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Summary: The onset of stomatal closure reduces transpiration during drought. In seed plants, drought causes declines in plant water status which increases leaf endogenous abscisic acid (ABA) levels required for stomatal closure. There are multiple possible points of increased belowground resistance in the soil–plant atmospheric continuum that could decrease leaf water potential enough to trigger ABA production and the subsequent decreases in transpiration.We investigate the dynamic patterns of leaf ABA levels, plant hydraulic conductance and the point of failure in the soil–plant conductance in the highly embolism‐resistant species Callitris tuberculata using continuous dendrometer measurements of leaf water potential during drought.We show that decreases in transpiration and ABA biosynthesis begin before any permanent decreases in predawn water potential, collapse in soil–plant hydraulic pathway and xylem embolism spread.We find that a dynamic but recoverable increases in hydraulic resistance in the soil in close proximity to the roots is the most likely driver of declines in midday leaf water potential needed for ABA biosynthesis and the onset of decreases in transpiration. [ABSTRACT FROM AUTHOR]

The mitochondrial plastid DNAs (MTPTs) in seed plants were reported more than 40 years ago and exhibited a high diversity regarding gene content, quantity, and size. However, the mechanism that resulted in the current diversity of MTPTs in angiosperms has not been fully discovered. In this study, we sequenced and characterized the complete organelle genomes of Limonia acidissima L. a monotypic species of Rutaceae. The newly generated and previously published organelle genomes of 42 species were used to explore the diversity of MTPTs regarding quantity, gene content, size, and coverage of chloroplast genome (cpDNA) regions. The results showed that the number of MTPTs ranged from three to 74, of which the lengths were from 100 to 53,731 bp. The highest coverage of MTPTs was found in the inverted repeat region, whereas the small single repeat region had the lowest coverage. Based on the previous data and current results, we propose a scenario for the diversity of MTPTs in angiosperms. In the first stage, the whole cpDNA might migrate to the mitogenome. Then, different genomic events, such as duplication, deletion, substitution, and inversion, have occurred continuously and independently and resulted in extremely variable profiles of mitogenomes among angiosperms. Our hypothesis provides a new and possibly reliable scenario for explaining the present circumstances of MTPTs in angiosperms. However, more genomic data should be mined, and more studies should be conducted to clarify this natural phenomenon in plants. [ABSTRACT FROM AUTHOR]

Periderm is a well‐known structural feature with vital roles in protection of inner plant tissues and wound healing. Despite its importance to plant survival, knowledge of periderm occurrences outside the seed plants is limited and the evolutionary origins of periderm remain poorly explored. Here, we review the current knowledge of the taxonomic distribution of periderm in its two main forms – canonical periderm (periderm formed as a typical ontogenetic stage) and wound periderm (periderm produced as a self‐repair mechanism) – with a focus on major plant lineages, living and extinct. We supplement the published occurrences with data based on our own observations and experiments. This updated body of data reveals that the distribution of wound periderm is more widespread taxonomically than previously recognized and some living and extinct groups are capable of producing wound periderm, despite canonical periderm being absent from their normal developmental program. A critical review of canonical and wound periderms in extant and fossil lineages indicates that not all periderms are created equal. Their organisation is widely variable and the differences can be characterised in terms of variations in three structural features: (i) the consistency in orientation of periclinal walls within individual files of periderm cells; (ii) the lateral coordination of periclinal walls between adjacent cell files; and (iii) whether a cambial layer and conspicuous layering of inward and outward derivatives can be distinguished. Using a new system of scoring periderm structure based on these criteria, we characterise the level of organisation of canonical and wound periderms in different lineages. Looking at periderms through the lens provided by their level of organisation reveals that the traditional image of periderm as a single generalised feature, is best viewed as a continuum of structural configurations that are all predicated by the same basic process (periclinal divisions), but can fall anywhere between very loosely organized (diffuse periclinal growth) to very tightly coordinated (organized periclinal growth). Overall, wound periderms in both seed plants and seed‐free plants have lower degrees of organisation than canonical periderms, which may be due to their initiation in response to inherently disruptive traumatic events. Wound and canonical periderms of seed plants have higher degrees of organisation than those of seed‐free plants, possibly due to co‐option of the programs responsible for organizing their vascular cambial growth. Given the importance of wound periderm to plant survival, its widespread taxonomic distribution, and its early occurrence in the fossil record, we hypothesise that wound periderm may have had a single origin in euphyllophytes and canonical periderm may have originated separately in different lineages by co‐option of the basic regulatory toolkit of wound periderm formation. In one evolutionary scenario, wound periderm regulators activated initially by tissue tearing due to tensional stresses elicited by woody growth underwent heterochronic change that switched their activation trigger from tissue tearing to the tensional stresses that precede it, with corresponding changes in the signalling that triggered the regulatory cascade of periderm development from tearing‐induced signals to signalling induced by tension in cells. [ABSTRACT FROM AUTHOR]

The island syndrome is defined as a suite of predictable and consistent differences between island and mainland organisms. In seed plants, much of what we know about the island syndrome comes from work in the Southwest Pacific, which is comprised of the three main islands of New Zealand and ten surrounding archipelagos. These surrounding archipelagos are all remote and relatively small. They were never connected to another landmass and their floras are derived by overwater dispersal, mostly from the main islands of New Zealand, making them an ideal system for the study of island evolution. In this review, we summarise work on the island syndrome conducted on New Zealand’s outlying islands, establish whether these findings are in line with global patterns of island biology or whether they are unique to this region, and propose directions for future research. [ABSTRACT FROM AUTHOR]

Introduction: Two economies of scale, predator satiation and pollination efficiency, have been proposed to explain the evolutionary mechanisms of mast seeding adopted by some long-lived plants. Plant height is strongly selected by pollination vectors and may also provide economies of scale; however, it remains unknown whether there is a close relationship between adult plant height and mast seeding intensity. Methods: Here, we analyzed mast seeding intensity of 158 plant species to test if adult plant height can select for mast seeding. Results: We show that mast seeding intensities are higher in taller plant species irrespective of phylogeny, life form, pollination vector, and type of Spermatophytes. We also show that anemophily rather than entomophily selects for taller plant species and higher mast seeding intensities. Discussion: The linear correlations and evolutionary links between adult plant height andmast seeding intensity provide evidence that mast seeding could have evolved as an adaptation to taller strategy of perennial plant species. [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]

Gene targeting (GT) allows precise manipulation of genome sequences, such as knock-ins and sequence substitutions, but GT in seed plants remains a challenging task. Engineered sequence-specific nucleases (SSNs) are known to facilitate GT via homology-directed repair (HDR) in organisms. Here, we demonstrate that Cas12a and a temperature-tolerant Cas12a variant (ttCas12a) can efficiently establish precise and heritable GT at two loci in Arabidopsis thaliana (Arabidopsis) through a sequential transformation strategy. As a result, ttCas12a showed higher GT efficiency than unmodified Cas12a. In addition, the efficiency of transcriptional and translational enhancers for GT via sequential transformation strategy was also investigated. These enhancers and their combinations were expected to show an increase in GT efficiency in the sequential transformation strategy, similar to previous reports of all-in-one strategies, but only a maximum twofold increase was observed. These results indicate that the frequency of double strand breaks (DSBs) at the target site is one of the most important factors determining the efficiency of genetic GT in plants. On the other hand, a higher frequency of DSBs does not always lead to higher efficiency of GT, suggesting that some additional factors are required for GT via HDR. Therefore, the increase in DSB can no longer be expected to improve GT efficiency, and a new strategy needs to be established in the future. This research opens up a wide range of applications for precise and heritable GT technology in plants. Key message: The combination of enhancers, Cas12a, and sequential transformation strategies enables efficient and precise heritable gene targeting in Arabidopsis. [ABSTRACT FROM AUTHOR]

