DNA methylation valley as a distinguishing feature occurs in root-specific expressed nicotine-related genes in .

Introduction: Nicotine, the main defense alkaloid of species, is synthesized exclusively in the roots. Several studies have shown that changes in DNA methylation patterns are associated with altered expression of genes involved in the biosynthesis of some secondary metabolites. It remains unknown whether DNA methylation pattern of nicotine-related genes differs in root and leaf tissues.

 (Polypodiales, Athyriaceae), a new fern species from southern Yunnan, China.

A new species in Athyriaceae, (section Anisogonium) is described and illustrated from southern Yunnan, China. exhibits the greatest morphological similarity to , particularly in lamina division, but can be reliably differentiated, based on lamina width and lobe shape. Molecular phylogenetic analysis demonstrates that the new species is closely related to , despite low morphological concordance.

Genetic origins and climate-induced erosion in economically important Asian walnuts.

The global climate is undergoing unprecedented changes, posing significant threats to species persistence. However, the spatiotemporal impacts on genetic diversity remain poorly understood, hindering species conservation and management. Walnuts, generally referred to as Juglans regia and J.

Arbuscular mycorrhizal association regulates global root-seed coordination.

Terrestrial plants exhibit immense variation in their form and function among species. Coordination between resource acquisition by roots and reproduction through seeds could promote the fitness of plant populations. How root and seed traits covary has remained unclear until our analysis of the largest-ever compiled joint global dataset of root traits and seed mass.

Phylogenetic Resolution and Conflict in the Species-Rich Flowering Plant Family Leguminosae.

The Tree of Life is central to evolutionary biology, yet resolving deep, recalcitrant phylogenetic relationships remains challenging due to complex processes such as incomplete lineage sorting (ILS), hybridization, and polyploidization. Although previous phylogenetic studies have advanced our understanding of Leguminosae (Fabaceae), a species-rich and ecologically diverse family, many deep relationships at the tribal and higher levels remain unresolved. Incorporating newly generated genome skimming data for 231 species with previously issued plastid genomic, mitochondrial genomic and transcriptomic data, we reconstructed a phylogeny of the family using whole plastomes, 39 mitochondrial genes, and 1559 low-copy nuclear genes, achieving dense taxonomic sampling across almost all recognized tribes and major unplaced lineages.

Genome sequencing and population genomics provide insights into the demographic history, genetic load, and local adaptation of an endangered Tertiary relict.

Endangered Tertiary relict trees represent an exceptional evolutionary heritage with small and isolated populations, yet little is known about how demographic history, local adaptation, and genetic load have affected their long-term survival and extinction risk. We performed whole-genome sequencing and population genomic analyses on Ulmus elongata L. K.

Increased diversity by cushion plants enhances alpine community productivity and stability.

The relationship between biodiversity and ecosystem functioning is well documented in multiple ecosystems such as grasslands and forests, yet in harsh alpine environments where the formation and maintenance of diversity face significant challenges, it remains largely underexplored. This study examines the role of multiple alpine cushion plant species in promoting plant diversity and enhancing ecosystem functioning through assessments of community biomass production and spatial stability. Cushion-constructed microcommunities (CCMC) exhibit a substantial increase in plant species richness, ranging from 83% to 150%, compared to bare ground areas.

Genomic Insights Into Local Adaptation Across Heterogeneous Understory Habitats and Climate Change Vulnerability.

Understanding adaptive evolution and survival risks in understory herbs is crucial for the effective conservation of biodiversity. How environmental gradients shape species local adaptation patterns is not well understood, nor is how populations of understory herbs respond to a changing climate. In this study, we conducted population genomic analyses of Adenocaulon himalaicum (Asteraceae) with a pan-East Asian distribution, representing a good model for dominant understory herbs to elucidate adaptation mechanisms in heterogeneous forest ecosystems.

Betanin-Mediated Antiherbivore Defense: Functional Significance of Red Pigmentation in Epidermal Salt Bladders of Chenopodium album Leaves.

Plant coloration, predominantly regulated by various natural plant pigments, has been hypothesized to serve crucial ecological functions in plant-animal interactions. Betalains are a rare class of plant pigments synthesized exclusively in specific families within the Caryophyllales order. Their biosynthesis is restricted by the availability of nitrogen.

MEPDB: Database of microExons in plants.

Microexons, ≤ 51-nucleotide (nt), particularly ultra-short ones (1-15 nt), are challenging to identify due to their small size and frequent absence in genome annotations, which limits understanding of their biological roles. Using our developed pipeline, we identified 2398 small internal microexons across 10 diverse plant species, and most of them were not annotated in the reference genomes. These microexons are grouped into 45 conserved microexon clusters based on microexon-tags, which include the coding microexons and portions of flanking exon sequences.

Microrchidia ATPases and DNA 6mA demethylase ALKBH1 act antagonistically on PRC2 to control chromatin structure and stress tolerance.

The Microrchidia (MORC) proteins are conserved GHKL-type ATPases required for chromatin condensation and gene silencing in animals and plants. Here we show that MORC proteins function with Polycomb-Repressive Complex 2 (PRC2) to control chromatin structure, gene expression and stress responses in rice. Rice MORC6b interacts with and stabilizes PRC2 for trimethylated histone H3 lysine 27 (H3K27me3) deposition preferentially at bivalent domains marked by both H3K4me3 and H3K27me3 to repress genes enriched for stress responses.

A new model for the global patterning of spores and pollen grains.

