Search Results (74)

SnRK kinases, central regulators of plant stress response, remain uncharacterized in Taxus—an ancient gymnosperm valued for paclitaxel production. This study aimed to identify the Taxus SnRK family and elucidate its functional roles. Specifically, we identified SnRK genes through genomic analysis and assessed tissue-specific expression via transcriptomics, while regulatory networks were deciphered using WGCNA. To overcome experimental constraints, a PEG-mediated protoplast transient expression system was developed using calli, followed by dual-luciferase assays. Consequently, 19 SnRK genes (2 SnRK1, 4 SnRK2, 13 SnRK3) were identified, with tissue-specific expression revealing TaSnRK1.2 upregulation under methyl jasmonate (MeJA) and in stress-resilient tissues (bark/root). Subsequently, WGCNA uncovered a bark/root-specific module containing TaSnRK1.2 with predicted TF interactions (TaGRAS/TaERF). Critically, homologous dual-luciferase assays demonstrated TaSnRK1.2 activates TaGRAS and TaERF promoters (4.34-fold and 3.11-fold induction, respectively). This study establishes the Taxus SnRK family and identifies TaSnRK1.2 as a hub integrating stress signals (e.g., MeJA) to modulate downstream TF networks, while the novel protoplast system enables future functional studies in this medicinal plant. Full article

Chromosome rearrangements during plant evolution can lead to alterations in genome structure and gene function, thereby influencing species adaptation and evolutionary processes. Gymnosperms, as an ancient group of plants, offer valuable insights into the morphological, physiological, and ecological characteristics of early terrestrial flora. The reconstruction of ancestral karyotypes in gymnosperms may provide critical clues for understanding their evolutionary history. In this study, we inferred the ancestral gymnosperm karyotype (AGK), which comprises 12 chromosomes, and conducted a collinearity analysis with existing gymnosperm genomes. Our findings indicate that chromosome numbers have remained remarkably stable throughout the evolution of gymnosperms. For species with multiplied chromosome numbers, such as gnetophytes, weak collinearities with the AGK were observed. Comparisons between the AGK and gnetophyte genomes revealed a biased pattern regarding retained duplication blocks. Furthermore, our analysis of transposable elements in Welwitschia mirabilis identified enriched regions containing LINE-1 retrotransposons within the syntenic blocks. Syntenic analysis between the AGK and angiosperms also demonstrated a biased distribution across chromosomes. These results provide a fundamental resource for further characterization of chromosomal evolution in gymnosperms. Full article

This study analyzes the lacustrine hydrocarbon source rocks of the Lower Cretaceous in the Erdengsumu sag of the Erlian Basin, evaluating their characteristics and identifying areas with oil resource potential, while also investigating the ancient lake environment, material source input, and controlling factors, ultimately developing a sedimentary model for lacustrine hydrocarbon source rocks. The findings suggest the following: (1) The lower Tengger Member (K₁bt₁) and the Aershan Formation (K₁ba) are the primary oil-producing strata, with an effective hydrocarbon source rock exhibiting a lower limit of total organic carbon (TOC) at 0.95%. The Ro value typically remains below 0.8%, indicating that high-maturity oil production has not yet been attained. (2) The oil generation threshold depths for the Dalestai and Sayinhutuge sub-sags are 1500 m and 1214 m, respectively. The thickness of the effective hydrocarbon source rock surpasses 200 m, covering areas of 42.48 km² and 88.71 km², respectively. The cumulative hydrocarbon generation intensity of wells Y1 and Y2 is 486 × 10⁴ t/km² and 26 × 10⁴ t/km², respectively, suggesting that the Dalestai sub-sag possesses considerable petroleum potential. The Aershan Formation in the Chagantala sub-sag has a maximum burial depth of merely 1800 m, insufficient to attain the oil generation threshold depth. (3) The research area’s productive hydrocarbon source rocks consist of organic matter types I and II₁. The Pr/Ph range is extensive (0.33–2.07), signifying a reducing to slightly oxidizing sedimentary environment. This aligns with the attributes of small fault lake basins, characterized by shallow water and robust hydrodynamics. (4) The low ratio of ∑nC₂₁₋/∑nC₂₂₊ (0.36–0.81), high CPI values (>1.49), and high C₂₉ sterane concentration suggest a substantial terrestrial contribution, with negligible input from aquatic algae–bacterial organic matter. Moreover, as sedimentation duration extends, the contribution from higher plants progressively increases. (5) The ratio of the width of the deep depression zone to the width of the depression in the Erdengsumu sag is less than 0.25. The boundary fault scale is small, its activity is low, and there is not much input from the ground. Most of the source rocks are in the reducing sedimentary environment of the near-lying gently sloping zone. Full article

