Search

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.

Pherosphaera fitzgeraldii, the Dwarf Mountain Pine, is a critically endangered conifer restricted to cliff ledges within waterfall spray zones in the Greater Blue Mountains Area of New South Wales, Australia. This species is under threat from pollution, invasive weeds, and limited recruitment, which are contributing to its declining population. Using a comprehensive conservation genomic approach, we assessed the population health of P. fitzgeraldii and developed strategic recommendations for its management.Genomic analysis of P. fitzgeraldii revealed the presence of two distinct genetic groups despite the limited distribution of the species. This genetic structure aligns with prevailing wind currents, indicating potential restrictions to pollen or seed exchange between subpopulations. Furthermore, limited gene flow was observed even among nearby subpopulations, emphasizing the risk of increased genetic differentiation due to ongoing isolation. Clonality is widespread in some subpopulations, and all subpopulations displayed signs of inbreeding and genetic depletion despite subdioecy, indicative of historical constraints on gene flow and small population sizes.We offer genomic-based recommendations for prioritizing conservation sites, enhancing genetic diversity in ex situ collections, and guiding future management. Further studies to uncover the sex determination mechanism of P. fitzgeraldii could help maintain balanced sex ratios in ex situ collections and support future genetic rescue efforts. This study underscores the value of genomics in informing protection and recovery of unique threatened species.

Abstract 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.

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]

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]

Fossil plants, including large trunks, stems, some branches, and twigs, were collected from the Maastrichtian (68.9 Ma), upper Dorotea Formation in the Magallanes–Austral Basin, 16 km north of the Cerro Guido–Las Chinas complex in the southern Chilean Magallanes region. These fossil trunks range from 0.2 to 2.2 m in length. Petrographic slides were made in three sections (transverse, radial and tangential) and analysed under a light microscope to study the permineralized fossils. The woods and stems belong to Austroginkgoxylon gen. et sp. nov., Agathoxylon antarcticum, Podocarpoxylon paradoxi sp. nov., Podocarpoxylon mazzonii, Palmoxylon subantarcticae and Notomalvaceoxylon magallanense gen. et sp. nov. The growth rings of gymnosperms and anatomical characters of angiosperms were analysed to obtain palaeoecological data. Interactions between gymnosperm roots growing into the secondary xylem of an angiosperm (nurse logs) are recorded. The data obtained from the fossil woods suggest warm and humid conditions in this southern South American locality during the Late Cretaceous, providing a unique opportunity to study continental environments at high southern latitudes, which are poorly represented on a global scale. [ABSTRACT FROM AUTHOR]

Sequencing, assembly, and annotation of the 26.5 Gbp 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 44.9 Mbp. 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 500 Kbp in length and one reaching 2 Mb. Nearly 19 Gbp 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.

Aim of study: A defoliating insect, Calomicrus foveolatus, feeding on the Andalusian endemic fir Abies pinsapo (Pinaceae) is herein reported for the first time. Until now, this chrysomelid beetle was known to feed exclusively on Quercus spp. (Fagaceae). Area of study: The study was carried out in the forests of A. pinsapo, restricted to protected mountainous areas of western Málaga and eastern Cádiz in southern Spain. Material and methods: Since 2001 we carried out monitoring for potentially damaging insects at five sites of the pinsapo forests at least once a year. The monitoring visits were increased to 2-3 times a year at the sites that contained the phytophagous species. Main results: Calomicrus foveolatus was observed feeding on pinsapo needles in sites of Sierra de las Nieves National Park, in Málaga province. Besides, damaged pinsapos were also observed in Sierra de Grazalema Natural Park in Cádiz Province. Feeding activity consisted of partial and superficial damage from gnawing on the upper side of the needles; eventually producing death of the needles and finally death of the entire shoot. The recognition characteristics of the beetle and its injury on the needles and branches are described. Research highlights: It is described, for the first time, the attack of a phytophagous leaf beetle, C. foveolatus, to the endemic conifer A. pinsapo, in the National Park “Sierra de las Nieves” in the province of Málaga, Spain. Further monitoring of this beetle is necessary for the sustainable management of this protected fir endemic to the Baetic regions.

