Mountains serve as exceptional natural laboratories for studying biodiversity due to their heterogeneous landforms and climatic zones. The Himalaya, a global biodiversity hotspot, hosts rich endemic flora, supports vital ecosystem functions, and offers a unique window into multifaceted plant diversity patterns. This review synthesizes research on Himalayan plant diversity, including species, phylogenetic, functional, and genetic dimensions, highlighting knowledge gaps and solutions. Research on Himalayan plant diversity has developed significantly. However, gaps remain, especially in studies on phylogenetic and functional diversity. The region's vegetation ranges from tropical rainforests to alpine ecosystems, with species richness typically following a hump-shaped distribution along elevation gradients. The eastern Himalaya exhibits higher plant diversity than the central and western regions. Low-elevation communities were found to be more functionally diverse, whereas high-elevation communities displayed greater ecological specialization. Communities at mid-elevations tend to show greater phylogenetic diversity than those at higher and lower elevations. The eastern and western flanks of the Himalaya retain high levels of genetic diversity and serve as glacial refugia, whereas the central region acts as a hybrid zone for closely related species. Himalayan plant diversity is shaped by historical, climatic, ecological and anthropogenic factors across space and time. However, this rich biodiversity is increasingly threatened by environmental change and growing anthropogenic pressures. Unfortunately, research efforts are constrained by spatial biases and the lack of transnational initiatives and collaborative studies, which could significantly benefit from interdisciplinary approaches, and other coordinated actions. These efforts are vital to safeguarding the Himalayan natural heritage.

The plastid genome (plastome) represents an indispensable molecular resource for studying plant phylogeny and evolution. Although plastome size is much smaller than that of nuclear genomes, accurately and efficiently annotating and utilizing plastome sequences remain challenging. Therefore, a streamlined phylogenomic pipeline spanning plastome annotation, phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome. Here, we develop PlastidHub, a novel web application employing innovative tools to analyze plastome sequences. In comparison with existing tools, key novel functionalities in PlastidHub include: (1) standardization of quadripartite structure; (2) improvement of annotation flexibility and consistency; (3) quantitative assessment of annotation completeness; (4) diverse extraction modes for canonical and specialized sequences; (5) intelligent screening of molecular markers for biodiversity studies; (6) gene-level visual comparison of structural variations and annotation completeness. PlastidHub features cloud-based web applications that do not require users to install, update, or maintain tools; detailed help documents including user guides, test examples, a static pop-up prompt box, and dynamic pop-up warning prompts when entering unreasonable parameter values; batch processing capabilities for all tools; intermediate results for secondary use; and easy-to-operate task flows between file upload and download. A key feature of PlastidHub is its interrelated task-based user interface design. Give that PlastidHub is easy to use without specialized computational skills or resources, this new platform should be widely used among botanists and evolutionary biologists, improving and expediting research employing the plastome. PlastidHub is available at https://www.plastidhub.cn.

Subgenus Melanocrommyum is the second largest subgenus of Allium, with a wide distribution ranging from the Canary Islands to northwestern India. This study investigates the phylogeny, biogeographic patterns, and morphological character evolution of the subgenus using 117 accessions representing 107 taxa across the 19 currently recognized sections within Allium subgenus Melanocrommyum. Although the subgenus is monophyletic, significant incongruence exists between morphological and molecular data. Our plastome-based phylogenetic analysis identified five distinct lineages (A–E), corresponding to the geographic distributions of the species. However, plastome lineages (A–E) and ITS clusters (A–G) were incongruent. Biogeographic and molecular dating analyses suggest that Melanocrommyum evolved in association with tectonic uplift events in Central Asia during the Late Miocene or Oligocene. Our finding that Melanocrommyum plastomes have lost infA and one copy rps19 gene indicate that the subgenus has undergone a relatively recent diversification. We also found that narrow leaves and fasciculate to semi-globose inflorescences may represent ancestral traits within the subgenus. This study provides new insights into the biogeographic history and trait evolution of Melanocrommyum, suggesting recent diversification influenced by tectonic events and climate change, while highlighting the complexity of molecular and morphological data integration.

