Mapping chromatin quantitative trait loci (cQTLs) is crucial for elucidating the regulatory mechanisms governing gene expression and complex traits. However, current cQTL mapping methods suffer from limited detection power, particularly at existing sample sizes, and are constrained by peak-calling accuracy. To address these limitations, we present CACTI, a novel method that improves cQTL mapping by leveraging correlations between neighboring regulatory elements. Across diverse histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3 and H3K36me3) and cell types, CACTI identifies 51%-255% more cQTL signals compared to conventional single-peak-based approaches. Using CACTI, we generate a comprehensive cQTL map for the five histone marks across multiple cell types and perform colocalization analyses with GWAS loci from 44 complex traits. CACTI cQTLs colocalize with 6%-47% of GWAS loci, which is on average 15%-424% more than the standard cQTL mapping method across different marks. 24%-75% of colocalized GWAS loci show no colocalization with eQTLs. This underscores CACTI's unique ability to uncover regulatory mechanisms that would otherwise remain undetected by eQTL analysis alone, significantly improving the functional interpretation of GWAS findings.
Prickly pear cacti spines that become embedded in the skin are associated with local and systemic inflammatory conditions as well as allergic contact dermatitis. Preclinical studies have suggested that extracts from the prickly pear cactus may be used in medicine due to their anti-inflammatory properties. This manuscript discusses complications and therapeutic possibilities related to the cacti.
The rise of biodiversity is shaped by variation in speciation rates. Across many taxonomic groups, both trait values and the rates at which traits evolve have been proposed to influence diversification, but these factors can act independently. Here, we test two competing hypotheses in the cactus family, that speciation depends on flower length variation or on the rate of evolutionary change in flower length. Across >750 species in 107 genera, we find that flower length is only weakly related to speciation, whereas the rate of flower-length evolution is a strongly positive predictor. Moreover, flower length and rate of evolutionary change in flower length are only weakly correlated, indicating that rapid change, rather than any particular floral morphology, underlies cactus diversification. These results challenge expectations that specialized morphologies accelerate diversification, suggesting instead that in cacti, it is the tempo of floral change, rather than any particular floral form, that explains their extraordinary diversity.
Developmental genetic studies in model species have unveiled genes that modulate organ size. The roles of homologs of these genes in angiosperms with complex ontogenies such as the "flower shoots" of Cactaceae have not yet been analyzed. Here we present histological, cellular, and transcriptome analysis from flower buds in two developmental stages for two cacti species with contrasting flowers: Disocactus speciosus and D. eichlamii. Analyses of cell area, cell number, and overall tepal size from floral buds were performed to determine if differential cell proliferation and expansion occurred. We also performed transcriptome analyses derived from size 1 and 2 floral buds, differential gene expression analysis, followed by KEGG enrichment. Comparative histological and cellular analyses in Disocactus tepals indicate that while size 1 cells are similar in size in both species, a prolonged expansion phase takes place in D. speciosus. Transcriptome analyses suggest similar overall expression patterns per size, but differential expression of genes related to tepal growth were documented like BIG PETALp (BPp), down-regulated in size 1 vs size 2 in D. eichlamii. In this species we found BIG BROTHER (BB) up-regulated in size 1 vs size 2. In contrast, in D. speciosus, we found two copies of BB, one copy up-regulated and the other down-regulated, as well as NAC100 which could be related with the final size of the flower in this species. This study integrates cellular and molecular data related with the development of differential organ size in Cactaceae. We found that a prolonged period of cell proliferation and expansion in D. speciosus tepals in contrast with D. eichlamii tepals seems to correlate with its final size, while transcriptome analyses point to several DEGs that should be further investigated through gene expression analyses as well as other reverse genetics approaches.