Representatives of Dermestidae (skin, larder, and carpet beetles) play a crucial role as decomposers in global ecosystems, facilitating the recycling of animal and plant biomass to sustain nutrient cycling. Despite their widespread ecological presence and functional importance, the fossil record of their larval stages has remained sparse, with previous documentation limited to occasional discoveries. This study significantly expands the larval fossil record by identifying 36 amber-preserved specimens from the Cretaceous, Eocene, and Miocene time slices, obtained from deposits distributed globally. By challenging the historical view of larval fossil rarity, we reveal morphological changes in defensive setae over geological time, demonstrating that Cretaceous and later fossil larvae possess significantly longer absolute and relative setal lengths compared to their extant counterparts. These findings, bolstered by quantitative comparisons of setal and body dimensions across fossil and extant representatives, indicate evolutionary adaptations in defensive structures dating back at least 100 million years. Our results offer new insights into the paleobiology of the group Dermestidae, highlighting how the morphology of larvae potentially reflects historical ecological pressures and resources availability. This study emphasizes the importance of integrating fossil evidence with comparative morphology to elucidate the evolutionary trajectories and functional roles of larvae in ancient terrestrial ecosystems. Full article

Understanding morphological descriptions of plants documented by ancient peoples over 1000 years ago and identifying the species they described are critical for reconstructing the natural geographic distribution of plant taxa, tracking taxonomic variations, and inferring historical climate dynamics. Analyzing shifts in plant communities and climatic conditions during this period is essential to unravel the interplay among floristic composition, climate fluctuations, and anthropogenic impacts. However, research in this field remains limited, with greater emphasis placed on plant taxa from hundreds of millions of years ago. Investigations into flora and climate during the last two millennia are sparse, and pre-millennial climatic conditions remain poorly characterized. In this study, a historical text written 1475 years ago was analyzed to compile plant names and morphological features, followed by taxonomic identification. The research identified three gymnosperm species (one in Pinaceae, two in Cupressaceae), 1 Tamaricaceae species (dicotyledon), and 19 dicotyledon species. However, three plant groups could only be identified at the genus level. Using textual analysis and woody plant coexistence methods, the climate of 1475 years ago in western Henan Province, located in the middle-lower Yellow River basin in East Asia, was reconstructed. Results indicate that the mean temperature of the coldest month (MTCM) was approximately 1.3 °C higher than modern values. In comparison, the mean temperature of the warmest month (MTWM) and mean annual temperature (MAT) were lower than present-day levels. This suggests slightly cooler overall conditions with milder seasonal extremes in ancient Luoyang—a finding supported by contemporaneous studies. Furthermore, annual precipitation (AP), precipitation of the warmest quarter (PWQ), and precipitation of the coldest quarter (PCQ) in the Luoyang region 1475 years ago exceeded modern measurements, despite the area’s monsoonal climate. This suggests significantly higher atmospheric moisture content in ancient air masses compared to today. This study provides floristic and climatic baseline data for advancing our understanding of global climate variability at millennial scales. Full article