Hybridization and introgression have long obscured relationships within Adenophora and its relatives, complicating generic delimitation. Leveraging deep genome skimming (DGS) data, we generated a large dataset, including thousands of single-copy nuclear (SCN) genes and plastomes, to untangle this reticulate history. Specifically, 9.89 terabytes (TB) of DGS data from 165 samples—representing 48 species and 13 subspecies of Adenophora (out of ca. 72 species) plus 24 outgroup species—yielded 1506 SCN genes and 77 plastid coding sequences. Tree-like phylogenies inferred with both coalescent- and concatenation-based methods revealed pronounced gene tree heterogeneity. Subsequent analysis showed that incomplete lineage sorting contributed minimally to this discordance; instead, hybridization and introgression were the primary drivers of early diversification. Integrating phylogenomic, morphological, and geographic evidence, we propose a revised generic framework for this group. Adenophora is expanded to include Campanula delavayi and the Korean Peninsula endemic genus Hanabusaya. We also recommend reinstating Hyssaria as a distinct Central Asian genus and introducing two new genera, Boreoasia and Rosomala.

Deep genome skimming (DGS) has emerged as a promising approach to recover orthologous nuclear genes for large-scale phylogenomic analyses. However, its reliability with low DNA quality and quantity typical of archival specimens, such as herbarium material, remains largely unexplored. We used Rhododendron as a case study to evaluate best practices for DGS in phylogenetic analyses at both deep and shallow scales. We first investigated locus recovery variation with sequencing depth, before evaluating the phylogenetic utility of different sets of loci, including Angiosperms353, target nuclear exons, and extended exon-flanking regions. We found DGS effectively recovered nuclear genes from herbarium specimens, with ～15×coverage performing similarly to deeper sequencing. The recovery of target exon and flanking regions was improved by using supercontigs as a reference, offering a potential solution to limited sequencing depth. The high-integrity nuclear sequences recovered robust phylogenetic relationships within Rhododendron. Notably, exon-flanking regions showed significant potential for resolving relationships at shallow scales. Genes recovered with taxon-specific references had less missing data than those recovered by Angiosperms353 and generated higher-resolution phylogenetic trees. This study demonstrates the utility of DGS data for obtaining numerous nuclear genes from herbarium specimens for phylogenetic studies, and makes recommendations for best practices regarding sequencing coverage, locus selection, and bioinformatic approaches.

Hybridization is a driving force in ecological transitions and speciation, yet direct evidence linking it to adaptive differentiation in natural systems remains limited. This study evaluates the role of hybridization in the speciation of Pinus densata, a keystone forest species on the southeastern Tibetan Plateau. By creating artificial interspecific F1s and a long-term common garden experiment on the plateau, we provide in situ assessments on 44 growth and physiological traits across four seasons, along with RNA sequencing. We found significant phenotypic divergence between P. densata and its putative parental species P. tabuliformis and P. yunnanensis, with P. densata demonstrating superior growth and dynamic balance between photosynthesis and photoprotection. The F1s closely resembled P. densata in most traits. Gene expression revealed 19%–10% of 34,000 examined genes as differentially expressed in P. densata and F1s relative to mid-parent expression values. Both additive (4%) and non-additive gene actions (5%–6% in F1s, 10%–12% in P. densata) were common, while transgressive expression occurred more frequently in the stabilized natural hybrids, illustrating transcriptomic reprogramming brought by hybridization and further divergence by natural selection. We provide compelling evidence for hybridization-derived phenotypic divergence at both physiological and gene expression levels that could have contributed to the adaptation of P. densata to high plateau habitat where both parental species have low fitness. The altered physiology and gene expression in hybrids serve both as a substrate for novel ecological adaptation and as a mechanism for the initiation of reproductive isolation.

As climate change triggers unprecedented ecological shifts, it becomes imperative to understand the genetic underpinnings of species’ adaptability. Adaptive introgression significantly contributes to organismal adaptation to new environments by introducing genetic variation across species boundaries. However, despite growing recognition of its importance, the extent to which adaptive introgression has shaped the evolutionary history of closely related species remains poorly understood. Here we employed population genetic analyses of high-throughput sequencing data to investigate the interplay between genetic introgression and local adaptation in three species of spruce trees in the genus Picea (P. asperata, P. crassifolia, and P. meyeri). We find distinct genetic differentiation among these species, despite a substantial gene flow. Crucially, we find bidirectional adaptive introgression between allopatrically distributed species pairs and unearthed dozens of genes linked to stress resilience and flowering time. These candidate genes most likely have promoted adaptability of these spruces to historical environmental changes and may enhance their survival and resilience to future climate changes. Our findings highlight that adaptive introgression could be prevalent and bidirectional in a topographically complex area, and this could have contributed to rich genetic variation and diverse habitat usage by tree species.