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]

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]

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]

The leafminers on gymnosperms receive much less attention than those on either angiosperms or ferns. Given the distinctly different leaf shape and leaf venation found in gymnosperms, they would be expected to host significantly different leafminer groups. Very few comprehensive reports on gymnosperm-feeding leafminers have been presented.Based on the well-studied fauna in North America and Europe, we compiled a list of 133 species, 30 genera and 13 families of gymnosperm-feeding leafminers. The gymnosperm-mining families (in descending order of leafminer number) included Tortricidae, Gelechiidae, Argyresthiidae, Yponomeutidae, Batrachedridae, Pyralidae, Adelidae, Agromyzidae, Blastobasidae, Bucculatricidae, Coleophoridae, Curculionidae and Noctuidae. There were 109 species, 22 genera and ten families in North America and 34 species, 19 genera and nine families in Europe. We compiled a list of 102 species and 16 genera of host plants, belonging to four families: Pinaceae, Cupressaceae, Taxaceae and Zamiaceae. There were 84 host species, 15 genera and three host families in North America and 46 host species, ten genera and three host families in Europe. Dominant gymnosperm-mining families and dominant host families were generally the same in the two continents.

Cycas pectinata Buch.-Ham. is an ancient gymnosperm that is now confined to pockets of habitats in the Indian subcontinent but was once widely distributed. Its decline is attributable to habitat loss, and has reached the point where C. pectinata is listed as 'Vulnerable' in the IUCN Red List. C. pectinata is the only species of Cycas found in Bhutan, and in this biodiversity-rich area it is present as a relic of great scientific and conservation value because of its rarity and long evolutionary history. Although it is well known in India, it has not been studied in detail in Bhutan. This study assessed populations and threats to C. pectinata in two places in Bhutan. Field visits were made to document the distribution, habitats, and associated threats to the populations. Plants were observed growing in steep rugged terrain in the open Chir Pine forest. Populations are significantly threatened due to human activities such as habitat destruction and over collection as ornamental plant. Possible expansion of populations is naturally threatened by low seed production and by predators. [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]

This study identified two palynological assemblages, namely Bayanhuasporites-Cycadopites-Protoconiferus and Cicatricosisporites-Cedripites-Perinopollenites, in the Tongbomiao Formation in the Hongqi Sag in the Hailar Basin, Inner Mongolia, China for the first time. The former is distributed in the lower part of the Tongbomiao Formation and is characterized by abundant gymnosperm pollen and diverse fern spores. Among them, the gymnosperm pollen is dominated by Paleoconifer (4.98%–31.62%) and Cycadopite (8.55%–25.23%) pollen grains and also includes other pollen grains such as Classopollis, Parcisporites, Erlianpollis, Callialasporites, and Jiaohepollis. The fern spores in the former palynological assemblage contain Bayanhuasporite (0–8.96%), Granulatisporites (0.93%–6.97%), and some important Cretaceous genera, such as Cicatricosisporites, Concavissimisporites, Densoisporites, Hsuisporites, Foraminisporis, and Leptolepidites. The Cicatricosisporites-Cedripites-Perinopollenites palynological assemblage is distributed in the upper part of the Tongbomiao Formation. Gymnosperm (77.30%), Pinaceae (31.9%), and Paleoconiferus (19.02%) pollen predominate this palynological assemblage, and Quadraeculina, Erlianpollis, and Jiaohepollis pollen are also common in this assemblage. The fern spores in this palynological assemblage include abundant Cicatricosisporites (4.29%). Besides, Concavissimisporites, Aequitriradites, and Leptolepidites are also common in this palynological assemblage. No angiosperm pollen has been found in both palynological assemblages. The identification of both palynological assemblages provides important evidence for the biostratigraphic correlation between the Hailar Basin and its adjacent areas. It also enables the reconstructions of the Berriasian-Valanginian (Early Cretaceous) vegetation and the paleoclimate on the eastern Mongolian Plateau during 141–132 Ma. The vegetation reconstructed on the palynological data of the represented by Hailar Basin in eastern Mongolian Plateau (141.6–141.4 Ma), form conifer forest or conifer broad-leaved mixed forest to conifer forest with shrubs and grassland, the climate belongs to warm temperate and warm-subtropicalt, the highest temperature is estimated to reach 35–38°C. Form 132.3 Ma, the vegetation type is conifer forest, and its paleoclimate is sub-humid warm temperate, the highest temperature is estimated to reach 24–29°C.©2022 China Geology Editorial Office.

