysis results showed that negative selection effects were detected in all 50 common genes. Among them, six genes in conifers had higher ω values than non‐conifers, and 12 genes had lower ω values. The evolutionary rate analysis results showed that 9 of 50 common genes differed between conifers and non‐conifers. It is more obvious that in non‐conifers, the rates of psbA (trst, trsv, ratio, dN, dS, and ω) were 2.6‐ to 3.1‐fold of conifers. In conifers, trsv, ratio, dN, dS, and ω of ycf2 were 1.2‐ to 3.6‐fold of non‐conifers. In addition, the evolution rate of ycf2 in the IR was significantly reduced. psbA is undergoing dynamic change, with an abnormally high evolution rate as a small portion of it enters the IR region. Although conifers have lost the typical IR regions, we detected no change in the substitution rate or selection pressure of most protein‐coding genes due to gene function, plant habitat, or newly acquired IRs. [ABSTRACT FROM AUTHOR]

Sequencing, assembly, and annotation of the 26.5Gbp hexaploid genome of coast redwood (Sequoia sempervirens) was completed leading toward discovery of genes related to climate adaptation and investigation of the origin of the hexaploid genome. Deep-coverage short-read Illumina sequencing data from haploid tissue from a single seed were combined with long-read Oxford Nanopore Technologies sequencing data from diploid needle tissue to create an initial assembly, which was then scaffolded using proximity ligation data to produce a highly contiguous final assembly, SESE 2.1, with a scaffold N50 size of 44.9Mbp. The assembly included several scaffolds that span entire chromosome arms, confirmed by the presence of telomere and centromere sequences on the ends of the scaffolds. The structural annotation produced 118,906 genes with 113 containing introns that exceed 500Kbp in length and one reaching 2Mb. Nearly 19Gbp of the genome represented repetitive content with the vast majority characterized as long terminal repeats, with a 2.9:1 ratio of Copia to Gypsy elements that may aid in gene expression control. Comparison of coast redwood to other conifers revealed species-specific expansions for a plethora of abiotic and biotic stress response genes, including those involved in fungal disease resistance, detoxification, and physical injury/structural remodeling and others supporting flavonoid biosynthesis. Analysis of multiple genes that exist in triplicate in coast redwood but only once in its diploid relative, giant sequoia, supports a previous hypothesis that the hexaploidy is the result of autopolyploidy rather than any hybridizations with separate but closely related conifer species. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Hydrasperman pteridosperms (seed ferns) were widespread and diverse in Carboniferous equatorial wetlands of Euramerica, and although present in Permian equatorial wetlands in Cathaysia, little is known about their ovules (unfertilised seeds) from this phytogeographical realm. Hydrasperman ovules are recognisable from their distinctive pollen chamber organisation, but those previously noted from the Permian floras of Cathaysia are imperfectly characterised and require further study to confirm their affinity and identity. Here we document the hydrasperman ovule Conostoma cf. kestospermum from coal-balls in the early Permian aged Taiyuan Formation of North China for which preliminary findings were previously published in a Chinese language book on the coal-ball floras of China. We provide additional information on the organisation and structure of the ovules and for the first time consider their palaeoecological and palaeogeographical significance. We conclude that significant taxonomic filtering occurred in the migration of wetland plant species between Euramerica and Cathaysia in the late Pennsylvanian, with the majority of hydrasperman pteridosperms going extinct in Euramerica at the end of the Carboniferous as a result of habitat loss and climate change. The few hydrasperman genera and species that persisted into the Cathaysian flora were relicts and a minor component of Permian equatorial wetland floras. [ABSTRACT FROM AUTHOR]

Some tree species have distributions on both sides of the Strait of Gibraltar and the Strait of Sicily. It is a challenge to determine whether such distributions result from the Tertiary or Pleistocene or from more recent dispersal related to human activities. Tetraclinis articulata (Cupressaceae) is a gymnosperm that offers an ideal model to deal with this problem because it has a limited area of distribution and has been used only moderately by humans. Three hundred and twenty-three individuals from 30 populations covering the entire distribution of the species were analysed. A multiple approach was developed: (1) by assessing the genetic structure through two molecular techniques, AFLP and nSSR markers, which were used to evaluate the genetic diversity of these populations and the relationships among them and (2) by estimating past distributions. Four lineages of populations that are geographically intermixed to a certain extent are documented here. Results obtained are discussed in the context of palaeontological records and climatic models. There is evidence of an ancient widespread distribution, including Europe, and the subsequent appearance of four isolated lineages that, nowadays, are partially intermixed. Nevertheless, the origin of the current populations could not be fully ascertained through this work, although logical deductions are discussed that consider human activities or, much less probably, wind dispersal of seeds out of refugia in northern Africa-southern Europe during the Quaternary, including shore connections. [ABSTRACT FROM AUTHOR]