Understanding plant diversity within geographical ranges and identifying key species that drive community variation can provide crucial insights for the management of grasslands. However, the contribution of both local sites and plant species to beta diversity in grassland ecosystems has yet to be accurately assessed. This study applied the ecological uniqueness approach to examine both local contributions to beta diversity (LCBD) and species contributions to beta diversity (SCBD) across six major geographical ranges in alpine grasslands. We found that LCBD was driven by species turnover, with climate, plant communities, and their interactions influencing LCBD across spatial scales. LCBD values were high in areas with low evapotranspiration, high rainfall variability, and low species and functional richness. Precipitation seasonality predicted large-scale LCBD dynamics, while plant community abundance explained local LCBD variation. In addition, we found that SCBD were confined to species with moderate occupancy, although these species contributed less to plant biological traits. Our findings are crucial for understanding how ecological characteristics influence plant beta diversity in grasslands and how it responds to environmental and community factors. In addition, these findings have successfully identified key sites and priority plants for conservation, indicating that using standardized quadrats can support the assessment of the ecological uniqueness in grassland ecosystems. We hope these insights will inform the development of conservation strategies, thereby supporting regional plant diversity and resisting vegetation homogenization.

Global warming leads to snow cover loss in the alpine ecosystem, exposing seeds to extreme diurnal temperature fluctuations during the growing season. The risk of freezing increases as seeds have increased moisture content. Studying the survival mechanisms of seeds at low temperatures can help analyze changes in alpine meadow populations and target conservation efforts. Here, we used three species of Poaceae as a model to understand freezing stress. Fully imbibed Elymus dahuricus, Festuca elata, and Lolium multiflorum seeds were subjected to programmed cooling at fast and slow rates (-1.0/0.05 ℃/min) and then assessed for survival. Differential Scanning Calorimetry was used to analyze thermal transitions during cooling. HE-stained paraffin sections and a Transmission Electron Microscope were employed to observe internal morphology and ultrastructural changes. E. dahuricus seeds exhibited greater tolerance to low temperatures than those of the other two species, with an LT₅₀ of approximately -20 ℃ for both cooling rates and maintained relatively intact ultrastructure. The observed the low-temperature exotherm (LTE) correlated with seed survival, with viability decreasing extensively below LTE. Fast cooling caused fewer changes to seed morphology and ultrastructure than slow cooling, suggesting that the primary survival mechanism during fast cooling is freezing avoidance through supercooling. Seeds exhibited greater freeze tolerance under slow than fast cooling, primarily by migrating intracellular water to extracellular spaces where it froze, causing considerable damage to cell ultrastructure and forming apparent cavities in some seeds.

In forests, a few large trees (L-trees) versus small–medium trees (S-trees) are often considered the major reservoir of aboveground carbon stock (AGCS). Here, we hypothesize that tree species’ functional strategies regulate AGCS by tree sizes in temperate deciduous forests across local scale environmental gradients. Using data from 99 plots, we modelled the multivariate effects of the tree-based (tree diversity, stand density and multidimensional tree size inequality) versus the trait-based (multi-trait diversity and single-trait dominance) attributes of L-trees versus S-trees, along topographic and soil conditions, to predict AGCS through four L-trees threshold size (i.e., ≥ 50 cm fixed-diameter, top 95th percentile, ≥ top 50% cumulative AGCS descending-ranked ordered, and mean threshold size) approaches. The tree-based and trait-based attributes of L-trees and S-trees shaped species co-occurrence processes but L-trees regulated AGCS more effectively (31.29–93.20%) than S-trees and abiotic factors across four thereshold size approaches and two concepts. Although L-trees threshold size and tree-based attributes mattered for AGCS, the dominant resource-acquisitive strategy of structurally complex L-trees having higher specific leaf area but lower leaf dry matter content and lesser multi-trait dispersion could promote AGCS better than the resource-conservative strategy (low specific leaf area) of S-trees. Capturing tree species’ functional strategies, synergies and trade-offs across tree sizes can enhance our understanding of how to achieve nature-based carbon neutrality and lessen climate change. Thus, forest management and restoration initiatives should prioritize high-functioning tree species with dominant productive traits while conserving multi-trait diversified species in temperate deciduous forests.