We present CACTI, a masked autoencoding approach for imputing tabular data that leverages the structure in missingness patterns and contextual information. Our approach employs a novel median truncated copy masking training strategy that encourages the model to learn from empirical patterns of missingness while incorporating semantic relationships between features - captured by column names and text descriptions - to better represent feature dependence. These dual sources of inductive bias enable CACTI to outperform state-of-the-art methods - an average R 2 gain of 7.8% over the next best method (13.4%, 6.1%, and 5.3% under missing not at random, at random and completely at random, respectively) - across a diverse range of datasets and missingness conditions. Our results highlight the value of leveraging dataset-specific contextual information and missingness patterns to enhance imputation performance. Code is publicly available at github.com/sriramlab/CACTI.
The structural and dynamic properties of columnar cacti are key inputs for stability analyses; however, no previous studies have been able to resolve these properties from full-scale tests in situ. I present an approach using non-destructive ambient vibration data to measure the resonance properties (modal frequencies and mode shapes) of single-stem saguaro cacti and resolve key biomechanical properties. I tested the approach on 11 spears in the Tucson, Arizona region, United States. Saguaro fundamental frequencies ranged between 0.55 and 3.7 Hz with damping ratios of 1.5-2.1%. Additional higher-order modes were identified below 10 Hz. Fundamental frequencies scaled linearly with the ratio of stem diameter to height-squared, but deviated from analytical theory due to an observed increase in Young's modulus for taller plants. Calculated ratios between second- and first-order bending frequencies also deviated from beam theory, indicating that stiffness decreases vertically for a given stem, especially for taller spears. These deviations both likely arise from the morphology of internal wooden ribs, which provide the main flexural rigidity. Numerical modeling at one site confirmed the cantilever approximation and height-dependent stiffness, revealing an empirically derived Young's modulus that decreased exponentially from 107 Pa at the top of the stem to 108 Pa at its base. Twelve days of monitoring at another site showed that frequencies drift with diurnal cycles, suggesting softening of the outer tissue as temperatures warm during the day. This non-destructive approach for structural assessment provides valuable data for biomechanical characterization and stability and ecological analyses.
The hyperarid-semiarid gradient of the western Andes, from the coastal Atacama Desert to central Mediterranean Chile, hosts exceptional plant endemism driven by palaeoclimatic oscillations, rugged topography and long-term isolation. Here, we use the columnar cactus genus Leucostele as a model to (1) quantify the influence of geographic isolation and topographic heterogeneity on genome-wide divergence, and (2) test whether zones of secondary contact foster genetic admixture. We genotyped 151 individuals from 20 populations of Leucostele using 9397 SNPs to assess spatial genetic structure, isolation by distance and the influence of terrain ruggedness and geographic isolation on admixture. Spatial ancestry analyses delineated ten latitudinal genetic clusters, with 8 populations exhibiting >75 % ancestry assignment to a single cluster and 12 showing varying degrees of admixture. Genetic differentiation increased with geographic distance, revealing strong isolation by distance across the Atacama Desert to southern central Chile. Admixture, quantified as Shannon entropy, varied among populations and decreased significantly with both increasing terrain ruggedness and greater geographic isolation. Our study reveals that rugged topography and spatial isolation promote genomic divergence by limiting gene flow and fostering distinct genetic clusters while less rugged terrain facilitates secondary contact and admixture, showing that these barriers remain permeable and reproductive isolation is incomplete. This dual influence of topographic heterogeneity underpins the dynamic evolutionary mosaic observed across the coastal Atacama Desert-central Chile gradient.
Pollination niches, which encompass the factors influencing pollen exchange among angiosperms, are fundamental to understanding reproductive success and the intricate eco-evolutionary dynamics of plants. In this study, we investigated pollination niche shift among four sympatric Eriosyce cacti with restricted distributions in the South American Mediterranean region. Utilizing a comprehensive approach-including pollination niche analysis, pollinator color perception studies, reproductive output assessments, molecular phylogenetics, gene flow analyses, and species distribution modeling-we revealed a significant pollination niche displacement in E. chilensis and its variety, E. chilensis var. albidiflora. These taxa transitioned from a hummingbird-pollinated system prevalent in the Eriosyce sect. Neoporteria, characteristic of their sister species E. litoralis, to a bee-pollination strategy akin to that of the co-occurring species E. mutabilis. This shift highlights a simultaneous convergence of E. chilensis toward E. mutabilis and divergence from E. litoralis in pollination strategies, providing adaptive advantages by reducing pollen limitation and enhancing seed production. The morphological and flowering phenological similarities between E. chilensis and E. mutabilis suggest the evolution of a shared advertising display, potentially indicative of floral mimicry, wherein both species benefit from attracting shared bee pollinators. Genomic analyses reveal distinct pollinator-driven selection pressures, with E. chilensis/E. albidiflora exhibiting traits that promote reproductive isolation from E. litoralis, supporting a scenario of rapid speciation occurring within the past half of million years in the absence of geographic barriers. These findings underscore the pivotal role of pollinator interactions in shaping angiosperm speciation and biodiversity, highlighting their dynamic influence on ecological and evolutionary processes.
