Biology subjects

Thakur, D.

Publications and source records attributed to Thakur, D..

13 recordsLinked to original sources

bioRxiv2026

Interactive effects of Nutrient Enrichment and Water Scarcity on Floral signaling and visitation

- Floral traits remain an underexplored frontier in global change biology compared to their vegetative counterparts. As anthropogenic change involves simultaneous shifts in resource availability, focusing on isolated stressors may overlook complex biological responses. Characterizing the interactive effects of these stressors is therefore crucial to move beyond additive models and accurately predict the stability of pollination services in a transforming world. - The individual and interactive effects of nutrient enrichment and water scarcity were investigated on the floral traits and pollinator visitation rates of five grassland species. - While species identity emerged as the dominant driver of overall trait variation, across-species responses were also present. Among the abiotic drivers, nutrient enrichment emerged as the primary influence, significantly increasing flower number and achromatic contrast while decreasing floral area, chromatic contrast and chroma. Conversely, water scarcity primarily reduced plant height and increased floral chroma and hue. The two factors also often interacted in their effects. The changes in visual traits scaled up to changes in pollinator visitation, but the specific effects were largely species-specific. - Ultimately, our findings demonstrate that anthropogenic stressors act in divergent ways to reshape floral phenotypes and pollinator visitation, advancing our understanding of plant-pollinator interactions under compounding global pressures.

ecology↗

bioRxiv2026

Computational predictions and evolutionary analysis of LrK10 kinase-related putative PSTOL1 gene homeologs in wheat and orthologs of its wild relatives.

Phosphorus Starvation Tolerance 1 in rice (OsPSTOL1, known as Phosphorus uptake 1, Pup1) is a receptor-like cytoplasmic protein kinase that confers tolerance to phosphorus deficiency. The OsPSTOL1 gene possesses a Ser/Thr kinase and shows high amino-acid sequence similarity with the leaf rust receptor-like kinase (OsLrK10). We hypothesize that the putative wheat TaPSTOL1 and TaLrK10 have a common ancestral origin and that putative TaPSTOL1 diverged recently acquiring new structural modifications and biological functions in the process. In this study, we identified all putative TaPSTOL1 homeologs and examine the evolutionary relationship between TaPSTOL1 and TaLrK10 in Triticum species. Our results indicate that the putative TaPSTOL1 diverged recently without possessing the amino-terminal domain, which is a typical characteristic of TaLrK10. We observed numerous conversions tracts between these two genes and the substitution pattern of randomly selected amino acids indicates that dynamic selection pressures acted on both genes. The putative TaPSTOL1 shows high nucleotide diversity compared to TaLrK10 within Triticum species. Further, a multiple-sequence analysis reveals that the third exon of TaLrK10 appears to have been duplicated and diverged as a putative single-exon based TaPSTOL1 in bread wheat. Overall, our comparative analysis indicates that both TaPSTOL1 and TaLrK10 appears to have diverged from a common ancestor, acquiring distinct structural organizations and biological functions.

genomics↗

bioRxiv2025

Drought and methyl jasmonate memory interact to determine plant functioning under current drought stress in a perennial grass

As droughts become more common due to climate change, survival may rely not only on a plants immediate response but also on what it has learned from past challenges. However, we still know little about how plants integrate different types of experiences, such as recurrent drought and hormonal cues, from previous generations. In this study, we examined whether clonal offspring of Festuca rubra plants previously exposed to drought or the stress hormone methyl jasmonate (MeJA) inherited biological memories that help them tolerate new drought stress. Using a factorial design, we combined untargeted LC- MS metabolomics with morpho-physiological measurements to evaluate these memory effects. We found that each type of memory changed plant metabolism and physiology, but the most notable changes occurred when both memories were present, and plants faced recurrent drought conditions again. This interaction between drought memory, MeJA memory, and current stress did not just add effects, it created entirely new metabolic responses, not seen in any single treatment. These combined memories fine-tuned water conservation, photosynthesis, and extensive metabolomic reshuffling, revealing a deeper level of drought resilience. Our results uncover a layered memory system in plants where past stresses do not act in isolation but interact to reshape future responses. This offers new insight into how plants prepare for stress and suggests practical strategies for priming drought tolerance across plant generations.

plant biology↗

bioRxiv2025

Shift from acquisitive to conservative plant strategies with increasing drought and temperature extremes in an alpine shrub