Ancient tea plantations possess extremely important economic and cultivation value. In China, ancient tea plantations with trees over 100 years old have been preserved. However, the status of soil microorganisms, soil fertility, and soil heavy metal pollution in these ancient tea plantations remains unclear. This study took four Dancong ancient tea plantations in Fenghuang, Chaozhou City, and Guangdong Province as the research objects. Soil samples were collected from the surface layer (0–20 cm) and subsurface layer (20–40 cm) of the ancient tea trees. The rhizosphere soil microbial diversity and soil nutrients were determined. On this basis, the soil fertility was evaluated by referring to the soil environmental quality standards so as to conduct a comprehensive evaluation of the soil in the Dancong ancient tea plantations. This study found that Proteobacteria, Acidobacteriota, Chloroflexi, and Actinobacteria were the dominant bacteria in the rhizosphere soil of the Dancong ancient tree tea plantation. Ascomycota and Mortierellomycota are the dominant fungal phyla. Subgroup_2, AD3, Acidothermus, and Acidibacter were the dominant bacterial genera. Saitozyma, Mortierella, and Fusarium are the dominant fungal genera. The redundancy analysis (RDA) revealed that at the bacterial phylum level, Verrucomicrobia showed positive correlations with alkali-hydrolyzable nitrogen (AN), available potassium (AK), and total nitrogen (TN); Proteobacteria exhibited a positive correlation with available phosphorus (AP); and Gemmatimonadetes was positively correlated with total potassium (TK). At the fungal phylum level, Ascomycota demonstrated a positive correlation with TK. TN, AN, and TK were identified as key physicochemical indicators influencing soil bacterial diversity, while TN, AN, AP, and AK were the key physicochemical indicators affecting soil fungal diversity. This study revealed that the soil of Dancong ancient tea plantations has reached Level I fertility in terms of TN, TP, SOM, and AP. TK and AN show Level I or near-Level I fertility, but AK only meets Level III fertility for tea planting, serving as the main limiting factor for soil fertility quality. Considering the relatively abundant TK content in the tea plantations, potassium-solubilizing bacteria should be prioritized over blind potassium fertilizer application. Meanwhile, it is particularly noteworthy that AN and SOM are at extremely high levels. Sustained excess of AN and SOM may lead to over-proliferation of dominant microorganisms, inhibition of other functional microbial communities, and disruption of ecological balance. Therefore, optimizing nutrient input methods during fertilization is recommended. Full article

Cycads, renowned as “living fossils”, are among the most ancient extant seed plants, playing a crucial role in understanding plant evolution and sex differentiation. Despite their importance, research on their genetics and sex differentiation remains scarce. This study investigates three species, represented by six samples, collected from various regions in Fujian Province, China, using whole-genome resequencing on the Illumina platform. The sequence data underwent rigorous quality control, alignment, and variant detection, focusing on SNP and InDel distribution and annotation. Among the studied species, Cycas revoluta exhibited the highest number of SNPs and the greatest heterozygosity values. Based on SNP data, phylogenetic trees and principal component analysis revealed distinct clusters, with the three C. revoluta samples forming one cluster, while the two C. szechuanensis samples and the C. taiwaniana sample were grouped separately. Gene function using COG and GO annotations, and KEGG enrichment analysis, all highlighted differences in genomic structure and functional gene distribution between male and female cycads. Notably, genes associated with sex differentiation, such as MADS-box and auxin-responsive protein genes, were shown, while other transcription factors showed distinct annotations and enrichment patterns based on sex. This study improves our understanding of genetic variation, evolutionary relationships, and gene enrichment in cycads, providing a foundation for conservation, cultivation, and insights into sex differentiation mechanisms in these ancient plants. Full article

Apocarotenoids are ancient signaling molecules that have played crucial roles in biological communication and adaptation across evolutionary history. Originating in cyanobacteria, these molecules have diversified significantly in plants, where they contribute to stress perception, developmental regulation, and environmental responses. While some apocarotenoids, such as abscisic acid (ABA) and strigolactones (SLs), have been formally classified as plant hormones due to the identification of specific receptors, many others remain functionally enigmatic despite their profound effects on gene regulation and plant physiology. In this study, we focus on β-carotene-derived apocarotenoids that lack identified receptors, shedding light on their potential signaling roles beyond traditional hormone pathways. By synthesizing current knowledge, we highlight key gaps in understanding their biosynthesis, transport, perception, and downstream effects. Addressing these gaps is essential for unraveling the full scope of apocarotenoid-mediated signaling networks in plants. A deeper understanding of these molecules could not only redefine plant hormone classification but also open new avenues for improving crop resilience and stress adaptation in the face of climate change. Full article

Trans-species polymorphisms (TSPs) are fundamental to preserving ancient genetic diversity, yet the evolutionary forces driving their long-term maintenance remain largely unexplored. Here, we investigate genome-wide TSPs in two Cucumis species, cucumber and melon, using whole-genome sequencing data from over 1200 accessions. A total of 5149 TSPs were identified, which predominantly located in genic and promoter regions. Coalescent analysis indicated that both gene flow and balancing selection have contributed to the persistence of these ancestral alleles. Moreover, among the 99 genes with shared coding-region polymorphisms, two genes that cluster by alleles rather than by species provide evidence of long-term balancing selection. These genes are involved in the immune and stress response processes with pleiotropic effects. Our findings elucidate the complex evolutionary forces driving TSPs in Cucumis, providing mechanistic insights into the maintenance of intraspecific genetic diversity in plants across deep evolutionary timescales. Full article