Comparing field and horticultural (common garden) conditions is particularly relevant to understanding many aspects of plant physiology, phenotypic plasticity, and environmental adaptation. Species that reproduce through vegetative propagation offer a unique opportunity to study gene expression changes in the same genetic material across wild and controlled environments. Here, we investigate patterns of differential gene expression in five target species of the genus Cereus Mill. (Cactaceae), which occur across distinct biomes. The studied species include Cereus jamacaru DC, C. calcirupicola Ritter, C. pierre-braunianus Esteves, C. hildmannianus K.Schum, and C. fernambucensis Lem. Epidermal tissue was collected from three adult individuals per species in the wild, alongside stems for greenhouse cultivation under standardized soil, lighting, nutritional, and watering conditions. After one year, epidermal tissue was recollected from the same individuals for RNA extractions. Whole transcriptomes from wild and common garden samples (30 transcriptomes) were analyzed for differential gene expression and co-expression patterns. Genes upregulated under wild conditions (WT) predominantly related to stress response and defense pathways, contrasting with those expressed in common garden (CG) conditions. Gene expression plasticity across diverse metabolic pathways highlights significant environmental responses, with distinct patterns linked to the phytogeographic domain and biome-specific factors. Cereus species demonstrate significant gene expression plasticity, with stress-response and metabolic regulation genes enabling adaptation to diverse environmental pressures. This flexibility underscores their ecological and evolutionary resilience in arid and nutrient-poor habitats.
Biological invasions impact ecosystems worldwide, including through changing the behaviour of native species. Here, we used camera traps to investigate the effects of invasive Opuntia spp. on the habitat use of 12 mammal species in Laikipia County, Kenya, an internationally important region of mammalian biodiversity. We found that Opuntia impacted mammal occupancy and activity. These effects were evident when Opuntia was considered at both site level and landscape scales; however, some mammal species showed different responses to increasing Opuntia at these two scales. The effects of Opuntia were generally context dependent, with their strength and direction varying among mammal species and between seasons. As well as having important implications for mammal conservation, ecosystem functioning and the future spread of Opuntia, our findings highlight behavioural changes in large mammals as a potentially important pathway through which invasive species impact ecosystems.
[This corrects the article DOI: 10.1016/j.heliyon.2022.e12618.].
Cipocereus minensis (Cactaceae) is a columnar, shrubby cactus endemic to the Campo Rupestre (Brazilian altitude grassland), often found associated with termite nests (Blattaria: Isoptera). This study investigates, for the first time, the association between cacti and termites, exploring the potential influence of termite nests on cactus production and phenology. Specifically, we assessed whether cacti in termite nests exhibited (i) different phenological pattern; (ii) greater reproductive structures produced; (iii) higher buds to immature fruits conversion rate; (iv) different responses in productivity related to temperature and rainfall; and (v) the termite species inhabiting the nests. Weekly quantitative phenological monitoring was conducted on 62 cacti (31 growing on termite nests, and 31 on rocky substrate) over 94 weeks (2018-2020). Temperature and rainfall were measured, and termites identified. Circular statistics were used to assess phenology, while GLMMs tested the effects of temperature, rainfall and substrate on the production of reproductive structures. For both substrates, C. minensis flowered and fruited throughout the year, with two to three more pronounced peaks annually, mainly in the dry season. GLMMs indicated that substrate influenced how cacti responded to climate fluctuations, particularly temperature. Seven termite species were identified in 24 inhabited nests, with up to three species per nest, while seven nests were abandoned. Cacti associated with termite nests exhibited greater flower buds and fruit production, and were more affected by climate at the onset of the phenological cycle (timing). Termite nests may provide microclimatic regulation (temperature e moisture) and can promote nutrient cycling, acting as "fertility islands" in the nutrient-poor Campo Rupestre soil, suggesting that the cacti grown in this substrate have access to more resources, such as nutrients and moisture.