We report on a new phytoptid mite species, Oziella viscidan. sp., collected in Western Crimea from sea rush, Juncus maritimus (Juncaceae), and give supplementary descriptions of two rarely encountered nalepellid species of the genus Trisetacus from pines: T. confusus Livshits & Vasilieva, 1982 (in Vasilieva et al. 1982) from needle sheaths of Pinus nigra ssp. pallasiana (Pinaceae), an endemic subspecies restricted to Crimea, and T. brevisetus Livshits & Sekerskaya, 1982 (in Vasilieva et al. 1982) from needle sheaths of Pinus brutia ssp. pityusa (Steven) Silba, a relatively isolated subspecies of Turkish pine (P. brutia Tenore) growing in Georgia, Caucasus and Crimea. Oziella viscidan. sp. is remarkable in that most specimens were found inhabiting the basal part of leaves and stems of J. maritimus, an area covered by a transparent, sticky exudate apparently secreted by the plant epidermis. The mites were completely embedded in this substance and, rather than crawling with their legs, were observed moving through the viscous material while bending their opisthosoma in a serpentine or wormlike manner—an adaptation that appears to be currently unreported in eriophyoids and possibly reminiscent of locomotion of ancestral "protoeriophyoids" associated with soil. In comparison to females, males of O. viscidan. sp. and T. confusus have a more distinct prodorsal shield pattern consisting of a larger number of longer lines. Three new barcode gene sequences were obtained: MZ220550 (Cox1, O. viscidan. sp., 1159 bp), MZ224497 (18S, 2012 bp, T. brevisetus), and MZ224498 (18S, 2013 bp T. confusus). A BLAST search of the 18S sequences of T. brevisetus and T. confusus shows them as slightly closer to other 18S sequences of Trisetacus from Pinaceae (95.5%–96.3% identity) than to Trisetacus from Cupressaceae (93.6%–94.0% identity). Comparison of sequences of nalepellids currently present in GenBank suggest that a complete 18S sequence KJ841938.1 (2252 bp) from China belongs to an identified Trisetacus from Pinaceae rather than to Setoptus koraiensis as labelled, highlighting the necessity to review carefully the sequences of Eriophyoidea prior to using them in phylogenetic analyses, as well as the need to recollect and resequence S. koraiensis to clarify the nature of the problematic data from GenBank assigned to this species. [ABSTRACT FROM AUTHOR]

The gymnosperms are a taxon of plants that release large amounts of pollen. Some genera of this group are specifically studied because their pollen is known to be the cause of respiratory diseases. The medical interest in allergenic bioaerosol has led to the need for daily aerobiological monitoring. The technique applied involves the use of an instrument that aspirates a volume of air corresponding to human inhalation and the identification under the light microscope of the allergenic bio-particulate present. Morphology alone does not allow to distinguish the non-saccate pollen thus they are attributed to a single category, i.e., Cupressaceae-Taxaceae, without distinction between genera belonging to the different families. This research represents an attempt to overcome the difficulties in the recognition of non-saccate gymnosperm pollen. Twenty-one species belonging to the Araucariaceae, Cupressaceae, and Taxaceae families were selected in Perugia (Umbria, central Italy). The most common species and other less widespread ones were selected, all characterized by non-saccate pollen. The results obtained allowed us to identify four morphologies: aperturoidate, areolate-papillate, areolate-porate, and porate. This study provides further knowledge regarding the morphological characteristics of these pollen grains, in order to overcome the general definition of inaperturates attributed to the pollen of some gymnosperms. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Araucaria angustifolia is classified as a critically endangered species by the International Union for Conservation of Nature. This threat is worsened by the inefficiency of methods for ex-situ conservation and propagation. In conifers, somatic embryogenesis (SE) associated with cryopreservation is an efficient method to achieve germplasm conservation and mass clonal propagation. However, the efficiency of SE is highly dependent on genotype responsivity to the artificial stimulus used in vitro during cell line proliferation and later during somatic embryo development. In this study, we evaluated the activity of antioxidant enzymes and characterized mitochondrial functions during the proliferation of embryogenic cells of A. angustifolia responsive (SE1) and non-responsive (SE6) to the development of somatic embryos. The activities of the antioxidant enzymes GR (EC 1.6.4.2), MDHAR (EC 1.6.5.4), and POX (EC 1.11.1.7) were increased in SE1 culture, while in SE6 culture, only the activity of DHAR (EC 1.8.5.1) was significantly higher. Additionally, SE6 culture presented a higher number of mitochondria, which agreed with the increased rate of oxygen consumption compared to responsive SE1 culture; however, the mitochondrial volume was lower. Although the ATP levels did not differ, the NAD(P)H levels were higher in SE1 cells. NDs, AOX, and UCP were less active in responsive SE1 than in non-responsive cells. Our results show significant differences between SE1 and SE6 embryogenic cells regarding mitochondrial functions and antioxidant enzyme activities, which may be intrinsic to the in vitro proliferation phase of both cell lines, possessing a crucial role for the induction of in vitro maturation process. [ABSTRACT FROM AUTHOR]

