Transgenic and gene-editing technologies are essential for gene functional analysis and crop improvement. However, the pleiotropic effects and unknown mechanisms of morphogenic genes have hindered their broader application. In this study, we employed the one-step de novo shoot organogenesis (DNSO) method, and demonstrated that overexpression of the morphogenic gene Arabidopsis thanalia GROWTH-REGULATING FACTOR 5 (AtGRF5) significantly enhanced genetic transformation efficiency in cucurbit crops by promoting callus proliferation and increasing dense cells during regeneration. High-resolution time-series transcriptomics and single-cell RNA sequencing revealed that AtGRF5 overexpression induced auxin-related genes and expanded stem cell populations during cucumber DNSO. Using DNA-affinity purification sequencing (DAP-seq) in combination with spatiotemporal differential gene expression analysis, we identified CsIAA19 as a key downstream target of AtGRF5, with its modulation playing a pivotal role in regeneration. Rescuing CsIAA19 in AtGRF5-overexpressing explant reversed the enhanced callus proliferation and regeneration. To address growth defects caused by AtGRF5 overexpression, we developed an abscisic acid-inducible AtGRF5 expression system, significantly improving transformation and gene-editing efficiency across diverse genotypes while minimizing pleiotropic effects. In summary, this research provides mechanistic insights into AtGRF5-mediated transformation and offers a practical solution to overcome challenges in cucurbit crop genetic modification.

MYB transcription factors (TFs), one of the largest TF families in plants, are involved in various plant-specific processes as the central regulators, such as in phenylpropanoid metabolism, cell cycle, formation of root hair and trichome, phytohormones responses, reproductive growth and abiotic or biotic stress responses. Here we summarized multiple roles and explained the molecular mechanisms of MYB TFs in plant development and stress adaptation. The exploration of MYB TFs contributes to a better comprehension of molecular regulation in plant development and environmental adaptability.

The modern cultivated tomato (Solanum lycopersicum) was domesticated from Solanum pimpinellifolium native to the Andes Mountains of South America through a “two-step domestication” process. It was introduced to Europe in the 16th century and later widely cultivated worldwide. Since the late 19th century, breeders, guided by modern genetics, breeding science, and statistical theory, have improved tomatoes into an important fruit and vegetable crop that serves both fresh consumption and processing needs, satisfying diverse consumer demands. Over the past three decades, advancements in modern crop molecular breeding technologies, represented by molecular marker technology, genome sequencing, and genome editing, have significantly transformed tomato breeding paradigms. This article reviews the research progress in the field of tomato molecular breeding, encompassing genome sequencing of germplasm resources, the identification of functional genes for agronomic traits, and the development of key molecular breeding technologies. Based on these advancements, we also discuss the major challenges and perspectives in this field.

Synthetic microbial communities (SynComs) are a promising tool for making full use of the beneficial functions imparted by whole bacterial consortia. However, the complexity of reconstructed SynComs often limits their application in sustainable agriculture. Furthermore, inter-strain interactions are often neglected during SynCom construction. Here, we propose a strategy for constructing a simplified and functional SynCom (sfSynCom) by using elite helper strains that significantly improve the beneficial functions of the core symbiotic strain, here Bradyrhizobium elkanii BXYD3, to sustain the growth of soybean (Glycine max). We first identified helper strains that significantly promote nodulation and nitrogen fixation in soybean mediated by BXYD3. Two of these helper strains assigned to the Pantoea taxon produce acyl homoserine lactones, which significantly enhanced the colonization and infection of soybean by BXYD3. Finally, we constructed a sfSynCom from these core and helper strains. This sfSynCom based on the core-helper strategy was more effective at promoting nodulation than inoculation with BXYD3 alone and achieved effects comparable to those of a complex elite SynCom previously constructed on the basis of potential beneficial functions between microbes and plants alone. Our results suggest that considering interactions between strains as well as those between strains and the host plant might allow construction of sfSynComs.

Land plants use diverse hormones to coordinate their growth, development and responses against biotic and abiotic stresses. Salicylic acid (SA) is an essential hormone in plant immunity, with its levels and signaling tightly regulated to ensure a balanced immune output. Over the past three decades, molecular genetic analyses performed primarily in Arabidopsis have elucidated the biosynthesis and signal transduction pathways of key plant hormones, including abscisic acid, jasmonic acid, ethylene, auxin, cytokinin, brassinosteroids, and gibberellin. Crosstalk between different hormones has become a major focus in plant biology with the goal of obtaining a full picture of the plant hormone signaling network. This review highlights the roles of SA in plant immunity and summarizes our current understanding of the pairwise interactions of SA with other major plant hormones. The complexity of these interactions is discussed, with the hope of stimulating research to address existing knowledge gaps in hormone crosstalk, particularly in the context of balancing plant growth and defense.

The past decade has witnessed rapid developments in gene discovery, biological big data (BBD), artificial intelligence (AI)-aided technologies, and molecular breeding. These advancements are expected to accelerate crop breeding under the pressure of increasing demands for food. Here, we first summarize current breeding methods and discuss the need for new ways to support breeding efforts. Then, we review how to combine BBD and AI technologies for genetic dissection, exploring functional genes, predicting regulatory elements and functional domains, and phenotypic prediction. Finally, we propose the concept of intelligent precision design breeding (IPDB) driven by AI technology and offer ideas about how to implement IPDB. We hope that IPDB will enhance the predictability, efficiency, and cost of crop breeding compared with current technologies. As an example of IPDB, we explore the possibilities offered by CropGPT, which combines biological techniques, bioinformatics, and breeding art from breeders, and presents an open, shareable, and cooperative breeding system. IPDB provides integrated services and communication platforms for biologists, bioinformatics experts, germplasm resource specialists, breeders, dealers, and farmers, and should be well suited for future breeding.