Invasive alien species (IAS) significantly threaten global biodiversity and ecosystem stability. Despite increasing management efforts, a critical knowledge gap existed in understanding commonalities and disparities among national strategies. We analyzed several IAS management lists from 23 countries and the European Union, focusing specifically on vascular plant species within these lists. List composition, characteristics, and associated management measures were analyzed. Key patterns in species prioritization across national lists and intercontinental exchange of invasive alien plants (IAPs) were identified. Pistia stratiotes, Pontederia crassipes, Salvinia molesta, Cabomba caroliniana, Ulex europaeus were identified as globally recognized threats, being listed by at least 33.3% of analyzed countries and invading five or more continents. Aquatic plants were found to be more frequently included in management lists. A significant directional invasion pattern between the Eastern and Western Hemispheres was identified. Species native to Asia were observed to dominate as significant donors of IAPs across continents. The analysis of list management strategies highlighted substantial gaps in achieving Target 6 of the Kunming-Montreal Global Biodiversity Framework, particularly in species prioritization and inclusion of potential IAPs. In response to these challenges, a tiered classification system for invasive alien species list was proposed, encompassing High-Priority, Watchlist, Potential, and Priority Site categories, which aimed at enhancing management effectiveness by tailoring strategies to different invasion stages and ecological contexts. This study could contribute to understanding global IAPs management strategies and serve as a reference for policymakers and conservation managers to identify priority IAPs and refine management approaches.

Exotic plant invasions and increased atmospheric carbon dioxide (CO₂) concentration have been determined to independently affect soil nematodes, a key component of soil biota. However, little is known about the long-term effects of these two global change factors and their interactive effects. Over three consecutive years, we cultivated invasive alien plant Xanthium strumarium and its two phylogenetically related natives under both ambient (aCO₂) and elevated (eCO₂) atmospheric CO₂ concentrations, and determined the effects of the invader and natives on soil nematodes under different CO₂ concentrations and the relevant mechanism. The abundance of total soil nematodes and that of the dominant trophic group (herbivores) were significantly affected by plant species and CO₂ concentration, and these effects were dependent on the experimental duration, however, the Shannon-diversity of nematodes was not affected by these factors. Under aCO₂, both invasive and native species significantly increased the total nematode abundance and that of the dominant trophic group with increasing experimental duration, and the amplitude of the increase was greater under the invader relative to the natives. The eCO₂ increased total nematode abundance (second year) and that of the dominant trophic group (third year) under the invader, but not under the natives (or even decreased) with increasing experimental duration. Root litter had greater effects on soil nematode abundance than leaf litter and root exudates did. This study indicates that eCO₂ would aggravate effects of invasive plants on soil nematodes by increasing abundance, and these effects would vary with the duration.

Ca²⁺ signaling plays crucial roles in plant stress responses, including defense against insects. To counteract insect feeding, different parts of a plant deploy systemic signaling to communicate and coordinate defense responses, but little is known about the underlying mechanisms. In this study, micrografting, in vivo imaging of Ca²⁺ and reactive oxygen species (ROS), quantification of jasmonic acid (JA) and defensive metabolites, and bioassay were used to study how Arabidopsis seedlings regulate systemic responses in leaves after hypocotyls are wounded. We show that wounding hypocotyls rapidly activated both Ca²⁺ and ROS signals in leaves. RBOHD, which functions to produce ROS, along with two glutamate receptors GLR3.3 and GLR3.6, but not individually RBOHD or GLR3.3 and GLR3.6, in hypocotyls regulate the dynamics of systemic Ca²⁺ signals in leaves. In line with the systemic Ca²⁺ signals, after wounding hypocotyl, RBOHD, GLR3.3, and GLR3.6 in hypocotyl also cooperatively regulate the transcriptome, hormone jasmonic acid, and defensive secondary metabolites in leaves of Arabidopsis seedlings, thus controlling the systemic resistance to insects. Unlike leaf-to-leaf systemic signaling, this study reveals the unique regulation of wounding-induced hypocotyl-to-leaf systemic signaling and sheds new light on how different plant organs use complex signaling pathways to modulate defense responses.

The study of plant diversity is often hindered by the challenge of integrating data from different sources and different data types. A standardized data system would facilitate detailed exploration of plant distribution patterns and dynamics for botanists, ecologists, conservation biologists, and biogeographers. This study proposes a gridded vector data integration method, combining grid-based techniques with vectorization to integrate diverse data types from multiple sources into grids of the same scale. Here we demonstrate the methodology by creating a comprehensive 1°×1° database of western China that includes plant distribution information and environmental factor data. This approach addresses the need for a standardized data system to facilitate exploration of plant distribution patterns and dynamic changes in the region.