Background and AimsTrait-based approaches have advanced our understanding of plant strategies, yet they often focus on leaf-level traits, overlooking the functional roles of stem anatomy and twig characteristics. We investigated intraspecific trait variation in Salix flabellaris, an alpine dwarf shrub, along climatic gradients in the Himalayas. Our goal was to identify distinct axes of trait variation related to stem, twig, and leaf traits, assess their environmental drivers, and evaluate population-specific growth responses to recent climate change. MethodsWe measured anatomical and morphological traits in stem, twig, and leaves across central and marginal populations along three Himalayan transects. Environmental gradients included variation in growing season temperature and soil moisture. Basal area increment from 2000 to 2021 was analyzed to assess long-term growth trends in different areas. ResultsTrait dimensions were largely independent, reflecting distinct ecological strategies: (1) stem anatomical trade-off between hydraulic safety and conductivity; (2) twig dimension balancing construction costs and mechanical strength; and (3) leaf dimension along the exploitative-conservative axis. Higher temperatures enhanced performance manifested as larger twigs and reduced tissue construction costs but only under sufficient soil moisture conditions. Central populations at mid-elevations displayed the favorable trait combinations and highest growth rates. In contrast, marginal populations (higher and lower elevations) showed traits indicating structural reinforcement and conservative resource use. Climate warming over recent decades enhanced stem growth primarily in high-elevation populations, where low-temperature constraints were relaxed. ConclusionsThis study demonstrates that stem, twig, and leaf traits represent distinct yet complementary strategies, with environmental filtering shaping their expression along climate gradients. Central populations exhibit highest growth under current conditions, while climate change is shifting growth advantages toward higher elevations. These findings highlight the need for integrated, multi-organ trait assessments to predict species performance, persistence, and potential range shifts under future climatic scenarios.

ecology↗

bioRxiv2025

Global Change Factors differentially impact Floral and Leaf Economic Traits

Background and AimsSince the Industrial Revolution, rising atmospheric CO{square}, warming, and more frequent droughts have significantly impacted ecosystems. While the response of leaf functional traits to these climate change factors have been widely studied, reproductive traits remain relatively understudied, despite their key role in the diversification and distribution of flowering plants. Here, we investigated how elevated CO{square}, warming, drought, and their interactions affect floral, leaf and seed traits in two model grassland species. We also examined how these factors influence trait coordination. MethodsTwo common grassland species, Lotus corniculatus and Crepis capillaris, were sampled from a 10-year climate manipulation experiment. We measured resource economic traits related to organ size, construction cost, and dry matter content in both leaves and flowers, along with seed size and number. Univariate and multivariate analyses were used to assess trait responses, and rank-abundance curves were employed to visualize changes in trait coordination across treatments. Key ResultsTrait responses to climate change factors varied between species. Drought emerged as the most influential factor, affecting only leaf traits in L. corniculatus, but impacting leaf, floral, and seed traits in C. capillaris. Across both species, climate change conditions increased leaf construction costs and reduced flower size. In addition, it led to larger leaves in L. corniculatus, and fewer seeds in C. capillaris. Under extreme climate change conditions, trait coordination became stronger in both species, although C. capillaris showed no coordination response specifically to drought. ConclusionOur results show that floral economic traits, like leaf traits, are responsive to individual and combined effects of climate change factors. This highlights their importance in shaping plant strategies under environmental stress and emphasizes the need to better integrate floral traits into the whole-plant economic framework.

ecology↗

bioRxiv2025

From smartphones to satellites: Uniting crowdsourced biodiversity monitoring and Earth observation to fill the gaps in global plant trait mapping

Plant functional traits are fundamental to ecosystem dynamics and Earth system processes, but their global characterization is limited by the availability of field surveys and trait measurements. Recent expansions in biodiversity data aggregation, including large collections of vegetation surveys, citizen science observations, and trait measurements, offer new opportunities to overcome these constraints. Here we demonstrate that combining these diverse data sources with high-resolution Earth observation data enables accurate modeling of key plant traits at up to 1 km resolution. Our approach achieves high predictive power, reaching correlations up to 0.63 (15 of 31 traits exceeding 0.50) and improved spatial transferability, effectively bridging gaps in under-sampled regions. By capturing a broad range of traits with high spatial coverage, these maps can enhance our understanding of plant community properties and ecosystem functioning globally, and can serve as useful tools in modeling global biogeochemical processes and informing worldwide conservation efforts. Ultimately, our framework highlights the power and necessity of crowdsourced biodiversity data in high-resolution plant trait modeling. We anticipate that advancements in biodiversity data collection and remote sensing capabilities will further refine global trait mapping, fostering a dynamic trait-based understanding of the biosphere.