Resource allocation theory posits that organisms distribute limited resources across functions to maximize their overall fitness. In plants, the allocation of resources among maintenance, reproduction, and growth influences short‐term economics and long‐term evolutionary processes, especially during resource scarcity. The evolution of specialized structures to divide labor between reproduction and growth can create a feedback loop where selection can act on individual organs, further increasing specializaton and resource allocation. Ferns exhibit diverse reproductive strategies, including dimorphism, where leaves can either be sterile (only for photosynthesis) or fertile (for spore dispersal). This dimorphism is similar to processes in seed plants (e.g., the production of fertile flowers and sterile leaves), and presents an opportunity to investigate divergent resource allocation between reproductive and vegetative functions in specialized organs. Here, we conducted anatomical and hydraulic analyses on Onoclea sensibilis L., a widespread dimorphic fern species, to reveal significant structural and hydraulic divergences between fertile and sterile leaves. Fertile fronds invest less in hydraulic architecture, with nearly 1.5 times fewer water‐conducting cells and a nearly 0.5 times less drought‐resistant xylem compared to sterile fronds. This comes at the increased relative investment in structural support, which may help facilitate spore dispersal. These findings suggest that specialization in ferns—in the form of reproductive dimorphism—can enable independent selection pressures on each leaf type, potentially optimizing spore dispersal in fertile fronds and photosynthetic efficiency in sterile fronds. Overall, our study sheds light on the evolutionary implications of functional specialization and highlights the importance of reproductive strategies in shaping plant fitness and evolution. [ABSTRACT FROM AUTHOR]

SUMMARY: L‐Arabinose (L‐Ara) is a plant‐specific sugar found in cell wall polysaccharides, proteoglycans, glycoproteins, and small glycoconjugates, which play physiologically important roles in cell proliferation and other essential cellular processes. L‐Ara is synthesized as UDP‐L‐arabinose (UDP‐L‐Ara) from UDP‐xylose (UDP‐Xyl) by UDP‐Xyl 4‐epimerases (UXEs), a type of de novo synthesis of L‐Ara unique to plants. In Arabidopsis, the Golgi‐localized UXE AtMUR4 is the main contributor to UDP‐L‐Ara synthesis. However, cytosolic bifunctional UDP‐glucose 4‐epimerases (UGEs) with UXE activity, AtUGE1, and AtUGE3 also catalyze this reaction. For the present study, we first examined the physiological importance of bifunctional UGEs in Arabidopsis. The uge1 and uge3 mutants enhanced the dwarf phenotype of mur4 and further reduced the L‐Ara content in cell walls, suggesting that bifunctional UGEs contribute to UDP‐L‐Ara synthesis. Through the introduction of point mutations exchanging corresponding amino acid residues between AtUGE1 with high UXE activity and AtUGE2 with low UXE activity, two mutations that increase relative UXE activity of AtUGE2 were identified. The crystal structures of AtUGE2 in complex forms with NAD+ and NAD+/UDP revealed that the UDP‐binding domain of AtUGE2 has a more closed conformation and smaller sugar‐binding site than bacterial and mammalian UGEs, suggesting that plant UGEs have the appropriate size and shape for binding UDP‐Xyl and UDP‐L‐Ara to exhibit UXE activity. The presented results suggest that the capacity for cytosolic synthesis of UDP‐L‐Ara was acquired by the small sugar‐binding site and several mutations of UGEs, enabling diversified utilization of L‐Ara in seed plants. [ABSTRACT FROM AUTHOR]

The collection of photos during the systematic monitoring activities is useful to witness the ecological role of marine phanerogams as hosts for a rich variety of organisms in coastal and transitional waters. Cymodocea nodosa is present in the Taranto seas. In Mar Piccolo, it reached high coverage in a short amount of time, up to 100%, due to the improvement in environmental conditions. The most recent observations showed that it offers a welcoming habitat for several vertebrates and invertebrates, native and non-indigenous, as well as to micro- and macroalgae. The NPPR-funded activities will make these observations more robust and structural. [ABSTRACT FROM AUTHOR]

Seagrasses provide key ecological services in coastal marine and estuarine environments. Human activities and environmental changes affect seagrasses compromising their structure and functioning. In this context, seagrass restoration has become a worldwide priority to halt and reverse degradation and to recover ecosystem functionality and associated services. Here, we investigate the sexual reproduction of Posidonia oceanica by describing the flowering and fruiting process. Furthermore, we compare the structural (survival and shoot density) and functional (daily leaf production, DLP) descriptors of seedlings with those derived from a P. oceanica transplantation performed through cuttings to assess their feasibility as an integrative source of vegetal material for restoration purposes. Despite many initial flowers and fruits, a small number of mature fruits are produced, confirming the low reproductive success of the phanerogam. A comparison of structural and functional features showed that seedlings and cuttings showed similar survival and shoot density rates after more than 2 years. In addition, DLP showed that seedlings increased in leaf length over the study period, reaching a similar value registered by cuttings. The study demonstrates the effectiveness of using seedlings in restoration efforts. It also emphasizes the importance of exploring P. oceanica reproductive ecology to better understand temporal and spatial variations in flowering, as well as fruiting success, at local and basin scales. [ABSTRACT FROM AUTHOR]

Summary: Leaf venation is a pivotal trait in the success of vascular plants. Whereas gymnosperms have single or sparsely branched parallel veins, angiosperms developed a hierarchical structure of veins that form a complex reticulum. Its physiological consequences are considered to have enabled angiosperms to dominate terrestrial ecosystems in the Late Cretaceous and Cenozoic.Although a hierarchical‐reticulate venation also occurs in some groups of extinct seed plants, it is unclear whether these are stem relatives of angiosperms or have evolved these traits in parallel. Here, we re‐examine the morphology of the enigmatic foliage taxon Furcula, a potential early Mesozoic angiosperm relative, and argue that its hierarchical vein network represents convergent evolution (in the Late Triassic) with flowering plants (which developed in the Early Cretaceous) based on details of vein architecture and the absence of angiosperm‐like stomata and guard cells.We suggest that its nearest relatives are Peltaspermales similar to Scytophyllum and Vittaephyllum, the latter being a genus that originated during the Late Triassic (Carnian) and shares a hierarchical vein system with Furcula.We further suggest that the evolution of hierarchical venation systems in the early Permian, the Late Triassic, and the Early Cretaceous represent 'natural experiments' that might help resolve the selective pressures enabling this trait to evolve. [ABSTRACT FROM AUTHOR]

Plant stems comprise nodes and internodes that specialize in solute exchange and elongation. However, their boundaries are not well defined, and how these basic units arise remains elusive. In rice with clear nodes and internodes, we found that one subclade of class I knotted1-like homeobox (KNOX1) genes for shoot meristem indeterminacy restricts node differentiation and allows internode formation by repressing YABBY genes for leaf development and genes from another node-specific KNOX1 subclade. YABBYs promote nodal vascular differentiation and limit stem elongation. YABBY and node-specific KNOX1 genes specify the pulvinus, which further elaborates the nodal structure for gravitropism. Notably, this KNOX1 subclade organization is specific to seed plants. We propose that nodes and internodes are distinct domains specified by YABBY-KNOX1 cross-regulation that diverged in early seed plants. [ABSTRACT FROM AUTHOR]

Summary: Ontogenetic shape change has long been recognized to be important in generating patterns of morphological diversity and may be especially important in plant reproductive structures. We explore how seed cone disparity in Cupressaceae changes over ontogeny by comparing pollination‐stage and mature cones.We sampled cones at pollen and seed release and measured cone scales using basic morphometric shape variables. We used multivariate statistical methods, particularly hypervolume overlap calculations, to measure morphospace occupation and disparity.Cone scales at both pollination and maturity exhibit substantial variability, although the disparity is greater at maturity. Mature cone scales are also more clustered in trait space, showing less overlap with other taxa than at pollination. These patterns reflect two growth strategies that generate closed cones over maturation, either through thin laminar scales or relatively thick, peltate scales, resulting in two distinct regions of morphospace occupation.Disparity patterns in Cupressaceae seed cones change over ontogeny, reflecting shifting functional demands that require specific patterns of cone scale growth. The evolution of Cupressaceae reproductive disparity therefore represents selection for trajectories of ontogenetic shape change, a phenomenon that should be widespread across seed plants. See also the Commentary on this article by Olson, 242: 1856–1859. [ABSTRACT FROM AUTHOR]