This data article presents a multimodal, non-invasive dataset documenting the physiology and growth stages of Stenocereus queretaroensis (pitayo), a native species from the arid and semi-arid regions of Southern Zacatecas, Mexico. In particular, Stenocereus spp. are important cacti in the region due to its nutritional properties, role as an economic resource, and cultural significance.It is worth emphasising that these cacti traditionally grow wild (i.e., without deliberate cultivation); accordingly, controlled cultivation is uncommon and remains understudied. With the aim of producing a formal, comprehensive analysis and compendium, the data were collected across multiple phenological stages to provide a complete representation of the plant development cycle, from vegetative growth through to fruiting. To achieve this, the collection process combined high-resolution multispectral imaging with field spectrometry in the 400-700 nm range. Standardized acquisition protocols were applied in field conditions to capture consistent reflectance data, and environmental variables such as illumination, temperature, and geographic coordinates were recorded for each session to ensure reproducibility. The dataset integrates several components: (i) multispectral images that provide spatial information on canopy and structural characteristics, (ii) field spectral signatures with detailed reflectance values for each sampled plant, and (iii) metadata describing phenological stage, acquisition date and time, environmental conditions, and equipment settings. For subsequent analysis, data was preprocessed and normalized to enable reliable comparisons between growth stages and across acquisition sessions, resulting in a clean, structured resource ready for computational analysis. In this regard, this dataset has been organized to facilitate its direct application across multiple research and development contexts. Specifically, potential applications include the training and validation of machine learning and computer vision models for automated phenological stage classification, harvest time estimation, and development of species-specific vegetation indices. Moreover, owing to its standardized design, the resource can serve as a benchmark for comparing methods, validating algorithms, and supporting reproducible workflows in precision agriculture and remote sensing. Beyond Stenocereus queretaroensis, the documented acquisition and preprocessing methodology can be replicated or adapted to generate similar multimodal datasets for other climate-resilient crops, particularly those cultivated in arid and semi-arid regions. This could enable comparative analyses across species and provide a reference for extending multimodal sensing approaches to underrepresented plants of ecological and economic importance.
The cactus Pelecyphora chihuahuensis is endemic to northern Mexico and represents an interesting subject on the integration of classical taxonomy with modern biotechnological tools to solve conservation issues. Because of its narrow ecological range and high ornamental value, the species is increasingly at risk from degradation of its habitats, climate change, and plant poaching. This review includes current knowledge on its taxonomic status, ecological distribution, and conservation needs, with a focus on biotechnological means to aid its preservation. Aspects such as molecular markers, next-generation sequencing, and previously reported GIS-based species distribution models provide valuable insights into its identity and ecological niche. Biotechnological tools for ex situ conservation include in vitro propagation and cryopreservation. Potential applications of CRISPR-Cas and synthetic biology in preserving rare cacti are also discussed. By uncovering gaps, this review opens a window of opportunity to urgently promote the sustainable management of P. chihuahuensis and related endangered cacti by merging biotechnology with ecology and taxonomy, the results presented here underscore the importance of integrating scientific findings into future research that supports the development and implementation of effective policies that prioritize the conservation and biocultural preservation of arid-land flora, ensuring that both ecological integrity and cultural values are maintained for these unique ecosystems.