Spores of fungi and seedless plants, and pollen grains of seed plants, are usually characterized by variable global patterns on the surface. However, the mechanisms responsible for the development of these patterns have not been fully understood. We hypothesize that the global pattern of a spore or pollen grain is induced by the stresses resulted from the mismatch between a faster-growing outer part and a slower-growing inner part within the grain and tried to verify the hypothesis by simplifying the developing spores and pollen grains as stressed core/shell structures, simulating the buckling patterns of such structures with different shapes and shell thicknesses through finite element method, and comparing the simulated models with natural spores and pollen grains observed under microscopes.

Extensive Introgression Failed to Erode Species Boundaries Among Multiple Sympatric Closely Related Species of Roscoea.

How species boundaries are maintained among sympatric closely related species experiencing gene flow is a puzzling question in evolutionary biology. Although introgression is commonly documented, the dynamics and gene function of introgression have rarely been explored to probe why frequent introgression does not necessarily destroy species boundaries in sympatry. In this study, we employ whole-genome resequencing data to examine introgression among five closely related species of Roscoea that coexist in a 'sky island' with seventeen distinct morphological traits.

Discovery of Bisindoles that Activate Tumor-Associated Macrophages and Enhance Antitumor Immunity.

The clinical successes in immunotherapy have been staggering but remain partially unsatisfactory. Small molecules may play an important role individually or in combination with antibiotics in this field. Therefore, the aim of this work is to identify small molecules that potentiate antitumor immunity.

Soil Phosphorus Availability Modulates Host Selectivity of Between Legumes and Grasses.

Host selectivity or preference plays a critical role in enabling parasitic plants to identify suitable hosts and influence plant community dynamics. Phosphorus (P) is known to affect the growth of root hemiparasitic plants and their interaction with single host species, but its role in shaping host selectivity across multiple hosts is unclear. In a pot experiment, we used a grass-legume co-culture design and evaluated whether the root hemiparasitic plant exhibits selective parasitism on legumes () versus grasses () and assessed the impact of soil P availability on this preference.

Clonal longevity and the enigmatic flowering of woody bamboos are associated with rates of protein evolution.

Rates of protein evolution (d/d) vary widely across the tree of life. In plants, both life-history traits and GC-biased gene conversion (gBGC) are thought to contribute to this variation, although disentangling their individual contributions remains a challenge. Using information on variation in life-history traits and molecular data in 148 species from Poaceae subfamilies Bambusoideae (mostly woody) and Pooideae (exclusively herbaceous), we investigated the relative importance of modes of reproduction and the non-selective forces of gBGC on protein evolutionary rates between the two subfamilies.

Genome duplications, genomic conflict, and rapid phenotypic evolution characterize the Cretaceous radiation of Fagales.

While many plant lineages display remarkable diversity in morphological form, our understanding of how phenotypic diversity, or disparity, arises in relation to genomic evolution over geologic scales remains poorly understood. Here, we investigated the relationship between phenotypic and genomic evolution in the Fagales, a lineage of woody plants that has been a dominant component of temperate and subtropical forests since the Late Cretaceous. We examine newly generated transcriptomic and trait datasets representing most extant genera and a rich diversity of Cretaceous fossil representatives.

Genome assembly at the chromosome level of Clinopodium barosmum.

Clinopodium barosmum (C. barosmum), a rare species within the genus Clinopodium of the Lamiaceae family in northwestern Yunnan, is highly valued for its exceptional ecological and medicinal properties. This study presents the successful assembly of the chromosome-level genome of C.

Reticulate allopolyploidy and subsequent dysploidy drive evolution and diversification in the cotton family.

Polyploidy and subsequent post-polyploid diploidization (PPD) are key drivers of plant genome evolution, yet their contributions to evolutionary success remain debated. Here, we analyze the Malvaceae family as an exemplary system for elucidating the evolutionary role of polyploidy and PPD in angiosperms, leveraging 11 high-quality chromosome-scale genomes from all nine subfamilies, including newly sequenced, near telomere-to-telomere assemblies from four of these subfamilies. Our findings reveal a complex reticulate paleoallopolyploidy history early in the diversification of the Malvadendrina clade, characterized by multiple rounds of species radiation punctuated by ancient allotetraploidization (Mal-β) and allodecaploidization (Mal-α) events around the Cretaceous-Paleogene (K-Pg) boundary.

Chemical synthesis of glycan motifs from the antitumor agent PI-88 through an orthogonal one-pot glycosylation strategy.

Chemical synthesis of monophosphorylated glycan motifs from the antitumor agent PI-88 has been achieved through an orthogonal one-pot glycosylation strategy on the basis of glycosyl -(1-phenylvinyl)benzoates, which not only accelerated synthesis, but also precluded the potential issues inherent to one-pot glycan assembly associated with thioglycosides. The following aspects were featured in synthetic approaches: 1) synthesis of trisaccharide and tetrasaccharide PI-88 glycans via [1 + 1 + 1] and [1 + 1 + 1 + 1] one-pot orthogonal glycosylation, respectively; 2) synthesis of PI-88 glycan motif pentasaccharide via [1 + 1 + 1] and [1 + 1 + 3] one-pot orthogonal glycosylation; 3) synthesis of hexasaccharide via [1 + 1 + 1] and [1 + 1 + 1 + 3] one-pot assembly.

Test Species Discrimination in Codonopsis (Campanulaceae) Using Genome Skimming Data.

To overcome the limitations of conventional barcoding loci, plastid genome (plastome) and nuclear ribosomal DNA (nrDNA) sequences recovered from genome skimming, proposed as 'super-barcodes' have been suggested as candidates for delimitating recently diverged species or complex plant groups. DNA super-barcodes must be further assessed for their effectiveness in other diverse plant groups. This research focused on the genus Codonopsis, a medicinally significant yet taxonomically complex group characterised by morphological similarity and high phenotypic plasticity in response to environmental conditions.