The evolution of the latitudinal diversity gradient (LDG), characterized by a peak in diversity toward the tropics, has captured significant attention in evolutionary biology and ecology. However, the inverse LDG (i‐LDG) mechanism, wherein species richness increases toward the poles, remains inadequately explored. Cycads are among one of the oldest lineages of extant seed plants and have undergone extensive diversification in the tropics. Intriguingly, the extant cycad abundance exhibits an i‐LDG pattern, and the underlying causes for this phenomenon remain largely elusive. Here, using 1,843 nuclear genes from a nearly complete sampling, we conducted comprehensive phylogenomic analyses to establish a robust species‐level phylogeny for Cycas, the largest genus within cycads. We then reconstructed the spatial‐temporal dynamics and integrated global environmental data to evaluate the roles of species ages, diversification rates, contemporary environment, and conservatism to ancestral niches in shaping the i‐LDG pattern. We found Cycas experienced decreased diversification rates, coupled with the cooling temperature since its origin in the Eocene from continental Asia. Different regions have distinctively contributed to the formation of i‐LDG for Cycas, with the northern hemisphere acting as evolutionary museums and the southern hemisphere serving as cradles. Moreover, water‐related climate variables, specifically precipitation seasonality and potential evapotranspiration, were identified as paramount factors constraining Cycas species richness in the rainforest biome near the equator. Notably, the adherence to ancestral monsoonal climates emerges as a critical factor in sustaining the diversity pattern. This study underscores the imperative of integrating both evolutionary and ecological approaches to comprehensively unravel the mechanisms underpinning global biodiversity patterns. [ABSTRACT FROM AUTHOR]

Beta diversity patterns are essential for understanding how biological communities are structured. Geographical and environmental factors, as well as species dispersal ability, are important drivers of beta diversity, but their relative importance may vary across spatial scales. In this study, we evaluate whether beta diversity changes across geographical scales and analyse how different drivers affect turnover patterns of native seed plants in an oceanic archipelago, the Azores (Portugal). Using a 500 × 500 m resolution grid, we selected cells that are covered by one of the following habitats: native forest, naturalized vegetation and seminatural pastures. We calculated species turnover at three spatial scales: 1) between islands, 2) between cells within each island, and finally 3) between cells of each of the habitats of interest in each island. We then calculated the contribution of dispersal syndromes (endozoochory, epizoochory, hydrochory and anemochory) to turnover at each of the scales. Lastly, we assessed the relationship between geographical and climatic distances and habitat type with turnover. Turnover was higher at the smallest spatial scale, particularly in seminatural pastures, and decreased with increasing spatial scales, a pattern potentially associated with the historical fragmentation and current patchy distribution of native forest and seminatural habitats in the Azores. Dispersal syndromes and habitat type had a negligible effect on turnover at all scales. Geographical distance had a positive effect on turnover at all scales, increasing its importance with scale. The relationship between turnover and climatic distance was only significant at the intermediate and small scales in specific islands and habitats. Therefore, scale plays an important role at determining the effect of the drivers of turnover, in particular geographical and climatic distance. These results highlight the need to carefully select the scale of analysis when studying turnover patterns, as well as identifying the potential drivers associated with each spatial scale. [ABSTRACT FROM AUTHOR]

Caffeic acid transferase (COMT) is a key enzyme in the lignin and melatonin synthesis pathways and plays an important role in plant growth and development. All seed plants have two characteristics: they have vascular tissues, phloem, and xylem, and they can produce and reproduce seeds. In order to understand the distribution and evolution of COMTs in seed plants, we performed physicochemical property analysis, subcellular localization, phylogenetic analysis, conserved motif analysis, and protein interaction network analysis of 44 COMT homologs from 26 seed plants through in silico. The results showed that in seed plants, the structure of COMT genes tends to be stable in different plant taxa, while the relationship between the chromosomal positions of different COMT genes in the same plant was more intricate. The conserved distribution of COMT in seed plants reflected its highly specialized function. [ABSTRACT FROM AUTHOR]

The oxidative pentose-phosphate pathway (OPPP) retrieves NADPH from glucose-6-phosphate, which is important in chloroplasts at night and in plastids of heterotrophic tissues. We previously studied how OPPP enzymes may transiently locate to peroxisomes, but how this is achieved for the third enzyme remained unclear. By extending our genetic approach, we demonstrated that Arabidopsis isoform 6-phosphogluconate dehydrogenase 2 (PGD2) is indispensable in peroxisomes during fertilization, and investigated why all PGD–reporter fusions show a mostly cytosolic pattern. A previously published interaction of a plant PGD with thioredoxin m was confirmed using Trx m2 for yeast two-hybrid (Y2H) and bimolecular fluorescent complementation (BiFC) assays, and medial reporter fusions (with both ends accessible) proved to be beneficial for studying peroxisomal targeting of PGD2. Of special importance were phosphomimetic changes at Thr6, resulting in a clear targeting switch to peroxisomes, while a similar change at position Ser7 in PGD1 conferred plastid import. Apparently, efficient subcellular localization can be achieved by activating an unknown kinase, either early after or during translation. N-terminal phosphorylation of PGD2 interfered with dimerization in the cytosol, thus allowing accessibility of the C-terminal peroxisomal targeting signal (PTS1). Notably, we identified amino acid positions that are conserved among plant PGD homologues, with PTS1 motifs first appearing in ferns, suggesting a functional link to fertilization during the evolution of seed plants. [ABSTRACT FROM AUTHOR]

Premise of research. The fossil record shows that seed plants appeared during the Devonian and started to become dominant in the Mississippian. However, the identity of their closest relatives remains uncertain with three candidates: Stenokoleales, Archeopteridalean progymnosperms, and Aneurophytalean progymnosperms. To clarify the relationships of these groups, it is necessary to document as many Devonian-Mississippian taxa as possible and increase taxon sampling in phylogenetic analyses. In this context, Stauroxylon beckii Galtier 1970 from Mississippian deposits of France is particularly interesting because of its similarities with both seed plants and some of their potential closest relatives. Here, we provide an updated description of Stauroxylon and discuss its affinities using morphoanatomical comparisons and phylogenetic analyses. Methodology. The holotype of S. beckii and a new specimen from the same formation are described using thin sections, cellulose acetate peels, and polished surfaces. The morphoanatomy of the specimens is compared with that of early seed plants and their putative relatives. Stauroxylon is also included in phylogenetic analyses of the radiatopses based on Toledo and colleague's matrix. Pivotal results. Stauroxylon beckii possess a cruciform protostele with protoxylem strands at the tips of the ribs, a central protoxylem strand, and produces second- and third-order axes in perpendicular planes. The new specimen differs by characters interpreted as developmental differences or intraspecific plasticity (organotaxis, secondary growth) and is also assigned to S. beckii. Both comparative approaches and phylogenetic analyses place Stauroxylon within the Aneurophytalean progymnosperms, a group previously only known in the Devonian. The inclusion of Stauroxylon strengthens previously established relationships within the radiatopsids. Stauroxylon also displays structural fingerprints important for leaf and pith evolution. Conclusions. Stauroxylon is interpreted as a Mississippian representative of the Aneurophytales. It provides new information on the relationships and morphoanatomical diversity of early seed plants and their closest relatives. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are a class of nonprotein-coding short transcripts that provide a layer of post-transcriptional regulation essential to many plant biological processes. MiR858, which targets the transcripts of MYB transcription factors, can affect a range of secondary metabolic processes. Although miR858 and its 187-nt precursor have been well studied in Arabidopsis (Arabidopsis thaliana), a systematic investigation of miR858 precursors and their functions across plant species is lacking due to a problem in identifying the transcripts that generate this subclass. By re-evaluating the transcript of miR858 and relaxing the length cut-off for identifying hairpins, we found in kiwifruit (Actinidia chinensis) that miR858 has long-loop hairpins (1,100 to 2,100 nt), whose intervening sequences between miRNA generating complementary sites were longer than all previously reported miRNA hairpins. Importantly, these precursors of miR858 containing long-loop hairpins (termed MIR858L) are widespread in seed plants including Arabidopsis, varying between 350 and 5,500 nt. Moreover, we showed that MIR858L has a greater impact on proanthocyanidin and flavonol levels in both Arabidopsis and kiwifruit. We suggest that an active MIR858L-MYB regulatory module appeared in the transition of early land plants to large upright flowering plants, making a key contribution to plant secondary metabolism. Widespread long-loop precursors MIR858L efficiently generate miR858 to affect proanthocyanidin and flavonol metabolism, and the long-loop precursor MIR858L likely originated from the TT2-like MYB gene [ABSTRACT FROM AUTHOR]