Selenicereus undatus (S.undatus) is an epiphyte cacti and it is largely grown in Asia. Drought, salinity and heavy metal stress are the major restricting factors in its growth and productivity in nature. Class III peroxidases (PODs) are important genes in response of plants to oxidative and abiotic stresses, as was found by a number of studies. Nevertheless, the genomic structure and functional analyses of POD genes in S. undatus have not been well investigated. In this study, the physiological and molecular responses of Selenicereus undatus to single and multi-factorial environmental stresses were investigated in comparison with melatonin supplementation. However, stress significantly increased the activities of peroxidase (POD), proline content and hydrogen peroxide (H₂O₂) accumulation, which were strongly attenuated by the application of melatonin through maintaining an equilibrium in redox status to promote growth. Transcriptome analysis observed obvious differential expression in the HuPOD gene family when under different stress treatments. In the S. undatus genome 75 HuPOD genes were identified and classified into five phylogenetic subgroups. Among them, HuPOD-02/05/06/12/13/29 were strongly up-regulated under combined stress while HuPOD-36/56 showed slight downregulation to single stresses conditions. KEGG enrichment analysis revealed that under single and multi-factorial stresses, differentially expressed HuPOD genes were significantly enriched in the MAPK signaling pathway, glutathione metabolism, and phenylpropanoid biosynthesis, suggesting pivotal roles in oxidative stress regulation and signal transduction in S. undatus. RT-qPCR validation confirmed RNA-seq expression patterns for five representative genes (HuPOD-01/10/36/56/62), with HuPOD-10/62 showing the highest induction under melatonin-supplemented stresses (Cd+S+D+M). These findings suggested that POD gene family may participate in the response to single and multifactorial stress in S.undatus This study provides a scientific basis for the further development and functional validation of the POD gene family in S.undatus.
Pediocactus bradyi, a semi-globose cactus endemic to northern Arizona, displays a root-contraction mechanism to survive extreme drought: its roots contract, pulling the stem below ground during dry periods, re-emerging once rains return. To quantify how root contraction shapes population dynamics, we developed an integral projection model based on 31 years of demographic data from a P. bradyi population on the Navajo Nation Off-Reservation Trust Land. We explored two scenarios: one including root contraction and one excluding it. We found that, being ∼10% of the individuals and mostly confined to smaller individuals, root contraction did not have an effect on the long-term population growth [λ = 1.041 (1.039, 1.303) with contraction vs. λ = 1.044 (1.035, 1.289) without]. Also, we show that larger individuals have higher survival and reproductive rates, while growth declines beyond 35 mm in diameter. An elasticity analysis confirmed that survival and growth are the main vital rates affecting population growth, followed by root elongation after contraction. Thus, while root contraction may improve individual survival, elongation is in fact more important at the population level. Therefore, as with most cacti species, conservation efforts should focus on ensuring the survival of large individuals irrespective of their root contraction status.
The development of high-efficiency fog collection technology is crucial for alleviating freshwater scarcity. Inspired by the efficient water-harvesting mechanisms of organisms such as the Namib Desert beetle and cacti, this study fabricates a biphilic surface on aluminum (Al), comprising elliptical superhydrophilic (SHL) microregions patterned within a superhydrophobic (SHB) background. The elliptical morphology of SHL microregions can be controlled by adjusting both the defocus distance of the cylindrical lens and the pulse width in a femtosecond laser system. Importantly, these microregions facilitated droplet formation and growth at their centers, regardless of orientation, due to the dominant influence of Laplace pressure gradients. In contrast, rectangular microregions exhibited no such capability. The biphilic surface exhibited significant improvements in fog collection efficiency, outperforming traditional SHB surfaces by factors of 14.2, 5.0, and 3.8 in environments with 70%, 85%, and 95% relative humidity, respectively. Furthermore, the surface patterned with elliptical microregions exhibited a marked advantage in fog collection performance compared to surfaces with rectangular microregions of equivalent area. By optimizing geometrically gradient micropatterns, this study highlights the critical role of edge morphology in controlling droplet self-transport, offering an innovative surface solution for efficient fog collection and expanding the application prospects of bioinspired fog-harvesting technologies.