The WUSCHEL-related homeobox (WOX) belongs to a plant-specific transcription factor gene family that plays crucial roles in plant growth and development. Barley ranks as the fourth global cereal crop and is recognized as a model crop for the study of cereal genetics. However, genome-wide characterization, functional validation, and stress-related studies of the WOX gene family in barley remain limited, hindering efforts to leverage their potential for improving salt tolerance and regeneration efficiency in breeding programs. In this study, we identified 12 HvWOX genes assigned from chromosome 1 to chromosome 5. Phylogenetic analysis revealed that these HvWOX genes can be classified into three clades (WUS, ancient, and intermediate). Gene structure analysis revealed that the exon numbers of HvWOX genes varied in the WUS and intermediate clades but were highly conserved in the ancient clade. Tissue-specific analysis revealed that the most common HvWOX genes were highly expressed in reproductive tissues such as anthers or ovaries. Cis-element analysis suggested that there were multiple stress- and hormone-responsive elements in the HvWOX gene promoters. In addition, overexpression of HvWOX8 in Arabidopsis significantly enhanced root elongation under salt stress (50–100 mM NaCl), suggesting its direct role in salt tolerance. Transcriptomic analysis further revealed that HvWOX8 modulates hormone signaling and electron transfer pathways during ATP synthesis under stress conditions. In conclusion, our results provided a comprehensive understanding of the gene characteristics, expression patterns, and potential roles of barley WOX genes. Full article

Gene duplication, as a prevalent phenomenon in the tree of life, provides a potential substrate for evolution. However, its role in the Aurantioideae remains unclear. In this study, we systematically identified, for the first time, a comprehensive landscape of five types of gene duplication in the genomes of 26 species within Aurantioideae, focusing on dissecting the duplication patterns, their potential evolutionary significance, and their impact on gene function and expression. Our results showed that the tandem duplication (TD) was a predominant duplication type and confirmed a shared ancient whole-genome duplication (γWGD) event within Aurantioideae. Ka/Ks indicated that all duplication types are under purifying selection pressure, with TD and proximal duplication (PD) undergoing rapid functional divergence. Gene Ontology (GO) enrichment analysis revealed functional specialization among different duplication types, collectively contributing to genome evolution. In addition, comparing the gene expression differentiation of the five gene duplication types between the outer and inner pericarps of Citrus maxima ‘Huazhouyou’, it was found that the proportion of gene expression differentiation in the exocarp was generally higher, suggesting tissue-specific functional roles for duplicated genes in the peel. Furthermore, gene conversion events revealed that Citrus sinensis and Citrus maxima ‘Huazhouyou’ experienced more gene conversion events, supporting that C. sinensis originated through hybridization with C. maxima as the maternal parent. Finally, the comparative analysis of gene families among 26 species in Aurantioideae revealed that small gene families (1–3 members) accounted for a substantial proportion in all species, indicating a lack of recent large-scale genome duplication events in this subfamily. These findings fill a gap in the understanding of gene duplication in Aurantioideae and provide a theoretical foundation for exploring the evolutionary mechanisms and breeding improvements within this group. Additionally, our study offers new insights into the contribution of gene duplication to functional diversification and ecological adaptation in other plants. Full article

Ancient introgression is an infrequent evolutionary process often associated with conflicts between nuclear and organellar phylogenies. Determining whether such conflicts arise from introgression, incomplete lineage sorting (ILS), or other processes is essential to understanding plant diversification. Previous studies have reported phylogenetic discordance in the placement of Xanthoceras, but its causes remain unclear. Here, we analyzed transcriptome data from 41 Sapindaceae samples to reconstruct phylogenies and investigate this discordance. While nuclear phylogenies consistently placed Xanthoceras as sister to subfam. Hippocastanoideae, plastid data positioned it as the earliest-diverging lineage within Sapindaceae. Our coalescent simulations suggest that this cyto-nuclear discordance is unlikely to be explained by ILS alone. HyDe and PhyloNet analyses provided strong evidence that Xanthoceras experienced ancient introgression, incorporating approximately 16% of its genetic material from ancestral subfam. Sapindoideae lineages. Morphological traits further support this evolutionary history, reflecting characteristics of both contributing subfamilies. Likely occurring during the Paleogene, this introgression represents a rare instance of cross-subfamily gene flow shaping the evolutionary trajectory of a major plant lineage. Our findings clarify the evolutionary history of Xanthoceras and underscore the role of ancient introgression in driving phylogenetic conflicts, offering a rare example of introgression-driven diversification in angiosperms. Full article