Vertebrate‐mediated seed dispersal is a common attribute of many living plants, and variation in the size and abundance of fleshy diaspores is influenced by regional climate and by the nature of vertebrate seed dispersers among present‐day floras. However, potential drivers of large‐scale variation in the abundance and size distributions of fleshy diaspores through geological time, and the importance of geographic variation, are incompletely known. This knowledge gap is important because fleshy diaspores are a key mechanism of energy transfer from photosynthesis to animals and may in part explain the diversification of major groups within birds and mammals. Various hypotheses have been proposed to explain variation in the abundance and size distribution of fleshy diaspores through time, including plant–frugivore co‐evolution, angiosperm diversification, and changes in vegetational structure and climate. We present a new data set of more than 800 georeferenced fossil diaspore occurrences spanning the Triassic–Oligocene, across low to mid‐ to high palaeolatitudes. We use this to quantify patterns of long‐term change in fleshy diaspores, examining the timing and geographical context of important shifts as a test of the potential evolutionary and climatic explanations. We find that the fleshy fruit sizes of angiosperms increased for much of the Cretaceous, during the early diversification of angiosperms from herbaceous ancestors with small fruits. Nevertheless, this did not cause a substantial net change in the fleshy diaspore size distributions across seed plants, because gymnosperms had achieved a similar size distribution by at least the Late Triassic. Furthermore, gymnosperm‐dominated Mesozoic ecosystems were mostly open, and harboured low proportions of specialised frugivores until the latest Cretaceous, suggesting that changes in vegetation structure and plant–frugivore co‐evolution were probably not important drivers of fleshy diaspore size distributions over long timescales. Instead, fleshy diaspore size distributions may be largely constrained by physical or life‐history limits that are shared among groups and diversify as a plant group expands into different growth forms/sizes, habitats, and climate regimes. Mesozoic gymnosperm floras had a low abundance of fleshy diaspores (<50% fleshy diaspore taxa), that was surpassed by some low‐latitude angiosperm floras in the Cretaceous. Eocene angiosperm floras show a mid‐ to high latitude peak in fleshy fruit abundance, with very high proportions of fleshy fruits that even exceed those seen at low latitudes both in the Eocene and today. Mid‐ to high latitude proportions of fleshy fruits declined substantially over the Eocene–Oligocene transition, resulting in a shift to more modern‐like geographic distributions with the highest proportion of fleshy fruits occurring in low‐latitude tropical assemblages. This shift was coincident with global cooling and the onset of Southern Hemisphere glaciation, suggesting that rapid cooling at mid‐ and high latitudes caused a decrease in availability of the climate conditions most favourable for fleshy fruits in angiosperms. Future research could be focused on examining the environmental niches of modern fleshy fruits, and the potential effects of climate change on fleshy fruit and frugivore diversity. [ABSTRACT FROM AUTHOR]

Mini zinc fingers constitute a class of microproteins that appeared early in evolution and expanded in seeds plants. In this review, the phylogenetic history, the functions and the mode of action of Mini zinc fingers in plants are reported and discussed. It appears that mini zinc fingers play an important role in the control of plant development. They are involved in the control of cell division and expansion, in the switch between the determinate/indeterminate state of the meristems and in the regulation of vegetative growth and floral organ development. Their biochemical mode of action seems to be diverse. In some studies, it has been reported that mini zinc fingers can directly bind to DNA and activate target gene expression, whereas other studies have shown that they can interact with and inhibit the activity of specific zinc finger homeodomain transcription factors or act as adaptor proteins necessary to aggregate polymeric protein complexes corresponding to chromatin remodelling factors negatively regulating the expression of specific genes. The diversity of mode of action for mini zinc finger microproteins suggests a wider range of biological functions than what has been that described in the literature thus far, and their involvement in the response to biotic and abiotic stresses should be further investigated in future studies. • Mini zinc fingers are a class of microproteins particularly prevalent in seed plants. • Mini zinc fingers perform their function via protein‒protein and/or protein‒DNA interactions. • Mini zinc fingers are major regulators of vegetative and reproductive plant development. • Mini zinc finger function in the plant response to stresses should be further explored. [ABSTRACT FROM AUTHOR]

The gaseous hormone ethylene plays pivotal roles in plant growth and development. The rate-limiting enzyme of ethylene biosynthesis in seed plants is 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS). ACS proteins are encoded by a multigene family and the expression of ACS genes is highly regulated, especially at a post-translational level. AtACS7, the only type III ACS in Arabidopsis, is degraded in a 26S proteasome-dependent pathway. Here, by using liquid chromatography–mass spectrometry/mass spectrometry (LC-MS/MS) analysis, two lysine residues of AtACS7, lys285 (K285) and lys366 (K366), were revealed to be ubiquitin-modified in young, light-grown Arabidopsis seedlings but not in etiolated seedlings. Deubiquitylation-mimicking mutations of these residues significantly increased the stability of the AtACS7K285RK366R mutant protein in cell-free degradation assays. All results suggest that K285 and K366 are the major ubiquitination sites on AtACS7, providing deeper insights into the post-translational regulation of AtACS7 in Arabidopsis. [ABSTRACT FROM AUTHOR]

The phytohormone abscisic acid (ABA) is synthesised by plants during drought to close stomata and regulate desiccation tolerance pathways. Conifers and some angiosperms with embolism‐resistant xylem show a peaking‐type (p‐type) response in ABA levels, in which ABA levels increase early in drought then decrease as drought progresses, declining to pre‐stressed levels. The mechanism behind this dynamic remains unknown. Here, we sought to characterise the mechanism driving p‐type ABA dynamics in the conifer Callitris rhomboidea and the highly drought‐resistant angiosperm Umbellularia californica. We measured leaf water potentials (Ψl), stomatal conductance, ABA, conjugates and phaseic acid (PA) levels in potted plants during a prolonged but non‐fatal drought. Both species displayed a p‐type ABA dynamic during prolonged drought. In branches collected before and after the peak in endogenous ABA levels in planta, that were rehydrated overnight and then bench dried, ABA biosynthesis was deactivated beyond leaf turgor loss point. Considerable conversion of ABA to conjugates was found to occur during drought, but not catabolism to PA. The mechanism driving the decline in ABA levels in p‐type species may be conserved across embolism‐resistant seed plants and is mediated by sustained conjugation of ABA and the deactivation of ABA accumulation as Ψl becomes more negative than turgor loss. Summary Statement: We find that abscisic acid biosynthesis is deactivated after leaf turgor loss point during extreme drought, but that the conjugation of ABA to inactive forms remains constant, leading to a decline in ABA levels in embolism‐resistant species. [ABSTRACT FROM AUTHOR]