ecology↗

bioRxiv2024

Control of odor sensation by light and cryptochrome in the Drosophila antenna

Olfaction is a sense employed by insects to differentiate safe from harmful food options, evaluate potential mates, and identify oviposition sites. Here, we found that the fruit fly, Drosophila melanogaster, responds differently to a set of repulsive odors depending on ambient light conditions. Ultraviolet (UV) or blue light reduces the behavioral aversion and electrophysiological responses of olfactory receptor neurons (ORNs) to certain repellent odors, such as benzaldehyde. We found that cryptochrome (cry) is strongly expressed in the antennal support cells that lie adjacent to ORNs, and mutation of cry eliminates the light-dependent reduction in aversion. Thus, these data demonstrate that support cells in an olfactory organ serve a sensory function as light receptor cells. It has been shown that light activation of Cry creates reactive oxygen species (ROS), and ROS activates the TRPA1 channel. We demonstrate that the TRPA1-C isoform is expressed and required in ORNs for benzaldehyde repulsion, and that TRPA1-C is activated in vitro by benzaldehyde. Overexpression of dual oxygenase, which generates hydrogen peroxide, reduced the aversion under dark conditions. Our data support the model that light-dependent creation of hydrogen peroxide persistently activates TRPA1-C. Consequently, the channel is no longer effectively activated by benzaldehyde. Since flies sleep much more at night, and begin feeding at dawn, we propose that the light-induced reduction in aversion to certain odors provides a mechanism to lower the barrier to feeding following the transition from night to day.

neuroscience↗

bioRxiv2024

Deciphering binding site conformational variability of substrate promiscuous and specialist enzymes

Substrate promiscuity is the ability of enzymes to catalyze reactions with alternate substrate(s) beyond their physiologically relevant ones. Such promiscuous activities expand enzymes functional landscape, enabling evolution or designing novel biochemical reactions. The molecular basis of substrate promiscuity remains elusive, though previous studies have suggested roles of active site structural features, such as flexibility, hydrophobicity, sub-sites, and electrostatics. Moreover, a recent hypothesis proposes the role of active site conformational variability in promiscuity. Accordingly, promiscuous enzymes could accommodate alternate substrate(s) through their pre-existing conformations, whereas specialists have a dominant conformation for their native substrates. To explore the role of active site conformational flexibility in substrate promiscuity, we compared the conformational states of two substrate promiscuous and specialist enzymes by analyzing their binding site structural dynamics from long-time explicit solvent molecular dynamics. Using tICA, we generated conformational states from simulations of the holo-conformation of enzymes. In addition to visual analysis of the variability of binding site conformation states, we performed quantitative estimation of the same using the native functionality score, which measures the contact similarity of conformations to the native structure. We observed that both specialist and generalist enzymes exhibited varied numbers of substrate binding site competent states, indicating that conformational flexibility to accept alternate substrates could exist in both groups of enzymes. Further, it caters to the view of substrate promiscuity as a continuum feature of enzymes.

bioinformatics↗

bioRxiv2024

Exon Nomenclature and Classification of Transcripts (ENACT): Systematic framework to annotate exon attributes

AbstractO_ST_ABSMotivationC_ST_ABSIsoform diversity is known to enhance a genes functional repertoire. Despite studies on transcriptome diversifying processes (Alternate splicing/transcription), their extent and correlated impact on proteome diversity remains rudimentarily understood. ResultsThe current study presents an innovative framework, "Exon Nomenclature and Annotation of Transcripts," that centralizes exonic loci while integrating protein sequence per entity with tracking and assessing splice site variability. The resulting annotation from framework enables exon features to be tractable, facilitating a systematic analysis of isoform diversity. Our findings and case studies unveil systemic exon inclusions roles in regulating diversity in CDS region. Availability and implementationAll data generated during this study are publicly available at www.iscbglab.in/enactdb/. Associated algorithmic procedures have been described in the methods section. Supplementary informationPDF file enclosing supplementary data attached.

bioinformatics↗

bioRxiv2024

Uncovering the translatome impact of transcriptome induced diversity in eukaryotes: framework and innovative insights

Isoform diversity is known to enhance a genes functional repertoire. Insights into the extent of such sequence variability generated through alternative splicing (AS), may unveil the layers of gene function/regulation. Despite studies on transcriptome diversifying processes, the impact of AS or related processes on sequence diversity still needs to be explored. Current study presents an innovative framework that centralizes exonic loci while integrating protein sequence per entity with attention to splice site variability assessment. The resulting framework enables exon (features) to be tractable, facilitating a systematic, detailed analysis of isoform diversity. We analyzed isoform diversity in five representative organisms and detailed the role of AS and related processes influencing exon inclusion in imparting sequence variation for human genome. Through analyses of exonic variations in two maximally diverged isoforms of human genes, we unraveled intricate splicing patterns prevalent in coding and non-coding regions. We observed that alternative splice sites, sequence changes, and skipping of exons are prevalent in coding exons, while the alternate first exon events are predominant in non-coding exons. Our findings offer a comprehensive understanding of isoform diversity as a function of exonic entity framework, providing valuable insights into the orchestration of exonic events in shaping the proteogenomic landscape.