Summary: 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. See also the Commentary on this article by Hetherington, 229: 1189–1191. [ABSTRACT FROM AUTHOR]

The evolutionary dynamics of polyploid genomes and consequences of polyploidy have been studied extensively in angiosperms but very rarely in gymnosperms. The gymnospermous genus Ephedra is characterized by a high frequency of polyploidy, and thus provides an ideal system to investigate the evolutionary mode of allopolyploid genomes and test whether subgenome dominance has occurred in gymnosperms. Here, we sequenced transcriptomes of two allotetraploid species of Ephedra and their putative diploid progenitors, identified expressed homeologs, and analyzed alternative splicing and homeolog expression based on PacBio Iso-Seq and Illumina RNA-seq data. We found that the two subgenomes of the allotetraploids had similar numbers of expressed homeologs, similar percentages of homeologs with dominant expression, and approximately equal numbers of isoforms with alternative splicing, showing an unbiased subgenome evolution as in a few polyploid angiosperms, with a divergence of the two subgenomes at ∼8 Ma. In addition, the nuclear DNA content of the allotetraploid species is almost equal to the sum of two putative progenitors, suggesting limited genome restructuring after allotetraploid speciation. The allopolyploid species of Ephedra might have undergone slow diploidization, and the unbiased subgenome evolution implies that the formation of large genomes in gymnosperms could be attributed to even and slow fractionation following polyploidization. [ABSTRACT FROM AUTHOR]

Identifying emerging invasive species is a priority to implement early preventive and control actions. In terms of the number of invasive tree species, forestry represents the second largest pathway of introduction, with an invasive debt likely existing for alien conifers in Europe. In the early 1900s, a network of arboreta was established in southern Belgium to assess the wood production potential of prospective conifer and broadleaved species. Here, we use eight arboreta as natural experiments to identify alien conifers presenting invasive behavior. Through systematic sampling, we quantified the natural regeneration of alien conifers and recorded local environmental variables. For each species, regeneration density, dispersal distances, and age structure were analyzed. Generalized mixed effects models were fitted to test the effect of planted area and tree-stand type on regeneration. The environmental space occupied by regenerating alien conifers was evaluated using principal component analysis. Out of 31 planted alien species, 15 (48%) were identified in natural regeneration, of which eight (26%) exhibited important regeneration density and dispersal distances. The most invasive species were Tsuga heterophylla and Abies grandis, confirming earlier field observations. Both large planted areas and areas planted with alien conifer species increased the density of regeneration. Species that had the highest regeneration density tolerated a wide range of environmental conditions, including shaded understory, which could lead to the invasion of mature, undisturbed forests. This study showed that 17% of the studied alien conifers are potentially invasive because they show important regeneration, long-distance dispersal, and, of importance, have already produced offspring that have matured and are capable of creating new satellite populations. In conclusion, our results provide a guideline for future planting operations, recommending extreme caution when planting these species in the temperate forests of Western Europe. [ABSTRACT FROM AUTHOR]