SUMMARY: DELAY OF GERMINATION 1 is a key regulator of dormancy in flowering plants before seed germination. Bryophytes develop haploid spores with an analogous function to seeds. Here, we investigate whether DOG1 function during germination is conserved between bryophytes and flowering plants and analyse the underlying mechanism of DOG1 action in the moss Physcomitrium patens. Phylogenetic and in silico expression analyses were performed to identify and characterise DOG1 domain‐containing genes in P. patens. Germination assays were performed to characterise a Ppdog1‐like1 mutant, and replacement with AtDOG1 was carried out. Yeast two‐hybrid assays were used to test the interaction of the PpDOG1‐like protein with DELLA proteins from P. patens and A. thaliana. P. patens possesses nine DOG1 domain‐containing genes. The DOG1‐like protein PpDOG1‐L1 (Pp3c3_9650) interacts with PpDELLAa and PpDELLAb and the A. thaliana DELLA protein AtRGA in yeast. Protein truncations revealed the DOG1 domain as necessary and sufficient for interaction with PpDELLA proteins. Spores of Ppdog1‐l1 mutant germinate faster than wild type, but replacement with AtDOG1 reverses this effect. Our data demonstrate a role for the PpDOG1‐LIKE1 protein in moss spore germination, possibly alongside PpDELLAs. This suggests a conserved DOG1 domain function in germination, albeit with differential adaptation of regulatory networks in seed and spore germination. Significance Statement: Seed and spore germination are considered analogous because they occur in the sporophyte (seed plants) and gametophyte (bryophytes). Here we show that an ortholog of Arabidopsis DELAY OF GERMINATION 1 (DOG1) controls spore germination in the moss P. patens, suggesting deep evolutionary conservation of germination control of reproductive diaspores. [ABSTRACT FROM AUTHOR]

SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode plant-specific transcription factors which are important regulators of diverse plant developmental processes. We took advantage of available genome sequences of streptophyte algae representatives to investigate the relationships of SPL genes between freshwater green algae and land plants. Our analysis showed that streptophyte algae, hornwort and liverwort genomes encode from one to four SPL genes which is the smallest set, in comparison to other land plants studied to date. Based on the phylogenetic analysis, four major SPL phylogenetic groups were distinguished with Group 3 and 4 being sister to Group 1 and 2. Comparative motif analysis revealed conserved protein motifs within each phylogenetic group and unique bryophyte-specific motifs within Group 1 which suggests lineage-specific protein speciation processes. Moreover, the gene structure analysis also indicated the specificity of each by identifying differences in exon–intron structures between the phylogenetic groups, suggesting their evolutionary divergence. Since current understanding of SPL genes mostly arises from seed plants, the presented comparative and phylogenetic analyzes from freshwater green algae and land plants provide new insights on the evolutionary trajectories of the SPL gene family in different classes of streptophytes. [ABSTRACT FROM AUTHOR]

The High Voltage Electrical Discharge (HVED) is a physical hydropriming method which alters the physicochemical properties of water, creating the plasma activated water (PAW). The mixture of highly reactive ions and molecules can break down the seed dormancy and speed up the growing process. Previous studies presented the promotional role of HVED technology on the germination, growth and polyphenol content. The aim of this study was to explore the effect of HVED technology on germination ability and vitality of three types of seeds with low germination rate. Selected species included carrot (Daucus carota L.), melilot (Melilotus albus Medik.), and mallow (Malva verticillata L.). In carrot and mallow, HVED (20Hz/30s) significantly promoted germination percentage, whilst in melilot seeds, germination was unchanged. HVED treatment enhanced the growth of shoots and roots in both carrot and mallow. In melilot, shorter treatment time of exposure to high voltage (30Hz/10s) resulted in longer shoots and roots. Perspectives of HVED as a method for improvement of germination exist, especially in mellow and carrot, but it is necessary to optimize the process parameters for each type of seed separately. [ABSTRACT FROM AUTHOR]

The plastids of algae and plants originated on a single occasion from an endosymbiotic cyanobacterium at least a billion years ago. Despite the divergent evolution that characterizes the plastids of different lineages, many traits such as membrane organization and means of fission are universal—they pay tribute to the cyanobacterial origin of the organelle. For one such trait, the peptidoglycan (PG) layer, the situation is more complicated. Our view on its distribution keeps on changing and little is known regarding its molecular relevance, especially for land plants. Here, we investigate the extent of PG presence across the Chloroplastida using a phylogenomic approach. Our data support the view of a PG layer being present in the last common ancestor of land plants and its remarkable conservation across bryophytes that are otherwise characterized by gene loss. In embryophytes, the occurrence of the PG layer biosynthetic toolkit becomes patchier and the availability of novel genome data questions previous predictions regarding a functional coevolution of the PG layer and the plastid division machinery-associated gene FtsZ3. Furthermore, our data confirm the presence of penicillin-binding protein (PBP) orthologs in seed plants, which were previously thought to be absent from this clade. The 5-7 nm thick, and seemingly unchanged, PG layer armoring the plastids of glaucophyte algae might still provide the original function of structural support, but the same can likely not be said about the only recently identified PG layer of bryophyte and tracheophyte plastids. There are several issues to be explored regarding the composition, exact function, and biosynthesis of the PG layer in land plants. These issues arise from the fact that land plants seemingly lack certain genes that are believed to be crucial for PG layer production, even though they probably synthesize a PG layer. [ABSTRACT FROM AUTHOR]

The discovery of this group of gymnosperms from the Palaeozoic era is one of the notable achievements of the palaeobotanist and it was of immense value to the palaeobotany & in phylogeny. It includes fernlike plants which were dominant in the Devonian period. They extend into the beginning of the Mesozoic era, later on, there was a mass extinction of the pteridospermales, due to the misconception, that they were initially considered ferns and fern-like plants. Williamson (1897) first considered these plants as an intermediate of the ferns and cycads due to the morphological and anatomical similarity of the organs. H. Potonie (1899) was the first to give their names as the Cycadofilicales. Oliver and Scott (1904) named this group as pteridospermales due to the similarity between the ferns and spermatophytes. In this review article features of the order pteridospermales and their phylogeny have been discussed. [ABSTRACT FROM AUTHOR]

Background: Mitochondrial genomes are essential for deciphering the unique evolutionary history of seed plants. However, the rules of their extreme variation in genomic size, multi-chromosomal structure, and foreign sequences remain unresolved in most plant lineages, which further hindered the application of mitogenomes in phylogenetic analyses. Results: Here, we took Dendrobium (Orchidaceae) which shows the great divergence of morphology and difficulty in species taxonomy as the study focus. We first de novo assembled two complete mitogenomes of Dendrobium wilsonii and Dendrobium henanense that were 763,005 bp and 807,551 bp long with multichromosomal structures. To understand the evolution of Dendrobium mitogenomes, we compared them with those of four other orchid species. The results showed great variations of repetitive and chloroplast-derived sequences in Dendrobium mitogenomes. Moreover, the intergenic content of Dendrobium mitogenomes has undergone expansion during evolution. We also newly sequenced mitogenomes of 26 Dendrobium species and reconstructed phylogenetic relationships of Dendrobium based on genomic mitochondrial and plastid data. The results indicated that the existence of chloroplast-derived sequences made the mitochondrial phylogeny display partial characteristics of the plastid phylogeny. Additionally, the mitochondrial phylogeny provided new insights into the phylogenetic relationships of Dendrobium species. Conclusions: Our study revealed the evolution of Dendrobium mitogenomes and the potential of mitogenomes in deciphering phylogenetic relationships at low taxonomic levels. [ABSTRACT FROM AUTHOR]