Saline–alkaline soils are a major environmental problem that limit plant growth and crop productivity. Plasma membrane H⁺-ATPases and the salt overly sensitive (SOS) signaling pathway play important roles in plant responses to saline–alkali stress. However, little is known about the functional genes and mechanisms regulating the transcription of H⁺-ATPases and SOS pathway genes under saline–alkali stress. In the present study, we identified that the plant AT-rich sequence and zinc-binding (TaPLATZ2) transcription factor are involved in wheat response to saline–alkali stress by directly suppressing the expression of TaHA2/TaSOS3. The knockdown of TaPLATZ2 enhances salt and alkali stress tolerance, while overexpression of TaPLATZ2 leads to salt and alkali stress sensitivity in wheat. In addition, TaWRKY55 directly upregulated the expression of TaPLATZ2 during saline–alkali stress. Through knockdown and overexpression of TaWRKY55 in wheat, TaWRKY55 was shown to negatively modulate salt and alkali stress tolerance. Genetic analyses confirmed that TaPLATZ2 functions downstream of TaWRKY55 in response to salt and alkaline stresses. These findings provide a TaWRKY55–TaPLATZ2–TaHA2/TaSOS3 regulatory module that regulates wheat responses to saline–alkali stress.

Reactive oxygen species (ROS) plays critical roles in modulating plant growth and stress response and its homeostasis is fine tuned using multiple peroxidases. H₂O₂, a major kind of ROS, is removed rapidly and directly using three catalases, CAT1, CAT2, and CAT3, in Arabidopsis. Although the activity regulations of catalases have been well studied, their degradation pathway is less clear. Here, we report that CAT2 and CAT3 protein abundance was partially controlled using the 26S proteasome. To further identify candidate proteins that modulate the stability of CAT2, we performed yeast-two-hybrid screening and recovered several clones encoding a protein with RING and vWA domains, CIRP1 (CAT2 Interacting RING Protein 1). Drought and oxidative stress downregulated CIRP1 transcripts. CIRP1 harbored E3 ubiquitination activity and accelerated the degradation of CAT2 and CAT3 by direct interaction and ubiquitination. The cirp1 mutants exhibited stronger drought and oxidative stress tolerance, which was opposite to the cat2 and cat3 mutants. Genetic analysis revealed that CIRP1 acts upstream of CAT2 and CAT3 to negatively regulate drought and oxidative stress tolerance. The increased drought and oxidative stress tolerance of the cirp1 mutants was due to enhanced catalase (CAT) activities and alleviated ROS levels. Our data revealed that the CIRP1–CAT2/CAT3 module plays a vital role in alleviating ROS levels and balancing growth and stress responses in Arabidopsis.

The phytohormone jasmonates (JAs) regulate plant growth and defense responses. The reproductive organs of flowers are devastated by insect herbivores. However, the molecular mechanisms of floral defense remain largely unknown. Here, we found that the Arabidopsis JA receptor CORONATINE INSENSITIVE1 (COI1) and its substrates JA ZIM-domain (JAZ) repressors, and the mediator subunit MEDIATOR25-based MED25–MYC–MYB (MMM) complexes, including MYC2/3/4/5 and MYB28/29/76, mediated floral defense against the insects Helicoverpa armigera, Spodoptera exigua, and Spodoptera frugiperda. The flower-specific IIIa bHLH factors ABORTED MICROSPORES (AMS) and DYSFUNCTIONAL TAPETUM 1 (DYT1) were JAZ-interaction proteins. They interacted with members of the MMM complexes, inhibited the transcriptional activity of MYC2 and MYB28, and repressed floral defense against insects. AMS and DYT1 recruited the flower-specific MYB21/24, and these MYBs interacted with members of MMM complexes, inhibited the MYC2–MYB28 function, and suppressed floral defense against insects. Our study revealed that the JA–COI1–JAZ–MMM pathway mediated flower defense, and the AMS/DYT1–MYB21/24 module antagonized the MMM complexes to repress floral defense against insects.

Lodging reduces grain yield and quality in cereal crops. Lodging resistance is affected by the strength of the culm, which is influenced by the culm diameter, culm wall thickness, and cell wall composition. To explore the genetic architecture of culm diameter in rice (Oryza sativa), we conducted a genome-wide association study (GWAS). We identified STRONG CULM 2 (STRONG2), which encodes the mannan synthase CSLA5, and showed that plants that overexpressed this gene had increased culm diameter and improved lodging resistance. STRONG2 appears to increase the levels of cell wall components, such as mannose and cellulose, thereby enhancing sclerenchyma development in stems. SNP14931253 in the STRONG2 promoter contributes to variation in STRONG2 expression in natural germplasms and the transcription factor MYB61 directly activates STRONG2 expression. Furthermore, STRONG2 overexpressing plants produced significantly more grains per panicle and heavier grains than the wild-type plants. These results demonstrate that the MYB61–STRONG2 module positively regulates culm diameter and lodging resistance, information that could guide breeding efforts for improved yield in rice.

Floral color and odor serve as attractants for pollinators. It remains unclear how changes in these traits in color-change species interact with pollinators and impact a plant's reproductive success. Lonicera calcarata flowers change from white (Night 1 [N1] and Day 1 [D1]) through yellow (Night 2 [N2]) and orange (Day 2 [D2]) to orange-red (Night 3 [N3] and Day 3 [D3]). Our research showed that floral characters, stigma activity, nectar production and floral spectral reflectance decreased through the flowering phases. Floral odor mainly comprised fatty acids, aldehydes, monoterpenes and alcohols, especially n-hexadecanoic acid, hexadecanal and 3-carene. Floral odor peaked on N1 and N3, largely due to the presence of fatty acids. The emission of n-hexadecanoic acid was higher on N1 and N3 compared with other phases, while hexadecanal emission remained constant throughout the flowering stages. The emission of 3-carene was highest on N1. Lonicera calcarata was mainly pollinated by the moth Chorodna strixaria, the butterfly Acosmeryx naga and three bumblebees (Bombus melanurus, B. eximius, B. sonani) and they all preferred to visit white (younger) flowers. Moths had a preference for 3-carene and no significant preference for n-hexadecanoic acid and hexadecanal. Seed sets of nocturnal pollination and control treatments were not significantly different. Lonicera calcarata could produce seeds by self-pollination; cross-pollination significantly increased the seed set. Floral color guides pollinators to visit younger flowers with more floral rewards and higher stigma activity. Different chemical compounds in floral odor may not only attract pollinators but also avoid herbivore damage.

