Biology subjects

Heyduk, K.

Publications and source records attributed to Heyduk, K..

12 recordsLinked to original sources

bioRxiv2025

Techniques and challenges in studying photosynthetic diversity in freshwater aquatic vascular plants

While the photosynthetic diversity of aquatic plants rivals that of terrestrial species, the environmental conditions underlying that diversity fundamentally differ. Despite these environmental differences, aquatic and terrestrial plants have convergently evolved Carbon Concentrating Mechanisms (CCMs). However, characterization of these pathways in submerged plants has lagged behind terrestrial systems due to methodological constraints of the aquatic environment. Here we review and evaluate contemporary methods for detecting CCMs in aquatic plants. Physiological methods including gas exchange and isotopic analyses provide valuable insights in terrestrial plants but face significant challenges in aquatic systems. Biochemical assays of organic acid accumulation reliably detect CCMs in aquatic species but may struggle to detect weak or non-canonical CCMs in submerged plants. Finally, we propose a method for targeted molecular assays of phosphoenolpyruvate carboxylase (PEPC) expression that could provide a sensitive tool for characterizing photosynthetic diversity in a wide range of aquatic species. Our results show that methods and frameworks developed for terrestrial plants do not necessarily directly translate to aquatic systems. However, by extending these methods and integrating multiple lines of evidence we can improve our ability to characterize photosynthetic diversity in aquatic plants.

plant biology↗

bioRxiv2025

Island-wide population genomic analysis of the coastal shrub, beach naupaka (Scaevola taccada L.), on Oahu

PremisePlant species face a myriad of challenges including climate change and habitat destruction. On Oahu in Hawaii, Scaevola taccada L., a coastal dune shrub, is highly impacted by human activities, but is also experiencing environmental threats like sea level rise. Despite its ubiquity across Pacific islands, the extent and distribution of genetic diversity in this species is unclear. Further, it is currently unclear how many times S. taccada arrived on Oahu. MethodsWe surveyed population genomic diversity using ddRAD-seq in eight populations of S. taccada on Oahu. Using principal components and STRUCTURE analyses, we assessed whether genetic diversity was structured geographically across the island. Additionally, we generated whole genome sequences from five herbarium accessions and used a publicly available genome to construct a haplotype network to infer the number of times S. taccada arrived on Oahu. We analyzed climate data and leaf thickness measurements to understand how patterns of genetic diversity were correlated with environmental and trait variation. ResultsOur analyses pointed to a trend in which two populations in protected areas were both genetically differentiated from, and harbored less genetic diversity than, human dominated areas. Further analysis of genetic structure via a PCA and pairwise FST indicated a secondary geographic pattern in our dataset by which western beach populations were differentiated from eastern beach populations. The chloroplast haplotype network suggested a single arrival on Oahu. ConclusionsOur results demonstrate that S. taccada populations in protected natural areas harbored unique genetic variation compared to human dominated beach parks, but that protected populations also had significantly reduced genetic variation compared to other populations.

plant biology↗

bioRxiv2024

Integrative analysis of CAM photosynthesis reveals its impact on primary metabolism in Yucca

Crassulacean Acid Metabolism (CAM) is an adaptation that temporally separates carbon uptake at night from photosynthesis during the day. CAM has evolved repeatedly across vascular plants, as its emergence may depend on simple regulatory changes to deeply conserved metabolic pathways. Modern CAM research relies heavily on interpretation of transcriptomic data, though regulation occurs at multiple levels following transcription. Additionally, while most research to date has focused on a handful of genes and metabolites in the core CAM pathway, the co-option of conserved regulatory and functional genes is bound to have wide ranging effects on other aspects of primary metabolism. In this study, we integrate transcriptomic, proteomic, and metabolomic data to compare primary metabolism between the CAM species Yucca aloifolia and closely related C3 species, Y. filamentosa. We observe minimal correlation between protein abundance and mRNA expression, suggesting significant post-transcriptional regulation in CAM species. We also find evidence of shifts in gene expression and metabolite accumulation outside of the central CAM pathway suggesting that the shift to CAM has cascading effects across primary metabolism, especially nitrogen metabolism. Our findings provide insights into the metabolic shifts associated with CAM evolution and highlight the complexity of its regulation at multiple biological levels.

evolutionary biology↗

bioRxiv2023

Conservation applications of ecological niche modeling: non-native ferns may compete with native ferns for limited suitable habitat in Hawaiian dryland ecosystems

PremiseCompetition from naturalized species and habitat loss are common threats to native biodiversity and may act synergistically to increase competition for decreasing habitat availability. We use Hawaiian dryland ferns as a model for the interactions between land-use change and competition from naturalized species in determining habitat availability. MethodsWe use fine-resolution climatic variables and carefully curated occurrence data from herbaria and community science repositories to estimate the distributions of Hawaiian dryland ferns. We quantify the degree to which naturalized ferns tend to occupy native species suitable area and map remaining available habitat given land-use change. ResultsOf all native species, Doryopteris angelica has the lowest percentage of occurrences of naturalized species in its suitable area while D. decora has the highest. However, all Doryopteris spp. had a higher percentage overlap--while Pellaea ternifolia had a lower percentage overlap--than expected by chance. D. decora and D. decipiens have the lowest proportions (< 20%) of suitable area covering native habitat. DiscussionAreas characterized by shared environmental preferences of native and naturalized ferns may also decrease due to human development and fallowed agricultural lands. Our study demonstrates the value of placed-based application of a recently developed correlative ecological niche modeling approach for conservation risk assessment in a rapidly changing and urbanized island ecosystem.