The article discusses the antagonistic relationship between the plant hormones auxin and cytokinin in the development of shoots. The study focuses on the moss Physcomitrium patens and highlights the evolutionary preservation of this hormone interaction in controlling shoot growth. The article also explores the involvement of auxin and cytokinin in various developmental processes in vascular plants, such as apical dominance and growth activation. The authors emphasize the need to further investigate the mechanisms by which cytokinin removes the inhibitory effect of auxin. The article provides insights into the signaling pathways and transcriptional regulators involved in the antagonism between auxin and cytokinin. Overall, the article contributes to our understanding of the complex hormonal regulation of plant growth and development. [Extracted from the article]

Introduction: The dramatic fluctuations of climate conditions since the late Tertiary era have resulted in major species range shifts. These movements were conditioned by geographic barriers and species dispersal capacities. In land plants, gene flow occurs through the movement of male gametes (sperm cells, pollen grains), which carry nDNA, and diaspores (spores, seeds), which carry both cpDNA and nDNA, making them an ideal model to compare the imprints of past climate change on the spatial genetic structures of different genomic compartments. Based on a meta-analysis of cpDNA and nDNA sequence data in western Europe, we test the hypotheses that nDNA genetic structures are similar in bryophytes and spermatophytes due to the similar size of spores and pollen grains, whereas genetic structures derived from the analysis of cpDNA are significantly stronger in spermatophytes than in bryophytes due to the substantially larger size of seeds as compared to spores. Methods: Sequence data at 1-4 loci were retrieved for 11 bryophyte and 17 spermatophyte species across their entire European range. Genetic structures between and within southern and northern populations were analyzed through F and N statistics and Mantel tests. Results and discussion: Gst and Nst between southern and northern Europe derived from cpDNA were significantly higher, and the proportion of significant tests was higher in spermatophytes than in bryophytes. This suggests that in the latter, migrations across mountain ranges were sufficient to maintain a homogenous allelic structure across Europe, evidencing the minor role played by mountain ranges in bryophyte migrations. With nDNA, patterns of genetic structure did not significantly differ between bryophytes and spermatophytes, in line with the hypothesis that spores and pollen grains exhibit similar dispersal capacities due to their size similarity. Stronger levels of genetic differentiation between southern and northern Europe, and within southern Europe, in spermatophytes than in bryophytes, caused by higher long-distance dispersal capacities of spores as compared to seeds, may account for the strikingly higher levels of endemism in spermatophytes than in bryophytes in the Mediterranean biodiversity hotspot. [ABSTRACT FROM AUTHOR]

Aim: In Taiwan island, recent land‐bridge and oversea dispersal after the appearance of proto‐Taiwan (<6.5 Ma) is responsible for its biodiversity assembly. Radiations have also been widely reported in mountain systems. The tempo‐spatial route to the floral hotspot was determined through a meta‐analysis of the evolution of endemic plants. Location: Taiwan island and its adjacent regions. Taxon: Seed plants. Methods: Published dated phylogenies were compiled to infer the origin times represented by the stem ages. To determine the speciation mode, either in situ origin or dispersal origin, the ancestral range shift pattern and/or current distribution range of the sister taxa were used with 10 different biogeographical regions classified. Histograms quantifying the numbers of different origin modes within bins of 0.5 Ma were constructed. Probabilities of long‐distance dispersal (LDD) were evaluated. Results: The 125 sampled species originate between the late Eocene and late Pleistocene, of which 14 (11.2%) and 111 (88.8%) were derived before and after the emergence of proto‐Taiwan, respectively. Spatially, in situ speciation would have a bigger contribution to the formation of endemism than dispersal events (56.8% vs. 43.2%). The species with in situ origin (mean = 1.83 Ma) were significantly younger than those with dispersal origin (mean = 6.34 Ma). The main regions where dispersal occurred were South‐Central China (n = 29) and Southeast China (n = 28), followed by Japan (n = 14). High probabilities (60.8%) of LDD were found. Main Conclusions: Spatially, recent land‐bridge and oversea dispersal from the adjacent Asian flora is supported and the southern part of China was found to be the most important source. In situ speciation that may have correlated with mountain uplift, monsoon intensification and Pleistocene climatic fluctuations exerted greater contributions to the biodiversity there. Temporally, floral endemism predominantly occurred after the emergence of proto‐Taiwan. Additional investigations with more sophisticated sampling and genetic data are needed in the future. [ABSTRACT FROM AUTHOR]

The Midlands region of KwaZulu-Natal (KZN) Province in South Africa was hitherto a putative centre of floristic endemism (CFE) based on conjecture. The aim of this study was to empirically explore this concept by delineating unambiguous boundaries for this CFE and documenting the endemic spermatophytes within a conservation framework. The Greater Midlands Centre of Floristic Endemism (GMCFE), a more expanded study area than the parochial Midlands region of KZN, is formally described as southern Africa's 20th CFE. It is a mid-elevation region occupying the greater Midlands of KZN, with extensions of contiguous grasslands extending northwards into southern Mpumalanga and southwards into north-eastern Eastern Cape. This "foothills" CFE covers ca. 77,000 km2 of predominantly mesic C4 grassland, ranging in elevation from ca. 700–2200 m a.s.l. It is congruent with the "sub-escarpment ecoregion," essentially a composite of the Sub-escarpment Grassland and Savanna Bioregions and the sub-escarpment grasslands of southern Mpumalanga and northern KZN. The GMCFE hosts at least 220 endemic spermatophytes, of which almost a fifth belong to the family Apocynaceae. Families Asteraceae, Asphodelaceae, Fabaceae, and Iridaceae also contribute significantly. Genera Ceropegia, Aloe, Dierama, Kniphofia, Helichrysum, and Streptocarpus contribute the most endemics. More than half are forbs, and almost three-quarters are confined to the Grassland Biome. Endemic radiations are attributed to geodiversity and geological complexity (especially the strong lithological influence of dolerite); physiographic heterogeneity (particularly elevation gradients and variable terrain units); strategic proximity to hyper-diverse temperate and subtropical "border floras"; and localized pollinator-driven adaptive radiations. Of alarming concern is the high number of threatened plant taxa, with ca. 60% of the endemic flora Red Listed in threat categories (CE, E, and VU) or considered "rare". Extremely low levels of formal protection and poor ecological connectivity, coupled with high levels of land transformation and intensive utilization, render the GMCFE one of the most imperilled CFE in South Africa. Urgent conservation action is required to safeguard this unique and highly threatened "rangeland flora" and stem the biodiversity crisis gripping the region. [ABSTRACT FROM AUTHOR]

Background and Aims The tribe Paullinieae has the highest diversity of vascular variants among the seed plants. The developmental diversity is better understood in the species-rich genera Paullinia and Serjania ; however, the phylogeny and diversity of vascular variants in the smaller genera of Paullinieae remain understudied. Here we investigate the evolution of development of stem vasculatures in the small genus Urvillea. Methods We generate the first molecular phylogeny of Urvillea derived from 11 markers using a maximum likelihood and Bayesian approach. In combination with phylogenetic reconstruction, stochastic character mapping is used to assess evolutionary changes in stem ontogenies, determined from developmental anatomy of stems collected in the field or from herbarium and wood collections. Key Results Urvillea is supported as a monophyletic group and sister to Serjania. There are five stem ontogenies in Urvillea , including typical growth and four different vascular variants. Most stem ontogenies initiate with lobed stems in primary growth. Lobed stems in secondary growth are ancestral in Urvillea , but this ontogeny was lost multiple times. A reversal to typical growth occurred in non-climbing species. Phloem wedges, fissured stems, and ectopic cambia each evolved once independently. Phloem wedges is an intermediate developmental stage in the formation of fissured stems, which is characterized by a continuous fragmentation of vascular tissues. Lobed stems may generate constriction zones and lobes may split or not. Conclusions Urvillea is the third most diverse genus (after Serjania and Paullinia) with respect to the number of vascular variants within Paullinieae. One ontogeny (fissured stems) is exclusive to the genus. Differential cambial activity and ectopic cambia are the main ontogenetic processes generating stem diversity. The evolutionary history of vascular variants demonstrates the large developmental plasticity of the cambium in such a small genus and further demonstrates that complex anatomies have repeatedly evolved within Paullinieae lianas. [ABSTRACT FROM AUTHOR]