Understanding how East Asian subtropical evergreen broad-leaved forests (EBLFs) have evolved over time is not only vital for biodiversity conservation but also facilitates predictive modeling of ecosystem services under global change scenarios. During recent decades, numerous studies have been devoted to investigating the evolution of EBLFs. However, there are often contradictory interpretations of the different taxa associated with different geological events and environmental backgrounds. Here, we synthesize several key aspects of the spatiotemporal evolution of EBLFs. First, the EBLFs emerged concomitantly with the development of Asian monsoon systems, occurring no earlier than the Eocene. While the southernmost region was inhabited by tropical elements, EBLFs are not the direct relic of boreotropical flora because of the presence of a broad arid belt at that time. Rather, they represent a unique assemblage including boreotropical relics, tropical floras and deciduous broad-leaved forests. Second, the evolution of EBLFs should not be contextualized within an enclave, the adjacent vegetation systems to elucidate the potential connections between EBLFs and other biomes should be considered to avoid an isolated phenomenon. Third, the adaptive response of EBLFs to environmental changes caused by anthropogenic disturbance in subtropical regions remains understudied. Such a knowledge gap must be addressed to develop effective conservation strategies to sustain the ecosystem amid the dual pressure of climate change and human activity in the future. Finally, current research has predominantly focused on the dominant tree species in EBLFs, whereas comprehensive understanding requires expanding the investigation of associated flora, including understory trees and herbaceous plants. This review not only consolidates contemporary perspectives on the evolution of EBLFs but also proposes a framework to navigate the Anthropocene challenges. By bridging historical patterns with future projections, we aim to catalyze transformative research on EBLFs’ resilience and sustainable management, fostering further research and development regarding the resurgence.

The genus Micromonospora, a globally distributed actinomycete inhabiting diverse ecosystems, is widely recognized for its remarkable biosynthetic capacity and role as a prolific source of bioactive natural products. However, the members of the genus Micromonospora from extreme environments remain largely unstudied. In this study, we isolated 15 Micromonospora spp. strains from samples collected in desert and marine habitats. Based on polyphasic taxonomy approaches eight strains were identified and represent four novel species. Genome mining of the newly isolated strains revealed substantial biosynthetic potential for terpenes (n = 70, 22.9% of total biosynthetic gene clusters [BGCs]) and polyketides (n = 60, 19.6% of total BGCs). Subsequent pan-genomic analysis identified substantial numbers of terpene-related (n = 745, 33.8% of total biosynthetic genes [BGs]) and polyketide-related (n = 728, 33.0%) BGs in the core genome, highlighting their core biosynthetic potential. To further investigate their metabolic capacity, fermentation and metabolomic profiling were conducted to assess the secondary metabolite production capacity of all 15 strains. The results revealed a diverse array of alkaloids (averaging 75.3, 33.4% of total annotated secondary metabolites) and amino acid-derived peptides (averaging 56.3, 25.0% of total). These findings also highlight significant metabolic variations among strains and underscore the pivotal role of fermentation conditions in shaping their metabolic profiles. This study advances the taxonomic and functional understanding of Micromonospora spp. and presents a multi-omics framework combining genome mining and metabolomics to explore the biosynthetic potential of wild-type strains from extreme habitats.

A robust and stable phylogenetic framework is a fundamental goal of evolutionary biology. As the third largest insect order, Lepidoptera (butterflies and moths) are central to terrestrial ecosystems and serve as important models for biologists studying ecology and evolutionary biology. However, for such an insect group, the higher-level phylogenetic relationships among its superfamilies remain poorly resolved. Here, we increased taxon sampling among Lepidoptera (37 superfamilies and 68 families containing 263 taxa), obtaining a series of amino-acid data sets from 69 680 to 400 330 aa in length for phylogenomic reconstructions. Using these data sets, we explored the effect of different taxon sampling with significant increases in gene loci on tree topology using maximum-likelihood (ML) and Bayesian inference (BI) methods. Moreover, we also tested the effectiveness of topology robustness among the three ML-based models. The results demonstrated that taxon sampling is an important determinant in tree robustness of accurate phylogenetic estimation for species-rich groups. Site-wise heterogeneity was identified as a significant source of bias, causing inconsistent phylogenetic positions among ditrysian lineages. The application of the posterior mean site frequency (PMSF) model provided reliable estimates for higher-level phylogenetic relationships of Lepidoptera. Phylogenetic inference presented a comprehensive framework among lepidopteran superfamilies, and revealed some new sister relationships with strong supports (Papilionoidea is sister to Gelechioidea, Immoidea is sister to Galacticoidea, and Pyraloidea is sister to Hyblaeoidea, respectively). The current study provides essential insights for future phylogenomic investigations in species-rich lineages of Lepidoptera and enhances our understanding on phylogenomics of highly diversified groups.

Although considerable progress has recently been made in the phylogeny of Hymenasplenium, the genus remains poorly investigated; specifically, the diversification and historical biogeography of the genus have been little studied. Here, we infer an updated plastid DNA phylogeny and the first large-scale nuclear DNA phylogeny to understand the biogeography of the genus. The plastid phylogeny includes 312 accessions from across the genus′ distribution range (ca. 121% increase of the latest sampling), with special attention paid to island accessions from 14 Indian Ocean and Pacific islands, whereas the nuclear phylogeny includes 161 accessions of the Afro–Eurasian species. We identify one new major clade and two new subclades. Reticulate evolution was revealed both among subclades and among species in the Afro–Eurasian. Our divergence-time analyses show that most of the extant species diversity has arisen from diversification after the Oligocene despite a Cretaceous origin of the genus. Ancestral area reconstruction revealed that vicariance likely played a major role in building biogeographic patterns at deep evolutionary scales (the Afro–Eurasian clade and the American clade) in Hymenasplenium, while the intercontinental disjunctions within the Afro–Eurasian clade among Asia, Africa, and Oceania might have resulted from frequent long-distance dispersal events from Asia to Oceania and Africa.