Identifying emerging invasive species is a priority to implement early preventive and control actions. In terms of the number of invasive tree species, forestry represents the second largest pathway of introduction, with an invasive debt likely existing for alien conifers in Europe. In the early 1900s, a network of arboreta was established in southern Belgium to assess the wood production potential of prospective conifer and broadleaved species. Here, we use eight arboreta as natural experiments to identify alien conifers presenting invasive behavior. Through systematic sampling, we quantified the natural regeneration of alien conifers and recorded local environmental variables. For each species, regeneration density, dispersal distances, and age structure were analyzed. Generalized mixed effects models were fitted to test the effect of planted area and tree-stand type on regeneration. The environmental space occupied by regenerating alien conifers was evaluated using principal component analysis. Out of 31 planted alien species, 15 (48%) were identified in natural regeneration, of which eight (26%) exhibited important regeneration density and dispersal distances. The most invasive species were Tsuga heterophylla and Abies grandis, confirming earlier field observations. Both large planted areas and areas planted with alien conifer species increased the density of regeneration. Species that had the highest regeneration density tolerated a wide range of environmental conditions, including shaded understory, which could lead to the invasion of mature, undisturbed forests. This study showed that 17% of the studied alien conifers are potentially invasive because they show important regeneration, long-distance dispersal, and, of importance, have already produced offspring that have matured and are capable of creating new satellite populations. In conclusion, our results provide a guideline for future planting operations, recommending extreme caution when planting these species in the temperate forests of Western Europe. [ABSTRACT FROM AUTHOR]

Varied floristic works relevant to Kashmir Himalaya were thoroughly examined to compile taxonomic contributions of various taxonomists viz. a viz. diversity in gymnosperms of this region. Extensive field surveys and standard taxonomic methods were used to locate, collect, identify and prepare an updated list of the target group. A total of 25 species of gymnosperms belonging to 13 genera in 6 families and 4 orders have been documented from the Kashmir Himalaya. Wild gymnosperms are represented by 11 species with conifers forming the most dominant group. Among families, Pinaceae is highest represented with 6 species, while Taxaceae is least represented. Cultivated gymnosperms exceed wild growing species, and Cupressaceae is most dominant with 9 species whereas Ginkgoaceae is least represented. Out 25 species 19 (7 wild + 12 cultivated) are trees, 5 (3 wild + 2 cultivated) are shrubs and only 1 is sub-shrub. [ABSTRACT FROM AUTHOR]

Summary: 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. [ABSTRACT FROM AUTHOR]

Fungal endophytes inhabit plant tissues without causing disease symptoms. They are highly diverse and distributed globally in all plants that have been investigated. Host, geographic, and environmental effects on endophyte communities have been reported in several studies, but the direct effect of fungal growth rate on endophyte composition has not been tested. To understand the relationship between foliar endophyte composition and fungal growth and to examine the effect of host, elevation, and climatic factors on the foliar endophyte communities, this study examined the foliar endophyte communities of representative gymnosperms and Rhododendron spp. across different elevations of Hehuanshan and Taipingshan forests in Taiwan. The isolation frequency and diversity of foliar endophytes were higher at low elevations than at high elevations. The foliar endophyte community structure differed as a function of host family and forest vegetation type. Elevation, mean annual temperature, and precipitation were significantly correlated with the community structure. Fungal growth rate was correlated with the endophyte abundance, which indicates that fast-growing fungi might have a competitive advantage when coexisting with other fungi in a plant host. [ABSTRACT FROM AUTHOR]

SUMMARY: 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. [ABSTRACT FROM AUTHOR]

Cell wall thickness (Tcw) determines photosynthesis and leaf elasticity. However, only a few studies in angiosperms addressed cell wall composition implication in regulating photosynthesis and leaf water relations through mesophyll conductance (gm) and bulk modulus of elasticity (ε) adjustments, respectively. Thus, we compared the phylogenetically distant Ginkgo biloba L. and Helianthus annuus L. under control and water deprivation to study the relationship between changes in cell wall composition (cellulose, hemicelluloses, and pectins) with gm and ε. Although no changes were found for Tcw, both species differently modified cell wall composition, resulting in different physiological consequences. H. annuus increased cellulose, hemicelluloses, and pectins in a similar proportion, maintaining ε. Additionally, it reduced photosynthesis due to stomatal closure. G. biloba did not decrease photosynthesis and largely increased hemicelluloses, leaf mass area, and leaf density, enhancing ε. Nonetheless, no association between cell wall composition and gm was found in either of the two species. [ABSTRACT FROM AUTHOR]