The impact of low-dose-rate radiation on genetics is largely unknown, particularly in natural environments. The Fukushima Dai-ich Nuclear Power Plant disaster resulted in the creation of contaminated natural lands. In this study, de novo mutations (DNMs) in germ line cells were surveyed from double-digest RADseq fragments in Japanese cedar and flowering cherry trees exposed to ambient dose rates ranging from 0.08 to 6.86 μGy h−1. These two species are among the most widely cultivated Japanese gymnosperm and angiosperm trees for forestry and horticultural purpose, respectively. For Japanese flowering cherry, open crossings were performed to produce seedlings, and only two candidate DNMs were detected from uncontaminated area. For Japanese cedar, the haploid megagametophytes were used as next generation samples. The use of megagametophytes from open crossing for next generation mutation screening had many advantages such as reducing exposure to radiation in contaminated areas because artificial crossings are not needed and the ease of data analysis owing to the haploid nature of megagametophytes. A direct comparison of the nucleotide sequences of parents and megagametophytes revealed an average of 1.4 candidate DNMs per megagametophyte sample (range: 0–40) after filtering procedures were optimized based on the validation of DNMs via Sanger sequencing. There was no relationship between the observed mutations and the ambient dose rate in the growing area or the concentration of 137Cs in cedar branches. The present results also suggest that mutation rates differ among lineages and that the growing environment has a relatively large influence on these mutation rates. These results suggested there was no significant increase in the mutation rate of the germplasm of Japanese cedar and flowering cherry trees growing in the contaminated areas.

The emergence of resistant pathogenic bacterial strains has threatened the human beings and already developed remedial measures. Based on the traditional herbal therapeutic history, present study is aimed to assess in vitro and in silico inhibition potential of leaves extracts of Pinus roxburghii and Cedrus deodara against human pathogenic bacteria Staphylococcus aureus, Salmonella typhi and Pseudomonas aeruginosa. Hexane, methanol and acetone extracts of both plants were evaluated against above mentioned bacterial strains employing agar well diffusion technique. While docking analyses were performed to analyze the interaction of vital bioactive compounds and bacterial virulence proteins to get an idea about potential candidates for drug discovery. Both plant extracts exhibited greater antibacterial activities against S. aureus as compared to S. typhi and P. aeruginosa. The activity of different extracts also portrayed the role of polarity of solvent and compound to be extracted in each solvent i.e., activity of hexane extract > methanol > acetone with some variations. MIC (minimum inhibitory concentration) values of P. roxburghii extracts were less than that of C. deodara against tested strains, while variation was observed in MBCs (minimum bactericidal concentrations). Furthermore, molecular docking of studied plants bioactive compounds and bacterial proteins showed strong interactions (binding affinity) i.e., taxifolin > nortrachelogenin > bisabolene > valencene > caryophyllene. Antibacterial efficiencies of P. roxburghii and C. deodara suggested their application as effective therapeutic agents against diseases caused by mentioned bacterial strains. In silico analysis suggests the isolation and usage of bioactive components as potential antibacterial agents/drugs after further experimentations on animals.

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]

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 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.

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-β-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. [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.

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]

Homologs of Larix kaempferiDEFICIENS-AGAMOUS-LIKE 1 (LaDAL1) promote flowering in Arabidopsis. However, their functional role in the whole life-cycle is limited. Here, we analyzed the phenotypes and transcriptomes of Arabidopsis plants over-expressing LaDAL1. With respect to the defined life-cycle stage of Arabidopsis based on the meristem state, the results showed that LaDAL1 promoted seed germination, bolting, flower initiation, and global proliferative arrest, indicating that LaDAL1 accelerates the meristem reactivation, the transitions of vegetative meristem to inflorescence and flower meristem, and meristem arrest. As a marker gene of meristem, TERMINAL FLOWER 1 was down-regulated after LaDAL1 over-expression. These results reveal that LaDAL1 accelerates the life-cycle progression in Arabidopsis by promoting the transition of meristem fate, providing more and novel functional information about the conifer age-related gene DAL1. [ABSTRACT FROM AUTHOR]

Abstract 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.