Recent phylogenomic studies have confirmed that Scirtidae is one of the earliest-diverging groups of polyphagan beetles. Cretaceous fossils and genome-scale data have shown promise in elucidating the evolutionary history of Scirtidae. However, knowledge about the Mesozoic diversity of scirtids remains limited, and a recent phylogenomic study of Australasian Scirtinae failed to consider among-site compositional heterogeneity. In this study, we present a refined phylogeny of Scirtinae by analyzing ultraconserved element data under the better-fitting site-heterogeneous CAT-GTR+G4 model. A new scirtine fossil, Serracyphon philipsi gen. et sp. nov., is reported from mid-Cretaceous Kachin amber. This fossil is characterized by serrate antennae, uncarinated antennomere 1, absence of subocular carinae, and absence of a buttonhole on subgenal ridges. The placement of Serracyphon is evaluated within our updated phylogenomic framework for scirtine evolution. Additionally, we critically reevaluate the taxonomy of the “Scirtes” fossils previously described from the Eocene of the Isle of Wight.

Due to the high cost of whole-genome sequencing and the sampling difficulty of transcriptome sequencing in non-model plants, evolutionary studies often depend on next-generation sequencing (NGS) data. Nonetheless, current approaches typically focus on assembling chloroplast genomes or a few nuclear loci, leaving much of the genomic information from NGS underexploited. In this study, we employed multigenomic data sets and advanced analytical pipelines to reconstruct a robust phylogenetic framework for 39 Bupleurum. Nuclear gene data sets and organellar genomes derived from NGS were analyzed. We successfully reconstructed a robust phylogenetic framework for East Asia (EA) Bupleurum, in which two clades were strongly supported and all intersectional relationships were resolved. Phylogenetic discordance was mainly caused by incomplete lineage sorting and hybridization. Divergence dating estimated the origin of Bupleurum at ∼50.76 Ma, with the two subgenera (Penninervia and Bupleurum) diverging at 42.26 Ma. The EA lineages emerged around 22.85 Ma, with Group I diverging at 11 Ma and Group II at 8.72 Ma. Notably, diversification rates remained stable within both EA groups. Combined with geological events and gene–environment correlations, precipitation seasonality (PSN) showed the strongest phylogenetic signals with the Single Copy Orthologue (SCO) tree. The arid event in Central Asia may have driven the adaptation of EA Bupleurum (especially in EA Group II species) to arid, sun-exposed environments. By integrating phylogenetics, geology, and environmental data, this study provides a comprehensive understanding of the evolutionary history and adaptive strategies of Bupleurum in EA, offering valuable insight into the interplay between genetic and ecological factors in plant diversification.

Inferring general biogeographic patterns in the sub-Antarctic region has been challenging due to the disparate geological origins of its islands and archipelagos—ranging from Gondwanan fragments to uplifted seafloor and more recently formed volcanic islands—and the remoteness of these island systems, spread around the austral continental landmasses. Here, we conduct phylogenetic reconstruction, divergence time estimation, and Bayesian Island Biogeographic analyses to reconstruct the spatio–temporal colonization histories of seven vascular plant lineages, which are either widespread across the sub-Antarctic region (Acaena magellanica, Austroblechnum penna-marina, Azorella selago, Notogrammitis crassior) or restricted to an extremely remote sub-Antarctic province (Colobanthus kerguelensis, Polystichum marionense, Pringlea antiscorbutica). Our results reveal high biological connectivity within the sub-Antarctic region, with southern landmasses (Australia, New Zealand, South America) as key sources of sub-Antarctic plant diversity since the Miocene, supporting long-distance dispersal as the primary colonization mechanism rather than tectonic vicariance. Despite the geographic isolation of the sub-Antarctic islands, eastward and westward colonization events have maintained this connectivity, likely facilitated by eastward-moving marine and wind currents, short-term weather systems, and/or dispersal by birds. Divergence time estimates indicate that most species diverged within the Plio–Pleistocene, with crown ages predating the Last Glacial Maximum, suggesting that sub-Antarctic archipelagos acted as refuges for biodiversity. Our findings highlight the role of one of the most remote sub-Antarctic archipelagos as both a refugium and a source of (re)colonization for continental regions. These results underscore the urgent need for establishing priority conservation plans in the sub-Antarctic, particularly in the face of climate change.

Panax (Araliaceae) is a small genus containing several well known medicinally important species. It has a disjunct distribution between Eastern Asia and Eastern North America, with most species from eastern Asia, especially the Himalayan-Hengduan Mountains (HHM). This study used the genomic target enrichment method to obtain 358 nuclear ortholog loci and complete plastome sequences from 59 accessions representing all 18 species of the genus. Divergence time estimation and biogeographic analyses suggest that Panax was probably widely distributed from North America to Asia during the middle Eocene. During the late Eocene to Oligocene Panax may have experienced extensive extinctions during global climate cooling. It survived and diverged early in the mountains of Southwest China and tropical Indochina, where some taxa migrated northwestward to the HHM, eastward to central and eastern China, and then onward toward Japan and North America. Gene flow is identified as the main contributor to phylogenetic discordance (33.46%) within Panax. We hypothesize that the common ancestors of the medicinally important P. ginseng + P. japonicus + P. quinquefolius clade had experienced allopolyploidization, which increased adaptability to cooler and drier environments. During the middle to late Miocene, several dispersals occurred from the region of the HHM to contiguous areas, suggesting that HHM acted as a refugium and also served as a secondary diversification center for Panax. Our findings highlight that the interplay of orographic uplift and climatic changes in the HHM greatly contributed to the species diversity of Panax.