Glioblastoma is the most common and aggressive brain tumor in adults. However, due to the limitations of conventional treatments, as well as their side effects, there is a need to develop more effective and less harmful therapy strategies. There is evidence that plants endemic to northern Mexico possess biological activities that positively impact human health, particularly against cancer. Echinocereus engelmannii and Echinocereus pectinatus are cacti from the north of Mexico that produce bioactive compounds with antitumor activity. We obtained methanol extracts from previously isolated and fermented microorganisms associated with these cacti. Cell lines of extracts with cytotoxicity against glioblastoma cells U87, neuroblastoma cells SH-S5Y5, and Schwann neuronal cells (healthy control) were evaluated, using a colorimetric 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazole bromide (MTT) reduction technique. The selective cytotoxicity extracts were analyzed using liquid chromatography tandem mass spectrometry (LC/MS2). We isolated 19 endophytic and soil-associated microorganisms from both cacti. Two of them were selected for their high percentages of tumor growth inhibition. The microorganism ES4 possessed the best activity with an IC50 of 17.31 ± 1.70 µg/mL and a selectivity index of 3.11. We identified the bacterium Stenotrophomonas maltophilia by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) from the most active microorganisms against tumor growth. LC/MS2 characterized the HS4 extract, and the most abundant group (50.0%) identified included carboxylic acids and derivatives, particularly bisgerayafolin A, Cyclo (Pro-Leu), maculosin, and tryptophan. In conclusion S. maltophilia extract inhibit the growth of glioma cells, showing greater sensitivity in the U87 cell line.
Integrated datasets linking traits, spatial distributions, environmental variables and phylogenies are essential for comparative research, but remain limited for many plant taxa, including those which are most threatened. Cactaceae are a morphologically and ecologically diverse succulent family that are iconic components of ecosystems across the Americas, and face high extinction risk. To support future comparative research, we present CactEcoDB (The Cactus Ecological Database), an Open Access dataset of curated spatial, ecological, trait, phylogenetic, and diversification data for over 1,000 cactus species. CactEcoDB includes species-level trait data, geographic occurrence records, environmental variables, range size estimates, speciation rates, and the largest time-calibrated phylogeny of cacti to date. By integrating these diverse data in a single and accessible platform, CactEcoDB is intended as a community resource for ecological, evolutionary, biogeographic, and conservation-focussed studies involving cacti, one of the most celebrated yet threatened plant families.
Cacti, including pitaya (Hylocereus spp.), are rich in antioxidants that will undoubtedly gain importance under ongoing climate change as water resources decline. Yet the molecular basis linking composition to antioxidant function remains incompletely defined. We compared white-fleshed H. undatus and red-fleshed H. polyrhizus across physicochemical traits, integrating correlation, principal component analysis, and molecular docking to a human iron-regulatory protein (IRP1). White-fleshed fruits were larger and heavier (length 103.4 mm; width 60.2 mm; weight 204.7 g) than red-fleshed (71.9 mm; 54.5 mm; 126.3 g). Conversely, red-fleshed fruits showed higher total soluble solids (13.47 vs. 9.60 °Brix), total phenolics (379.7 vs. 183.0 mg L-1), total flavonoids (303.7 vs. 147.3 mg L-1), and antioxidant activity (52.3% vs. 30.0%). Organic acids and phenolics differed by species (e.g., higher citric acid in red; higher malic acid in white). Correlations indicated that greater soluble sugars were associated with higher phenolic accumulation, consistent with the elevated antioxidant capacity of red-fleshed fruit. The first two principal components explained 83.3% of the total variance (PC1 = 68.8%, PC2 = 14.5%) and separated samples along size/°Brix versus phenolic/ antioxidant axes. Docking predicted favorable binding of major acids and phenolics to IRP1, suggesting plausible antioxidant mechanisms. Findings support species-specific use, with red-fleshed H. polyrhizus serving as a nutrient-dense source of antioxidant compounds, while white-fleshed H. undatus offers advantageous pomological traits. Integrating compositional profiling with multivariate analysis and docking provides mechanistic context and practical implications for breeding, climate-resilient cultivation, and industrial applications. © 2025 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.