The purpose of the main research was to investigate the effects of methyl jasmonate (MeJA) (0.05, 0.25, 0.5, and 2.5 mM) on the pollen germination and tube elongation of Pinus nigra. Total pollen germination rate increased after MeJA treatments while the most enhancement was observed at 0.05-mM MeJA. No germination was observed at 2.5-mM MeJA. Although the unipolar and bipolar germination were observed in all groups, no significant changes were observed in unipolar and bipolar pollen germination rates after MeJA treatments. Tube length increased only at 0.05-mM MeJA. Although branched tubes were observed in all groups, branched tube rate increased only at 0.05-mM MeJA. Although two branched, three branched, and consecutive branched tubes were observed in all groups, the most common branching type was two branched type in all groups. Although anisotropy of actin filaments in the shank and apex of unbranched tubes decreased after MeJA treatments, the most decrease was observed at 0.05-mM MeJA. Also, anisotropy of actin filaments in the shank and in pre-branching region of branched tubes decreased only at 0.25-mM MeJA. Anisotropy of both two apexes of a branched tube changed only at 0.25- and 0.5-mM MeJA. Callose accumulation in the apex of unbranched and branched tubes increased in parallel with the increase in MeJA concentration. However, more callose is accumulated in one apex than the other apex of a branched tube. In conclusion, MeJA affected the actin organization, changed the callose distribution, and altered the pollen tube growth of Pinus nigra. [ABSTRACT FROM AUTHOR]

The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. Genomic data are limited in giant sequoia and producing a reference genome sequence has been an important goal to allow marker development for restoration and management. Using deep-coverage Illumina and Oxford Nanopore sequencing, combined with Dovetail chromosome conformation capture libraries, the genome was assembled into eleven chromosome-scale scaffolds containing 8.125 Gbp of sequence. Iso-Seq transcripts, assembled from three distinct tissues, was used as evidence to annotate a total of 41,632 protein-coding genes. The genome was found to contain, distributed unevenly across all 11 chromosomes and in 63 orthogroups, over 900 complete or partial predicted NLR genes, of which 375 are supported by annotation derived from protein evidence and gene modeling. This giant sequoia reference genome sequence represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management. [ABSTRACT FROM AUTHOR]

Epigenetic reprogramming during germ cell formation is essential to gain pluripotency and thus embryogenic potential. The histone modification H3K27me3, which is catalysed by the Polycomb repressive complex 2 (PRC2), regulates important developmental processes in both plants and animals, and defects in PRC2 components cause pleiotropic developmental abnormalities. Nevertheless, the role of H3K27me3 in determining embryogenic potential in gymnosperms is still elusive. To address this, we generated H3K27me3 profiles of Norway spruce (Picea abies) embryonic callus and non-embryogenic callus using CUT&RUN, which is a powerful method for chromatin profiling. Here, we show that H3K27me3 mainly accumulated in genic regions in the Norway spruce genome, similarly to what is observed in other plant species. Interestingly, H3K27me3 levels in embryonic callus were much lower than those in the other examined tissues, but markedly increased upon embryo induction. These results show that H3K27me3 levels are associated with the embryogenic potential of a given tissue, and that the early phase of somatic embryogenesis is accompanied by changes in H3K27me3 levels. Thus, our study provides novel insights into the role of this epigenetic mark in spruce embryogenesis and reinforces the importance of PRC2 as a key regulator of cell fate determination across different plant species. [ABSTRACT FROM AUTHOR]

Plants generally use soil inorganic nitrogen, ammonium (NH4+–N), and nitrate (NO3−–N) as sources of nitrogen, an essential nutrient. The assimilation processes after uptake differ considerably from ammonium to nitrate. Nitrate must be reduced to ammonium in plant tissue before it is synthesized to amino acids, while ammonium is directly and immediately synthesized to amino acids after its uptake. Nitrate reductase is an enzyme that catalyzes the first and rate‐limiting step of nitrate assimilation, reducing nitrate to nitrite. It is a substrate‐inducible enzyme, and the capacity to induce nitrate reductase varies greatly among plant species. In vivo nitrate reductase activity (NRA) is generally measured as a nitrite production rate during incubation using fine cut pieces of plant tissue, and it is applicable as an indicator on plant nitrate use. Here we present in vivo NRA of leaves from a total of 108 species including arboreal trees, small trees, shrubs, herbs, a vine and a moss. For 75 of the species, NRA in fine roots was also determined. At least 20 species in sampled plants were imported and planted for scientific or industrial purposes, but most sampled species were native to Japan. Several inventory studies of plant NRA have been conducted, mainly in Europe, and they provided information on the species‐specific capacity of nitrate use by plants in Europe. However, to our best knowledge, there has been hitherto no published inventory of the NRA of plants in Japan where many endemic species are distributed. Our dataset contains plant NRA with species, family name, life form, leaf lifespan (evergreen or deciduous), growth stage, the season of sample collection, growth conditions (natural or cultivated) and other treatments/conditions when applicable. The data provided by this study may contribute to future works that require information regarding the plant species characteristics for nitrate use capacity or nitrate preference. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2019-06.1/jalter-en. [Correction added on 7 September 2020, after first online publication: JaLTER URL has been updated.] [ABSTRACT FROM AUTHOR]