The maintenance of species boundaries between widespread and narrow endemic congeneric species in sympatric sites remains a fundamental question in ecology and evolutionary biology. For plants with specialized pollination mechanisms, pre- and postpollination isolation mechanisms likely play distinct roles in reproductive isolation and species integrity. Parnassia (Celastraceae) is characterized by one-by-one stamen movement and has its distribution center in southwest China, where many widespread and local endemic species coexist. To quantify pre- and postpollination barriers and their relative roles in maintaining species boundaries, we conducted field experiments with the widespread Parnassia wightiana Wall. ex Wight & Arn. and the local endemic Parnassia amoena Diels over two separate years at Jinfo Mountain, southwest China. We examined four prepollination barriers (ecogeography, blooming phenology, stamen movement, and pollinator type) and three postpollination barriers (fruit set, seed production, and seed viability). Our findings indicate that prepollination barriers played a more significant role in reproductive isolation than postpollination barriers. For the widely distributed P. wightiana, ecogeographical isolation was the primary barrier, followed by phenology and pollinator type isolation. In the narrow endemic P. amoena, which exhibits slower stamen movement, this feature contributed significantly to isolation, with phenological isolation being the second most important factor. Among postpollination barriers, seed viability was the most significant for both species. Our results indicate that prepollination barriers are the predominant isolation mechanism for these two sympatric Parnassia species, and stamen movement may serve as a novel type of prepollination barrier, particularly for the narrow endemic species.

Drought represents a paramount abiotic stressor constraining global agroforestry productivity. Plants have evolved multifaceted adaptive strategies involving active modulation of symbiotic microbial communities to mitigate drought stress. These plant-associated microbes enhance plant drought adaptation via five principal mechanisms: (i) extracellular polymeric substance-mediated biofilm formation on plant surface enhances hydroregulation and edaphic structural stability; (ii) osmoprotectant biosynthesis (e.g., proline) maintains cellular osmotic equilibrium; (iii) synthesizing antioxidants to reduce damage from reactive oxygen species and oxidative stress; (iv) regulating plant phytohormone metabolism by secreting hormones (e.g. indole-3-acetic acid) and 1-aminocyclopropane-1-carboxylic deaminase; (v) emitting signaling molecules (e.g. volatile organic compounds, hormones and enzymes) to activate plant drought adaptation. Future researches should focus on the development of host-specific drought-adaptive microbial consortia while elucidating phyllosphere–rhizosphere microbiome crosstalk, ultimately harnessing translational microbiome engineering to evaluate their efficacy in multi-environment agricultural systems.

The decline in tree growth has become a global issue. It is critically important to explore the factors affecting tree growth under the background of global climate change to understand tree growth models. A database was established based on Robinia pseudoacacia growth and its driving factors on China’s Loess Plateau. Linear regression and three machine learning methods, including support vector machine, random forest (RF) and gradient boosting machine were used to develop R. pseudoacacia growth models considering forest age, density, climate factors and topographic factors. The root mean square deviation method was adopted to quantitatively assess the relationship between tree growth and soil properties. The average tree height of R. pseudoacacia on the Loess Plateau was 8.8 ± 0.1 m, the average diameter at breast height (DBH) was 10.4 ± 0.1 cm and the average crown diameter was 3.2 ± 0.1 m. The RF model was a fast and effective machine learning method for predicting R. pseudoacacia growth, which showed the best simulation capability and could account for 67% of tree height variability and 55% of DBH variability. Model importance indicated that forest age and stand density were the main factors predicting R. pseudoacacia growth, followed by climate factors. The trade-off between R. pseudoacacia growth and soil properties revealed that soil texture and soil pH were the primary determinants of R. pseudoacacia growth in this region. Our synthesis provides a good framework for sustainable forest management in vulnerable ecological areas under future climate change.

The survival and reproduction of plants in a particular region are closely related to the local ecological niche. The use of species distribution models based on the ecological niche concept to predict potential distributions can effectively guide the protection of endangered plants, prevention and control of invasive plants, and plant introduction and ex-situ conservation. However, traditional methods and processes for predicting potential distributions of plants are tedious and complex, requiring the collection and processing of large amounts of data and the manual operation of multiple tools. Therefore, it is difficult to achieve large-scale prediction of the potential distributions of plants. To address these limitations, by collecting and organizing a large amount of basic data, occurrence records, and environmental data and integrating species distribution models and mapping techniques, a workflow to automatically predict the potential distributions of Chinese plants was established, thus the innovative work of predicting the potential distributions of 32 000 species of plants in China was completed. Furthermore, an online platform for predicting plant distributions in China based on visualization technology was developed, providing a basis for sharing the prediction results across a wide range of scientists and technologists. Users can quickly access information about the potential distributions of plants in China, providing a reference for the collection, preservation, and protection of plant resources. In addition, users can quickly predict the potential distribution of a certain plant in a certain region across China according to specific needs, thus providing technical support for biodiversity conservation.

We screened 161 eligible papers of experimental data across the Tibetan plateau for Meta-analysis, in order to systematically assess and validate potential application of plant resource allocation strategies, such as the optimal allocation hypothesis, the isometric allocation hypothesis, and the allometric allocation hypothesis under environmental changes, and to explore the effects of environmental factors (temperature change, grazing intensity) on plant resource allocation strategies in alpine grassland ecosystems on the Tibetan Plateau. Overall, we found that the aboveground and belowground growth relationship in alpine grasslands follows the allometric growth hypothesis, which was unaffected by warming, grazing and their interactions. In addition, the biomass transferred between aboveground and belowground, the former was decreased, while the later was increased under warming condition in alpine steppe implies that the resource allocation strategy in alpine steppe grassland may potentially follow the optimal allocation hypothesis. We further found that the effect of soil properties on biomass, not the biomass allocation, was different under warming and grazing condition in alpine grasslands, which further conforms the above conclusion. In addition, warming helped to mitigate the negative effects of grazing, which indicated that the interaction between warming and grazing is important in alpine grassland ecosystems. Overall, results of this study are of theoretical significance for understanding how moderate grazing affects the growth of plants in alpine grasslands under changing climate.