Summary: Seed germination is a vital developmental transition for the production of progeny by sexual reproduction in spermatophytes. The seed‐to‐seedling transition is predominately driven by hypocotyl cell elongation. However, the mechanism that underlies hypocotyl growth remains largely unknown.In this study, we characterized the actin array reorganization in embryonic hypocotyl epidermal cells. Live‐cell imaging revealed a basally organized actin array formed during hypocotyl cell elongation. This polarized actin assembly is a barrel‐shaped network, which comprises a backbone of longitudinally aligned actin cables and a fine actin cap linking these cables.We provide genetic evidence that the basal actin array formation requires formin‐mediated actin polymerization and directional movement of actin filaments powered by myosin XIs. In fh1‐1 and xi3ko mutants, actin filaments failed to reorganize into the basal actin array, and the hypocotyl cell elongation was inhibited compared with wild‐type plants.Collectively, our work uncovers the molecular mechanisms for basal actin array assembly and demonstrates the connection between actin polarization and hypocotyl elongation during seed‐to‐seedling transition. [ABSTRACT FROM AUTHOR]

SUMMARY: The non‐seed plants (e.g., charophyte algae, bryophytes, and ferns) have multiple human uses, but their contributions to agriculture and research have lagged behind seed plants. While sharing broadly conserved biology with seed plants and the major crops, non‐seed plants sometimes possess alternative molecular and physiological adaptations. These adaptations may guide crop improvements. One such area is the presence of multiple classes of insecticidal proteins found in non‐seed plant genomes which are either absent or widely diverged in seed plants. There are documented uses of non‐seed plants, and ferns for example have been used in human diets. Among the occasional identifiable toxins or antinutritive components present in non‐seed plants, none include these insecticidal proteins. Apart from these discrete risk factors which can be addressed in the safety assessment, there should be no general safety concern about sourcing genes from non‐seed plant species. Significance Statement: Lower plants such as ferns and mosses are underexplored resources for agriculture. Recent investigations have revealed that lower plants contain genes for insecticidal proteins that are now being leveraged for transgenic crop improvement. [ABSTRACT FROM AUTHOR]

Summary: Heterogeneity in gene trees, morphological characters, and composition has been associated with several major plant clades. Here, we examine heterogeneity in composition across a large transcriptomic dataset of plants to better understand whether locations of shifts in composition are shared across gene regions and whether directions of shifts within clades are shared across gene regions.We estimate mixed models of composition for both nucleotide and amino acids across a recent large‐scale transcriptomic dataset for plants.We find shifts in composition across both nucleotide and amino acid datasets, with more shifts detected in nucleotides. We find that Chlorophytes and lineages within experience the most shifts. However, many shifts occur at the origins of land, vascular, and seed plants. While genes in these clades do not typically share the same composition, they tend to shift in the same direction. We discuss potential causes of these patterns.Compositional heterogeneity has been highlighted as a potential problem for phylogenetic analysis, but the variation presented here highlights the need to further investigate these patterns for the signal of biological processes. [ABSTRACT FROM AUTHOR]

The study of reproductive mechanisms is of particular interest for a real understanding of seed plant evolution. Spermatophytes comprise angiosperms and four orders of gymnosperms (Cycadales, Ginkgoales, Coniferales, and Gnetales) whose main characteristic is the reproduction via seeds. Ginkgo and cycads form a sister clade to the other gymnosperms and occupy a key phylogenetic position in-between the extinct Paleozoic seed ferns and the other extant gymnosperms. This review focuses on the similarities and differences between the reproductive mechanisms of Ginkgo and Cycas, from the morphogenesis of the male and female organs to the pollination and fertilization events. Together with the morphological and cytological description, the latest available molecular data on the reproductive organ development of the two plant genera are discussed. This will, hopefully, pave the path for new studies aiming at filling the gaps in our understanding of the hormonal and genetic regulation of their reproductive mechanisms. The whole reproductive process is presented in detail, providing a comprehensive and organic picture together with complete illustrations and photographic material. Each phase of the reproductive process is dissected, pointing out the main similarities and differences found among the two genera. The comparison comprises the male and female reproductive organs development, with a focus on pollen ontogeny, shape, ultrastructure, and germination as well as ovule development and patterning, female gametophyte formation, and ovule integument differentiation. Particular attention is given to the pollination and fertilization events focusing on the role of reproductive fluids as well as zoogamy. [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]

Floristic regions, conventionally established using species distribution patterns, have often overlooked the phylogenetic relationships among taxa. However, how phylogenetic relationships influence the historical interconnections within and among biogeographic regions remains inadequately understood. In this research, we compiled distribution data for seed plants in Gansu, a region of significant biogeographic diversity located in northwestern China.We proposed a novel framework for floristic regions within Gansu, integrating distribution data and phylogenetic relationships of genera-level native seed plants, aiming to explore the relationship between phylogenetic relatedness, taxonomic composition, and regional phylogenetic delineation. We found that (1) phylogenetic relatedness was strongly correlated with the taxonomic composition among floras in Gansu. (2) The southeastern Gansu region showed the lowest level of spatial turnover in both phylogenetic relationships and the taxonomic composition of floristic assemblages across the Gansu region. (3) Null model analyses indicated nonrandom phylogenetic structure across the region, where most areas showed higher phylogenetic turnover than expected given the underlying taxonomic composition between sites. (4) Our results demonstrated a consistent pattern across various regionalization schemes and highlighted the preference for employing the phylogenetic dissimilarity approach in biogeographical regionalization investigations. (5) Employing the phylogenetic dissimilarity approach, we identified nine distinct floristic regions in Gansu that are categorized into two broader geographical units, namely the northwest and southeast. (6) Based on the phylogenetic graphic regions of China across this area. [ABSTRACT FROM AUTHOR]

Summary: Phytochromes are photoreceptors enabling plants to respond to various light conditions. Independent gene duplications resulted in small phytochrome families in mosses, ferns and seed plants. This phytochrome diversity is hypothesised to be critical for sensing and adapting to different light conditions, but experimental evidence for this idea is lacking for mosses and ferns.The moss model species Physcomitrium patens contains seven phytochromes grouped into three clades, PHY1/3, PHY2/4 and PHY5. Here, we used CRISPR/Cas9‐generated single and higher order mutants to investigate their role in light regulation of protonema and gametophore growth, protonema branching and induction of gametophores.We found both specific and partially overlapping roles for the three phytochrome clades in regulating these responses in different light conditions. PHY1/3 clade phytochromes act as primary far‐red light receptors, while PHY5 clade phytochromes are the primary red light receptors. PHY2/4 clade phytochromes have functions in both red and far‐red light. We also observed that PHY1/3 and PHY2/4 clade phytochromes promote gametophore growth in simulated canopy shade and also play a role in blue light.Similar to seed plants, gene duplications in the phytochrome lineage in mosses were followed by functional diversification into red and far‐red light‐sensing phytochromes. [ABSTRACT FROM AUTHOR]

Genome and transcriptome assembly data often contain DNA and RNA contaminations from external organisms, introduced during nucleotide extraction or sequencing. In this study, contamination of seed plant (Spermatophyta) transcriptomes/genomes with p25alpha domain encoding RNA/DNA was systematically investigated. This domain only occurs in organisms possessing a eukaryotic flagellum (cilium), which seed plants usually do not have. Nucleotide sequences available at the National Center for Biotechnology Information website, including transcriptome shotgun assemblies (TSAs), whole-genome shotgun contigs (WGSs), and expressed sequence tags (ESTs), were searched for sequences containing a p25alpha domain in Spermatophyta. Despite the lack of proteins containing the p25alpha domain, such fragments or complete mRNAs in some EST and TSA databases were found. A phylogenetic analysis showed that these were contaminations whose possible sources were microorganisms (flagellated fungi, protists) and arthropods/worms; however, there were cases where it cannot be excluded that the sequences found were genuine hits and not of external origin. [ABSTRACT FROM AUTHOR]