Key message: MiRNA transcriptome analysis of different tissues in poplar and larch suggests variant roles of miRNAs in regulating wood formation between two kinds of phyla. Poplar and larch belong to two different phyla. Both are ecological woody species and major resources for wood-related industrial applications. However, wood properties are different between these two species and the molecular basis is largely unknown. In this study, we performed high-throughput sequencing of microRNAs (miRNAs) in the three tissues, xylem, phloem and leaf of Populus alba × Populus glandulosa and Larix kaempferi. Differentially expressed miRNA (DEmiRNA) analysis identified 85 xylem-specific miRNAs in P. alba × P. glandulosa and 158 xylem-specific miRNAs in L. kaempferi. Among 36 common miRNAs, 12 were conserved between the two species. GO and KEGG analyses of the miRNA target genes showed similar metabolism in two species. Through KEGG and BLASTN, we predicted target genes of xylem differentially expressed (DEmiRNA) in the wood formation-related pathways and located DEmiRNAs in these pathways. A network was built for wood formation-related DEmiRNAs, their target genes and orthologous genes in Arabidopsis thaliana. Comparison of DEmiRNA and target gene annotation between P. alba × P. glandulosa and L. kaempferi suggested the different functions of DEmiRNAs and divergent mechanism in wood formation between two species, providing knowledge to understand wood formation mechanism in gymnosperm and angiosperm woody plants. [ABSTRACT FROM AUTHOR]

Curvularia includes plant pathogenic species with a worldwide distribution and a wide host range, particularly cereals and grass (Poaceae). Chinese fir (Cunninghamia lanceolata) is an important afforestation tree species in southern China, with a high economic value. Leaf blight disease on Chinese fir was discovered in Hunan and Zhejiang, China, and two fungal species were found to be associated with the symptoms. Using morphological and phylogenetic approaches, they were identified as Curvularia spicifera and Curvularia muehlenbeckiae. They were determined to be the pathogens by fulfilling Koch's postulates. Both showed a pathogenicity on Citrus reticulata and Citrus tangerina, which have a similar geographic distribution to Chinese fir. The similar geographic distribution of these hosts may increase the risk of disease. Based on a literature review, leaf blight caused by C. spicifera and C. muehlenbeckiae is recorded here on a gymnosperm for the first time. [ABSTRACT FROM AUTHOR]

In response to various stimuli, plants acquire resistance against pests and/or pathogens. Such acquired or induced resistance allows plants to rapidly adapt to their environment. Spraying the bark of mature Norway spruce (Picea abies) trees with the phytohormone methyl jasmonate (MeJA) enhances resistance to tree‐killing bark beetles and their associated phytopathogenic fungi. Analysis of spruce chemical defenses and beetle colonization success suggests that MeJA treatment both directly induces immune responses and primes inducible defenses for a faster and stronger response to subsequent beetle attack. We used metabolite and transcriptome profiling to explore the mechanisms underlying MeJA‐induced resistance in Norway spruce. We demonstrated that MeJA treatment caused substantial changes in the bark transcriptional response to a triggering stress (mechanical wounding). Profiling of mRNA expression showed a suite of spruce inducible defenses are primed following MeJA treatment. Although monoterpenes and diterpene resin acids increased more rapidly after wounding in MeJA‐treated than control bark, expression of their biosynthesis genes did not. We suggest that priming of inducible defenses is part of a complex mixture of defense responses that underpins the increased resistance against bark beetle colonization observed in Norway spruce. This study provides the most detailed insights yet into the mechanisms underlying induced resistance in a long‐lived gymnosperm. We explored the mechanisms underlying MeJA‐induced resistance in Norway spruce. We showed that a suite of spruce inducible defenses was primed following MeJA treatment and that they are part of a complex mixture of defense responses that underpins long‐lasting increased resistance. [ABSTRACT FROM AUTHOR]