Legumes play critical roles in agroecosystems by modulating nitrogen-fixing microorganisms to enhance soil fertility and promote crop productivity. Current research on the effects of legumes predominantly focuses on surface soil, lacking a comprehensive analysis of their overall impact across multiple soil layers and an in-depth understanding of associated microbial mechanisms. Here, the community structure of soil nitrogen-fixing microorganisms in three soil layers (0–20 cm, 20–50 cm and 50–100 cm) under legume and non-legume cultivation was investigated through metagenomic sequencing. We found that only in topsoil (0–20 cm) legume treatment exhibited a significantly higher relative abundance of nitrogen-fixing genes than non-legume treatment. Under legume cultivation, the relative abundance of nitrogen-fixing genes was significantly higher in the topsoil layer than in deeper layers, whereas non-legume treatment displayed an inverse depth-dependent pattern. Combining soil physicochemical properties, the relative abundance of nitrogen-fixing genes correlated significantly with soil moisture, total carbon (TC), and dissolved organic carbon (DOC) content. Both TC and DOC were identified as key drivers of these genes. Subsequently, a similar depth-dependent pattern within the relative abundance of soil carbon degradation genes was found in response to the cultivation of both crops. The relative abundances of soil carbon degradation genes were negatively correlated with nitrogen-fixing genes under legume treatment individually, distinct from non-legume treatment. Our findings highlight the depth-dependent impact of legumes on nitrogen fixation and the critical interaction between soil carbon degradation and nitrogen fixation, providing insights into carbon management in legume cultivation practices to enhance nitrogen fixation in future agriculture.

Soil respiration is an important pathway of carbon release from the terrestrial biosphere to the atmosphere, which plays a key role in ecosystem carbon cycling. However, the response and mechanism of soil respiration to nitrogen and phosphorus addition in legume plants are still unclear. Here, a pot experiment planted with soybean (Glycine max (L.) Merr.) was conducted to investigate the effects of nitrogen (N) and phosphorus (P) addition on soil respiration. Four treatments were designed: control, N addition, P addition, and both N and P addition. Soil respiration was measured twice a month from June to September in 2022. Our results showed that nutrient addition treatments presented significantly negative effects on soil respiration. In particular, nitrogen addition not only directly affected soil respiration, but also indirectly impacted soil respiration by altering soil nitrate nitrogen content. Elevated soil nitrate nitrogen content could inhibit soybean root nodule number and reduce biomass allocation to roots, thereby decreasing soil respiration. Furthermore, phosphorus addition and nitrogen–phosphorus co-addition strongly inhibited soybean nodulation by changing soil pH value, thus inhibiting soil respiration of soybean. The findings provide baseline information for optimizing nutrient management in legume crops.

Tree allometric models based on height (H) and diameter (D) are the most commonly used method to estimate forest biomass. Environments and stand characteristics are recognized to affect tree allometries. However, few studies have considered to incorporate these effects into allometric models, which restricts the use of these models in a wide domain. Adopting the power-law function Y = aG^b as a basic model where Y is either tree height or biomass and the corresponding G is tree diameter D at breast height or D²H, we developed a two-step approximation procedure to quantify the effects of environments and stand characteristics on allometric coeffcients a and b for Cunninghamia lanceolata and Pinus forest in China. Results show that most of the allometric coeffcients are dependent on stand characteristics for C. lanceolata forest, and on mean annual temperature, stand age and latitude for Pinus forest. The allometric models via the two-step approximation Y = f(α + α_jx_j) G^{f (β+βixi)} (x_j or x_i are key drivers associated with environments and stand characteristics. α, α_j,β and β_i are regression coeffcients) considerably improved the accuracy of tree height and biomass estimation. Compared to the basic model, the second approximation models signifcantly reduced the mean absolute bias between the observed and computed values by 25%–34% for C. lanceolata and by 21%–26% for Pinus forest, respectively. Our results highlight the necessity of incorporating environments and stand characteristics into the allometric models and provide a universal method to accurately estimate H-D-based tree biomass across a wider domain.

Interspecific plant–soil feedback (PSF)—the influence of soil conditioned by one plant species on another—is key to ecosystem processes but remains challenging to predict due to complex factors like species origin and phylogenetic relatedness. These aspects are underexplored, limiting our understanding of the mechanisms driving PSFs and their broader implications for ecosystem functioning and species coexistence. To shed light on the role of plant species origin and phylogenetic distance in interspecific PSFs, we conducted a greenhouse experiment with 10 native responding species and soils conditioned by 10 native and 10 exotic species resulting in 20 species pairs. These pairs represented a range of phylogenetic distances between both species, spanning up to 270 million years of evolutionary history since their last common ancestor. Conditioning by both native and exotic species reduced biomass production, with stronger inhibition observed for native-conditioned soils. Native-conditioned soils also exhibited lower phosphorus levels, higher basal and specific respiration, and greater cation exchange capacity, base saturation, and magnesium content compared to exotic-conditioned soils. Contrary to expectations, phylogenetic distance did not influence PSFs, regardless of conditioning species origin. Our findings suggest that co-evolution drives native plants to foster microbial communities with low carbon-use efficiency, highlighting soil biota’s critical role in PSFs. This advances our understanding of interactions between plant species origin and microbial communities and underlines the importance of microbial management for promoting native species and controlling invasives. The lack of phylogenetic distance effects aligns with prior studies, indicating evolutionary relatedness alone does not reliably predict PSF outcomes.

The intricate interplay among plant productivity and soil factors is a pivotal driver for sustaining the carbon sequestration capacity of coastal wetlands. Yet, it remains uncertain whether climate warming will reshape the cause-and-effect interactions between coastal plant productivity and soil factors. In this study, we combined a manipulative warming experiment with a convergent cross-mapping technique to quantify the causal relationships, which can be either unidirectional or bidirectional, between plants (gross primary productivity, GPP) and soil environment (e.g. soil temperature, moisture and salinity). Our findings revealed that warming amplified the interaction between GPP and soil salinity in the coastal wetland ecosystem. While soil temperature primarily drove this causal relationship in control plots, a more complex interaction emerged in warming plots: soil salinity not only directly influenced GPP but also indirectly affected it by altering soil temperature and moisture. Overall, warming increased the number of causal pathways linking GPP with soil environmental factors, such as the effect of soil salinity on GPP and the impacts of GPP on soil moisture. These findings provide experimental evidence of intensified plant–soil causality in coastal wetlands under climate warming.