bioinformatics↗

bioRxiv2023

Heterologous Expression and Characterization of ToxA1 haplotype from India and its interaction with for Spot Blotch Susceptibility in spring wheat

BackgroundToxA, a necrotrophic effector protein, is present in the genome of fungal species like Parastagnospora nodorum, Pyrenophora tritici-repentis and Bipolaris sorokiniana. Tsn1 is the sensitivity gene in the host whose presence indicates more susceptibility to ToxA carrying pathogen, and ToxA-Tsn1 interaction follows an inverse gene-for-gene relationship. Methods and ResultsThe present study involved cloning and expressing the ToxA1 haplotype from B. sorokiniana. It was found that the amplicon exhibited an expected product size of 471 bp. Sequence analysis of the ToxA1 nucleotide sequence revealed the highest identity, 99.79%, with P. tritici-repentis. The protein expression analysis showed peak expression at 16.5kDa. Phylogenetic analysis of the ToxA1 sequence from all the Bipolaris isolates formed an independent clade along with P. tritici-repentis and diverged from P. nodorum. ToxA-Tsn1 interaction was studied in 18 wheat genotypes (11 Tsn1 and 7 tsn1) at both seedling and adult stages, validating the inverse gene-for-gene relationship, as the toxin activity was highest in the K68 genotype (Tsn1) and lowest in WAMI280 (tsn1). ConclusionThe study indicates that the haplotype ToxA1 is prevailing in the Indian population of B. sorokiniana. It would be desirable for wheat breeders to select genotypes with tsn1 locus for making wheat resistant to spot blotch.

plant biology↗

bioRxiv2022

Differential effect of climate on structural and biochemical plant traits

Exploring patterns and causes of intraspecific trait variation is crucial for a better understanding of the effects of climate change on plant populations and ecosystems. However, our current understanding of the intraspecific trait variation is mainly based on structural (morphological) traits, and we have limited knowledge on patterns and causes of variation in biochemical traits (e.g., leaf pigments), which are also crucial for plant adaptation. As a result, we also do not know how similar the climatic effects on structural versus biochemical traits are. Using plant traits from 110 genotypes representing 11 Festuca rubra populations grown in 4 different climates, we studied trait covariation among structural traits (linked to fitness, resource use, gas exchange, and reproduction) and biochemical traits (linked to photosynthesis, photoprotection, and oxidative stress). We also disentangled the relative role of the climate of origin and the climate of cultivation in the structural versus biochemical traits and tested for adaptive plasticity in the traits. We found that 1) biochemical traits did not covary with structural traits and represent independent photoharvesting - photoprotection strategy dimension of functional variation; 2) interactive effects of climate of origin and cultivation were more pronounced for biochemical than structural traits. 3) Trait plasticity was affected by the climate of origin (precipitation and temperature as well as their interaction); 4) F. rubra showed both adaptive and mal-adaptive plasticity, and adaptiveness depended upon trait type, cultivation climate, and climate of origin. Overall, our results suggest that structural and biochemical plant traits respond differentially to climate and thus the response of one group of traits cannot be predicted from the other. Responses are also strongly determined by interactions between the climate of origin and cultivation. Thus, more studies on variation in biochemical traits, their correspondence to other traits, and their variation with climate are needed.

ecology↗

bioRxiv2021

Rhizome trait scaling relationships are modulated by climate and are linked to plant fitness

Background and AimRhizomes are important organs allowing many clonal plants to persist and reproduce under stressful climates with longer rhizomes indicating enhanced ability of the plants to spread vegetatively. We do not however, know either how rhizome construction costs change with increasing length or vary with environmental conditions. MethodsWe analysed the rhizome length vs mass scaling relationship, the plasticity in the scaling relationships, their genetic basis, and how scaling relationships are linked to plant fitness. We used data from 275 genotypes of a clonal grass Festuca rubra originating from 11 localities and cultivated under four contrasting climates. Data were analysed using standard major axis regression, mixed-effect regression models and a structural equation model. Key ResultsRhizome construction costs increased (i.e., lower specific rhizome length) with increasing length. The trait scaling relationships were modulated by cultivation climate and its effects also interacted with the climate of origin of the experimental plants. With increasing length, increasing moisture led to a greater increase in rhizome construction costs. Plants with lower rhizome construction costs showed significantly higher fitness. ConclusionsThis study suggests that rhizome scaling relationships are plastic, but also show genetic differentiation and are linked to plant fitness. Therefore, to persist under variable environments modulation in scaling relationships could be an important plants strategy.

ecology↗