Honey is a sweet substance laboriously collected and crafted from nectar by bees, and since ancient times, it has been deeply cherished by humans for its unique flavor and nutritional value. Litchi honey stands out among various types of honey with its unique flavor and sweet taste, and it is particularly favored by consumers. In accordance with the testing methodologies specified in relevant Chinese national standards, we conducted an exhaustive analysis of the physicochemical properties of six litchi honey samples in Southern China. The results showed that the moisture content fell within a range of 17.18% to 22.7%, while the electrical conductivity remained below 0.28 mS/cm, and amylase activity surpassed 7.7 mL/(g·h). The fructose content varied from 36.5% to 39.6%, with glucose content ranging between 30.57% and 37.63%. The combined total of these two monosaccharides was found to be within the spectrum of 69.63% to 77.23%, and sucrose content was recorded between 0.59% and 1.15%. The F/G was between 1.05 and 1.28, the proportion of fructose in reducing sugars ranged from 51.28% to 56.22%, and the maltose content was between 1.09% and 1.51%. The HMF content was measured between 1.04 and 3.49 mg/kg. Moreover, the presence of C-4 plant sugars was absent in all tested honey samples. These results definitively demonstrate that the physicochemical attributes of all litchi honey samples align with the standards set forth by Chinese national regulations and international authorities such as CODEX. During our in-depth examination of volatile constituents, we identified 26 common compounds, with trans-linalool oxide, linalool, lilac aldehyde B, lilac aldehyde D, α-terpineol, and cedrol emerging as pivotal in crafting the unique flavor and aroma profile of litchi honey. Additionally, the detection of methyl cyclosiloxane in litchi honey has garnered our attention, necessitating a comprehensive investigation into the honey production process. In conclusion, this study not only establishes a robust scientific basis for the quality assurance and product development of litchi honey but also provides valuable reference information for consumers in their selection of honey products. Full article

Studying paleoclimatic conditions across geological epochs is essential for understanding climate evolution and its influence on Earth’s biosphere. Leaf macrofossils serve as a crucial data source for reconstructing ancient climates due to their sensitivity to environmental changes. Advanced analytical methods, such as the Climate Leaf Analysis Multivariate Program (CLAMP) and the coexistence approach (CA), enable precise assessment of past climatic parameters using fossilized leaf remains. The Erzhilansay locality, dated to the early Miocene, represents a remarkable site with exceptionally preserved and diverse plant fossils, making it pivotal for paleoclimatic reconstructions. This study reveals that mean annual temperatures and summer temperatures in the early Miocene were relatively stable over millions of years. In contrast, winters were notably milder, exhibiting warmer and more consistent conditions. Precipitation levels were significantly higher, fostering the development of dense vegetation, unlike the arid environment seen today. These findings underscore the importance of employing integrated methodologies to reconstruct ancient climates and interpret geological-scale climate changes. The study also offers critical insights into climate dynamics, supporting the development of strategies to mitigate current environmental challenges. Full article

All multicellular organisms undergo senescence, but the continuous division of the vascular cambium in plants enables certain tree species to survive for hundreds or even thousands of years. Previous studies have focused on the development of the vascular cambium, but the mechanisms regulating age-related changes remain poorly understood. This study investigated age-related changes in the vascular cambium of P. euphratica trees aged 50 to 350 years. The number of cambium cells in the 50-year-old tree group was 10 ± 2, while the number of cambium cells in the 200-year-old and 350-year-old tree groups significantly decreased. The thickness of the cambium cells exhibited a similar trend. In addition, the net photosynthetic and transpiration rates continue to increase with age, but no notable differences were found in factors like average leaf area, palisade tissue thickness, and stomatal density. A total of 6491 differentially expressed genes (DEGs) were identified in the vascular cambium of P. euphratica at three distinct ages using RNA sequencing. The expression patterns of DEGs associated with cell division and differentiation, lignin biosynthesis, plant hormones, and transcription factors were analyzed. DEGs related to XTH, EXP, PAL, C4H, ABA, Br, GA, and others are highly expressed in older trees, whilst those encoding expansins, kinases, cyclins, 4CL, Auxin, Eth, SA, and others are more prevalent in younger trees. Gene family members, such as NAC, MYB, HD-ZIP III, WRKY, and GRF, have various regulatory functions in the vascular cambium. The findings offer insights into how ancient P. euphratica trees maintain vitality by balancing growth and aging, providing a foundation for future research on their longevity mechanisms. Full article