The relative limitation of microbes by soil organic carbon (SOC), nitrogen (N) and phosphorus (P) is linked with soil microbial activities, so how change of plant species diversity (PSD) affects microbial resource limitation would partly determine its impacts on SOC dynamics and nutrient cycling. However, the responses of microbial resource limitation to increasing PSD have poorly explored. Here, 45 plots covering a natural PSD gradient were used to investigate the effects of PSD on microbial resource limitation in a subtropical forest. Extracellular enzymatic stoichiometry along with a laboratory N and P addition experiment were used to determine microbial resource limitation. Contents of microbial biomass C, N and P significantly increased, but C:P and N:P ratios in microbial biomass were unchanged as PSD increased. Soil microbes were generally co-limited by C and P, but not by N across the 45 plots. Increasing PSD did not alter microbial N limitation, alleviated microbial C limitation and aggravated microbial P limitation. The alleviated microbial C limitation or aggravated microbial P limitation was attributed to increased soil C availability but decreased P availability, which resulted in stimulated soil C:P and N:P ratios and in turn greater C:P and N:P imbalance between soil and microbial biomass under higher PSD. Our results highlight the divergent effects of increasing PSD on microbial resource limitation. Considering that microbial C and P limitations are widespread, the patterns observed in the current study should be applicable broadly.

Over the past two decades, our understanding of Lauraceae, a large family of woody plants, has undergone significant advances in phylogeny, taxonomy, and biogeography. Molecular systematic studies have elucidated the basic relationships within the family with plastid phylogenomic analyses providing robust support for deep-level relationships between Lauraceae lineages, leading to the recognition of nine tribes: Hypodaphnideae, Cryptocaryeae, Cassytheae, Neocinnamomeae, Caryodaphnopsideae, Mezilaureae, Perseeae, Laureae, and Cinnamomeae, with Mezilaureae validated here. Nuclear genomes and comparative genomics studies have also clarified aspects of the family’s evolutionary history and metabolic diversity. Taxonomic studies have focused mainly on the most diverse regions, e.g., tropical Asia, tropical America, and Africa (Madagascar), with six new genera described and five reinstated since the last major overview of the family. The extensive fossil record suggests that Lauraceae diversified globally during the Late Cretaceous and Early Cenozoic. Biogeographic studies indicate that different lineages of the family are sorted into Gondwanan and Laurasian lineages, with patterns resulting from the disruption of boreotropical flora and multiple long-distance dispersal events. Phylogeographic studies, predominantly from East Asia, have shown patterns of in situ survival and demographic stability or expansion during the Quaternary. Nevertheless, many systematic relationships within the family remain unresolved and further research is needed into the complex biogeographic history and ecological roles of Lauraceae. A multifaceted approach integrating genomic studies, field work, morphological and ecological investigations is therefore needed to understand the evolution and diversity of this ecologically and economically significant plant family.

Comparative analyses in ecology and evolution often face the challenge of controlling for the effects of shared ancestry (phylogeny) from those of ecological or trait-based predictors on species traits. Phylogenetic Generalized Linear Models (PGLMs) address this issue by integrating phylogenetic relationships into statistical models. However, accurately partitioning explained variance among correlated predictors remains challenging. The phylolm.hp R package tackles this problem by extending the concept of “average shared variance” to PGLMs, enabling nuanced quantification of the relative importance of phylogeny and other predictors. The package calculates individual likelihood-based R² contributions of phylogeny and each predictor, accounting for both unique and shared explained variance. This approach overcomes limitations of traditional partial R² methods, which often fail to sum the total R² due to multicollinearity. We demonstrate the functionality of phylolm.hp through two case studies: one involving continuous trait data (maximum tree height in Californian species) and another focusing on binary trait data (species invasiveness in North American forests). The phylolm.hp package offers researchers a powerful tool to disentangle the contributions of phylogenetic and ecological predictors in comparative analyses.

The ecological and evolutionary mechanisms underlying montane biodiversity patterns remain unresolved. To understand which factors determined community assembly rules in mountains, biogeographic affinity that represents the biogeographic and evolutionary history of species should incorporate with current environments. We aim to address two following questions: 1) How does plant taxonomic and phylogenetic diversity with disparate biogeographic affinities vary along the subtropical elevational gradient? 2) How do biogeographic affinity and environmental drivers regulate the community assembly? We collected woody plant survey data of 32 forest plots in a subtropical mountain of Mt. Guanshan with typical transitional characteristics, including 250 woody plant species belonging to 56 families and 118 genera. We estimated the effects of biogeographic affinity, climate and soil properties on taxonomic and phylogenetic diversity of plant communities employing linear regression and structural equation models. We found that the richness of temperate-affiliated species increased with elevations, but the evenness decreased, while tropical-affiliated species had no significant patterns. Winter temperature directly or indirectly via biogeographic affinity shaped the assemblage of woody plant communities along elevations. Biogeographic affinity affected what kind of species could colonize higher elevations while local environment determined their fitness to adapt. These results suggest that biogeographic affinity and local environment jointly lead to the dominance of temperate-affiliated species at higher elevations and shape the diversity of woody plant communities along elevational gradients. Our findings highlight the legacy effect of biogeographic affinity on the composition and structure of subtropical montane forests.

Evergreen broad-leaved forests (EBLFs) are widely distributed in East Asia and play a vital role in ecosystem stability. The occurrence of these forests in East Asia has been a subject of debate across various disciplines. In this study, we explored the occurrence of East Asian EBLFs from a paleobotanical perspective. By collecting plant fossils from four regions in East Asia, we have established the evolutionary history of EBLFs. Through floral similarity analysis and paleoclimatic reconstruction, we have revealed a diverse spatio-temporal pattern for the occurrence of EBLFs in East Asia. The earliest occurrence of EBLFs in southern China can be traced back to the middle Eocene, followed by southwestern China during the late Eocene-early Oligocene. Subsequently, EBLFs emerged in Japan during the early Oligocene and eventually appeared in central-eastern China around the Miocene. Paleoclimate simulation results suggest that the precipitation of wettest quarter (PWetQ, mm) exceeding 600 mm is crucial for the occurrence of EBLFs. Furthermore, the heterogeneous occurrence of EBLFs in East Asia is closely associated with the evolution of the Asian Monsoon. This study provides new insights into the occurrence of EBLFs in East Asia.