Although plastid genome (plastome) structure is highly conserved across most seed plants, investigations during the past two decades have revealed several disparately related lineages that experienced substantial rearrangements. Most plastomes contain a large inverted repeat and two single‐copy regions, and a few dispersed repeats; however, the plastomes of some taxa harbour long repeat sequences (>300 bp). These long repeats make it challenging to assemble complete plastomes using short‐read data, leading to misassemblies and consensus sequences with spurious rearrangements. Single‐molecule, long‐read sequencing has the potential to overcome these challenges, yet there is no consensus on the most effective method for accurately assembling plastomes using long‐read data. We generated a pipeline, plastid Genome Assembly Using Long‐read data (ptGAUL), to address the problem of plastome assembly using long‐read data from Oxford Nanopore Technologies (ONT) or Pacific Biosciences platforms. We demonstrated the efficacy of the ptGAUL pipeline using 16 published long‐read data sets. We showed that ptGAUL quickly produces accurate and unbiased assemblies using only ~50× coverage of plastome data. Additionally, we deployed ptGAUL to assemble four new Juncus (Juncaceae) plastomes using ONT long reads. Our results revealed many long repeats and rearrangements in Juncus plastomes compared with basal lineages of Poales. The ptGAUL pipeline is available on GitHub: https://github.com/Bean061/ptgaul. [ABSTRACT FROM AUTHOR]

Anemochory (wind dispersal) represents a key dispersal strategy that has allowed seed plants (spermatophytes) to expand habitats. To facilitate anemochory, the spermatophytes use diverse wind dispersal mechanisms, including wings or plumes of the ovule or seed 1,2. Seed wings are integument outgrowths of an ovule, while seed plumes refer to a bundle of filaments. These two wind dispersal mechanisms are independently employed by many seed plants 1,2 , but are very rarely combined in a single taxon. Seed wings originated in the Late Devonian (Famennian) 3,4,5 while seed plumes first appeared in the Early Carboniferous (Mississippian) 6,7. An opening, or micropyle, in the integument characterizes the ovules of seed plants 7. This essential structure had not appeared until the Carboniferous, and it evolved through the gradual fusion of integumentary lobes 7,8. Famennian ovules demonstrate great diversity in integumentary lobes. Nevertheless, notably few of these earliest ovules exhibit wings or wing-like integumentary lobes and none possess plumes or micropyles. Here, we document a Famennian ovule Gnetopsis quadria sp. nov. from Anhui Province, China. It combines wing-like lobes and plumes as two dispersal mechanisms, and probably has a micropyle. Wang et al. describe a fossil specimen of Gnetopsis quadria with wing-like lobes and plumes as integumentary outgrowths. [ABSTRACT FROM AUTHOR]

Assessing the distribution of geographically restricted and evolutionarily unique species and their underlying drivers is key to understanding biogeographical processes and critical for global conservation prioritization. Here, we quantified the geographic distribution and drivers of phylogenetic endemism for ~320,000 seed plants worldwide and identified centers and drivers of evolutionarily young (neoendemism) and evolutionarily old endemism (paleoendemism). Tropical and subtropical islands as well as tropical mountain regions displayed the world’s highest phylogenetic endemism. Most tropical rainforest regions emerged as centers of paleoendemism, while most Mediterranean-climate regions showed high neoendemism. Centers where high neo-and paleoendemism coincide emerged on some oceanic and continental fragment islands, in Mediterranean-climate regions and parts of the Irano-Turanian floristic region. Global variation in phylogenetic endemism was well explained by a combination of past and present environmental factors (79.8 to 87.7% of variance explained) and most strongly related to environmental heterogeneity. Also, warm and wet climates, geographic isolation, and long-term climatic stability emerged as key drivers of phylogenetic endemism. Neo-and paleoendemism were jointly explained by climatic and geological history. Long-term climatic stability promoted the persistence of paleoendemics, while the isolation of oceanic islands and their unique geological histories promoted neoendemism. Mountainous regions promoted both neo-and paleoendemism, reflecting both diversification and persistence over time. Our study provides insights into the evolutionary underpinnings of biogeographical patterns in seed plants and identifies the areas on Earth with the highest evolutionary and biogeographical uniqueness—key information for setting global conservation priorities. [ABSTRACT FROM AUTHOR]

Background: Mitogenome sizes of seed plants vary substantially even among closely related species, which are often related to horizontal or intracellular DNA transfer (HDT or IDT) events. However, the mechanisms of this size variation have not been well characterized. Results: Here we assembled and characterized the mitogenomes of three species of Melastoma, a tropical shrub genus experiencing rapid speciation. The mitogenomes of M. candidum (Mc), M. sanguineum (Ms) and M. dodecandrum (Md) were assembled to a circular mapping chromosome of 391,595 bp, 395,542 bp and 412,026 bp, respectively. While the mitogenomes of Mc and Ms showed good collinearity except for a large inversion of ~ 150 kb, there were many rearrangements in the mitogenomes between Md and either Mc or Ms. Most non-alignable sequences (> 80%) between Mc and Ms are from gain or loss of mitochondrial sequences. Whereas, between Md and either Mc or Ms, non-alignable sequences in Md are mainly chloroplast derived sequences (> 30%) and from putative horizontal DNA transfers (> 30%), and those in both Mc and Ms are from gain or loss of mitochondrial sequences (> 80%). We also identified a recurrent IDT event in another congeneric species, M. penicillatum, which has not been fixed as it is only found in one of the three examined populations. Conclusions: By characterizing mitochondrial genome sequences of Melastoma, our study not only helps understand mitogenome size evolution in closely related species, but also cautions different evolutionary histories of mitochondrial regions due to potential recurrent IDT events in some populations or species. [ABSTRACT FROM AUTHOR]

Aim: Significant changes in species elevational ranges in mountains have been repeatedly documented, yet the direction, magnitude and drivers of these shifts remain controversial. Presently, there is still lacking evidence about the general nature of species elevational range shifts in eastern Eurasia in response to anthropogenic climate change. By using historical specimen records and recent field observations for 735 seed plant species across 29 China's mountains, we assessed changes in species' elevational centroids and their drivers. Location: China. Time Period: 1950–2018. Major Taxa Studied: Seed plant species. Methods: The elevation records of all sampled occurrences in each mountain during the two time periods were estimated, and the null models were developed to test the sampling bias. Ecological niche models (ENMs) were used to evaluate the relative importance of climate factors in constraining each species distribution. Generalized linear models (GLMs) to test the relationships between the centroid elevational range shifts of species and different divers. Results: We found that 54% of the species shifting upward and 46% downhill. However, species' elevational shifts significantly differed among species and mountains. Herbaceous and lowland species moved upward faster than woody and high‐elevation species. Species in temperate mountains and in mountains with taller elevational gradients moved upward, while species in subtropical mountains and in mountains with shorter elevational gradients moved downward. Precipitation changes experienced by species, species' climatic adaptations, several species' functional traits and mountain size all contributed to explain the magnitude of species' centroid elevational range shifts. Main Conclusions: Our results highlight complex biodiversity redistribution of seed plants across Chinese mountains, not necessarily conforming to the trend of species upward shifts in elevation. Changes in precipitation regimes may blur the simplistic assumption of isotherm tracking. This study fills an important geographic shortfall for our understanding of biodiversity redistribution under anthropogenic climate change. [ABSTRACT FROM AUTHOR]