Why this research Matters The inner bark plays important roles in tree stems, including radial exchange of water with the xylem and translocation of carbohydrates. Both processes affect the water content and the thickness of the inner bark on a diurnal basis. For the first time, we simultaneously measured the diurnal variations in the inner bark thickness of hinoki cypress (Chamaecyparis obtusa) by using point dendrometers and those of local xylem potential by using stem psychrometers located next to the dendrometers to determine how these variations were related to each other, to phloem turgor and carbohydrate transport. We also estimated the axial hydrostatic pressure gradient by measuring the osmolality of the sap extracted from the inner bark. The inner bark shrunk during the day and swelled during the night with an amplitude related to day‐to‐day and seasonal variations in climate. The relationship between changes in xylem water potential and inner bark thickness exhibited a hysteresis loop during the day with a median lag of 2 h. A phloem turgor‐related signal can be retrieved from the diurnal variations in the inner bark thickness, which was higher at the upper than at the lower position along the trunk. However, a downward hydrostatic pressure gradient was only observed at dawn, suggesting diurnal variations in the phloem sap flow velocity.

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms.

Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers.

Abstract Wood anatomical traits of xylem are the characteristics of tree rings at cellular and subcellular scales providing important insights on structural features and their linkage to the environment. Therefore, studying the relationship between anatomical traits and environmental changes not only provide physiological explanations, but also provide a new vision of studying the adaptation process and response strategies of tree growth to climate. In this paper, I review and synthesize literature on the influence of climatic parameters on wood anatomy from the different geographical regions using recent (2015–2020) published articles on the topic. This paper discusses the relationship between the anatomical features of angiosperm and gymnosperm xylem with climatic factors. Based on the literature, I then purpose to explore the temporal and spatial variations in the anatomical characteristics of xylem tree rings with environmental changes. Also, more studies can be conducted to assess the synergetic and antagonistic effects among different tree-ring proxies and to determine the specific roles and contributions of major climatic factors during different periods of tree-ring formation.

• The stem CH 4 emissions in wetlands are significantly higher than in uplands. • The stem CH 4 emissions of angiosperm are higher than gymnosperm trees. • The stem CH 4 emissions in coastal wetlands are less than in inland wetlands. • The source of stem CH 4 emissions in wetlands is from the soil. Growing evidence suggests that methane (CH 4) emissions from tree stems are a potentially significant atmospheric source. However, a comprehensive global assessment of the general pattern and the controlling factors of stem CH 4 emissions is still unavailable. Here, we present a global data-synthesis of 1081 observations from 62 studies to explore the patterns of stem CH 4 emission rate in upland and wetland ecosystems and their controlling factors. The global average stem CH 4 emission rate in uplands was 2.04 ± 0.61 nmol m −2 s −1, which was significantly lower than in wetlands (87.08 ± 19.49 nmol m −2 s −1). Angiosperm stem CH 4 emission rates were significantly higher than gymnosperm in both upland and wetland ecosystems. Meanwhile, stem CH 4 emission rate in inland wetlands (101.78 ± 27.44 nmol m −2 s −1) was significantly higher than in coastal wetlands (56.21 ± 19.23 nmol m −2 s −1). In both wetland and upland ecosystems, stem CH 4 emission rate decreased with increasing sampling height, but increased as soil CH 4 emission rate increased. However, the relationship between stem CH 4 emissions and soil CH 4 fluxes was much weaker for uplands, but very strong for wetlands. In wetlands, stem CH 4 emission rate was also regulated by plant properties, as it was negatively correlated with wood specific density, but positively correlated with stem lenticel density. In uplands, tree diameter negatively affected stem CH 4 emission rate. Overall, our results shed light on the magnitude and controlling factors of stem CH 4 emissions in upland and wetland ecosystems and could facilitate their upscaling to ecosystems and identify the role of stem CH 4 emissions in global CH 4 budgets. [Display omitted] [ABSTRACT FROM AUTHOR]