The angiosperm family Elaeagnaceae comprises three genera and ca. 100 species distributed mainly in Eurasia and North America. Little family-wide phylogenetic and biogeographic research on Elaeagnaceae has been conducted, limiting the application and preservation of natural genetic resources. Here, we reconstructed a strongly supported phylogenetic framework of Elaeagnaceae to better understand inter- and intrageneric relationships, as well as the origin and biogeographical history of the family. For this purpose, we used both nuclear and plastid sequences from Hyb-Seq and genome skimming approaches to reconstruct a well-supported phylogeny and, along with current distributional data, infer historical biogeographical processes. Our phylogenetic analyses of both nuclear and plastid data strongly support the monophyly of Elaeagnaceae and each of the three genera. Elaeagnus was resolved as sister to the well-supported clade of Hippophae and Shepherdia. The intrageneric relationships of Elaeagnus and Hippophae were also well resolved. High levels of nuclear gene tree conflict and cytonuclear discordance were detected within Elaeagnus, and our analyses suggest putative ancient and recent hybridization. We inferred that Elaeagnaceae originated at ca. 90.48 Ma (95% CI = 89.91-91.05 Ma), and long-distance dispersal likely played a major role in shaping its intercontinentally disjunct distribution. This work presents the most comprehensive phylogenetic framework for Elaeagnaceae to date, offers new insights into previously unresolved relationships in Elaeagnus, and provides a foundation for further studies on classification, evolution, biogeography, and conservation of Elaeagnaceae.

Intraspecific genetic variance and gene flow can support the adaptive evolution of species challenged by climate shifts or novel environmental conditions. Less well understood is how genome organization and gene flow interact in closely related species during evolutionary divergence and differentiation. Here we conducted genomic footprint analyses to determine how three species of Pterocarya (P. stenoptera, P. hupehensis, and P. macroptera), which are sympatric but occupy different elevational niches, adapted to the heterogeneous environment of the Qinling-Daba Mountains, China. We identified candidate genes for environmental adaptation (i.e., PIEZO1, WRKY39, VDAC3, CBL1, and RAF), and also identified regions of gene introgression between P. hupehensis and P. macroptera that show lower genetic load and higher genetic diversity than the rest of their genomes. The same introgressed regions are notably situated in areas of minimal genetic divergence yet they are characterized by elevated recombination rates. We also identified candidate genes within these introgressed regions related to environmental adaptation (TPLC2, CYCH;1, LUH, bHLH112, GLX1, TLP-3, and ABC1). Our findings have thus clarified the important role of gene flow in ecological adaptation and revealed genomic signatures of past introgression. Together, these findings provide a stronger theoretical basis for understanding the ecological adaptation and conservation of Quaternary relict woody plants in East Asia.

The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value. However, taxonomy and systematics of Salix is extremely difficult and relationships between main lineages, especially deep phylogenies, remain largely unresolved. In this study, we used genome-skimming, plastome assembly, and single-copy orthologs (SCOs) from 66 Salix accessions, along with publicly available plastome and sequence read archive (SRA) datasets to obtain a robust backbone phylogeny of Salix, clarify relationships between its main lineages, and gain a more precise understanding of the origin and diversification of this species-rich genus. The plastome and SCO datasets resolved Salix into two robust clades, with plastome-based phylogenies lacking inner resolution and SCO offering fully resolved phylogenies. Our results support the classification of Salix into five subgenera: Salix, Urbaniana, Triandrae, Longifoliae and Vetrix. We observed a significant acceleration in the diversification rate within the Chamaetia-Vetrix clade, while Salix exhibited increased rates of diversification spanning from the early Oligocene to the late Miocene. These changes coincided with contemporaneous tectonic and climate change events. Our results provide a foundation for future systematic and evolutionary studies of Salix. Additionally, we showed that genome skimming data is an efficient, rapid, and reliable approach for obtaining extensive genomic data for phylogenomic studies, enabling the comprehensive elucidation of Salix relationships.

Mimetic seeds attract birds to disperse seeds mainly by mimicking fleshy fruits or arillate seeds, however, they provide little nutritive reward for bird dispersers. The key characteristics of mimetic seeds are conspicuous seed color, hard seed coat, certain toxic secondary metabolites, and perhaps smooth waxy layer. In this review, we discuss the global distribution of mimetic seeds, the interaction of mimetic seeds with bird dispersers, and secondary metabolites that underlie key characteristics of mimetic seeds. Mimetic-seed species mainly occur in the tropics, with large numbers distributed along coastal areas. The interaction between mimetic-seed species and bird dispersers can be antagonistic, mutualistic, or both. These interactions are generally established by conspicuous visual cues and hard tactile cues from mimetic seeds. The formation and variation of key characteristics of mimetic seeds may contribute to the metabolism of several kind of secondary compounds. Here, we also discuss mimetic-seed dispersal in the context of an evolutionary game, and propose several aspects of mimetic-seed dispersal that remain unstudied. While this review is based on preliminary findings and does not account for other potential influencing factors such as climate, it is expected to contribute to an improved understanding of mimetic-seed dispersal.

Understanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change. Quercus is a keystone genus in Northern Hemisphere forests, and its wide distribution in diverse ecosystems and long evolutionary history make it an ideal model for studying the genomic basis of ecological adaptations. Here we used a newly sequenced genome of Quercus gilva, an evergreen oak species from East Asia, with 18 published Fagales genomes to determine how Fagaceae genomes have evolved, identify genomic footprints of ecological adaptability in oaks in general, as well as between evergreen and deciduous oaks. We found that oak species exhibited a higher degree of genomic conservation and stability, as indicated by the absence of large-scale chromosomal structural variations or additional whole-genome duplication events. In addition, we identified expansion and tandem repetitions within gene families that contribute to plant physical and chemical defense (e.g., cuticle biosynthesis and oxidosqualene cyclase genes), which may represent the foundation for the ecological adaptation of oak species. Circadian rhythm and hormone-related genes may regulate the habits of evergreen and deciduous oaks. This study provides a comprehensive perspective on the ecological adaptations of tree species based on phylogenetic, genome evolutionary, and functional genomic analyses.