ecology↗

bioRxiv2023

Predicting photosynthetic pathway from anatomy using machine learning

- Plants with Crassulacean acid metabolism (CAM) have long been associated with a specialized anatomy, including succulence and thick photosynthetic tissues. Firm, quantitative boundaries between non-CAM and CAM plants have yet to be established - if they indeed exist. - Using novel computer vision software to measure anatomy, we combined new measurements with published data across flowering plants. We then used machine learning and phylogenetic comparative methods to investigate relationships between CAM and anatomy. - We found significant differences in photosynthetic tissue anatomy between plants with differing CAM phenotypes. Machine learning based classification was over 95% accurate in differentiating CAM from non-CAM anatomy, and had over 70% recall of distinct CAM phenotypes. Phylogenetic least squares regression and threshold analyses revealed that CAM evolution was significantly correlated with increased mesophyll cell size, thicker leaves, and decreased intercellular airspace. - Our findings suggest that machine learning may be used to aid the discovery of new CAM species and that the evolutionary trajectory from non-CAM to strong, obligate CAM requires continual anatomical specialization.

evolutionary biology↗

bioRxiv2023

Short structural variation fuelled CAM evolution within an explosive bromeliad radiation

1.The subgenus Tillandsia (Bromeliaceae) belongs to one of the fastest radiating clades in the plant kingdom and is characterised by the repeated evolution of Crassulacean Acid Metabolism (CAM). Despite its complex genetic basis, this water-conserving trait has evolved independently across many plant families and is regarded as a key innovation trait and driver of ecological diversification in Bromeliaceae. By producing high-quality genome assemblies of a Tillandsia species pair displaying divergent photosynthetic phenotypes, and combining genome-wide investigations of synteny, TE dynamics, sequence evolution, gene family evolution and temporal differential expression, we were able to pinpoint the genomic drivers of CAM evolution in Tillandsia. Several large-scale rearrangements associated with karyotype changes between the two genomes and a highly dynamic TE landscape shaped the genomes of Tillandsia. However, our analyses show that rewiring of photosynthetic metabolism is mainly obtained through regulatory evolution rather than coding sequence evolution, as CAM-related genes are differentially expressed across a 24-hour cycle between the two species, but are no candidates of positive selection. Gene orthology analyses reveal that CAM-related gene families manifesting differential expression underwent accelerated gene family expansion in the constitutive CAM species, further supporting the view of gene family evolution as a driver of CAM evolution.

evolutionary biology↗

bioRxiv2022

Phylogenetic resolution of the Cannabis genus reveals extensive admixture

Population structure of Cannabis sativa L. was explored across nine independent collections that each contained a unique sampling of varieties. Hierarchical Clustering of Principal Components (HCPC) identified a range of three to seven genetic clusters across datasets with inconsistent structure based on use type indicating the importance of sampling particularly when there is limited passport data. There was broader genetic diversity in modern cultivars relative to landraces. Further, in a subset of geo-referenced landrace accessions, population structure was observed based on geography. The inconsistent structure across different collections shows the complexity within Cannabis, and the importance of understanding any particular collection which could then be leveraged in breeding programs for future crop improvement.

genomics↗

bioRxiv2021

Timing of gene expression and recruitment in independent origins of CAM in the Agavoideae (Asparagaceae).

CAM photosynthesis has evolved repeatedly across the plant tree of life, yet our understanding of the genetic convergence across independent origins remains hampered by the lack of comparative studies. CAM is furthermore thought to be closely linked to the circadian clock in order to achieve temporal separation of carboxylation and sugar production. Here, we explore gene expression profiles in eight species from the Agavoideae (Asparagaceae) encompassing three independent origins of CAM. Using comparative physiology and transcriptomics, we examined the variable modes of CAM in this subfamily and the changes in gene expression across time of day and between well-watered and drought-stressed treatments. We further assessed gene expression and molecular evolution of genes encoding phosphoenolpyruvate carboxylase (PPC), an enzyme required for primary carbon fixation in CAM. Most time-of-day expression profiles are largely conserved across all eight species and suggest that large perturbations to the central clock are not required for CAM evolution. In contrast, transcriptional response to drought is highly lineage specific. Yucca and Beschorneria have CAM-like expression of PPC2, a copy of PPC that has never been shown to be recruited for CAM in angiosperms, and evidence of positive selection in PPC genes implicates mutations that may have facilitated the recruitment for CAM function early in the evolutionary history of the Agavoideae. Together the physiological and transcriptomic comparison of closely related C3 and CAM species reveals similar gene expression profiles, with the notable exception of differential recruitment of carboxylase enzymes for CAM function.

plant biology↗

bioRxiv2020

Hybridization history and repetitive element content in the genome of a homoploid hybrid, Yucca gloriosa (Asparagaceae)

Hybridization in plants results in phenotypic and genotypic perturbations that can have dramatic effects on hybrid physiology, ecology, and overall fitness. Hybridization can also perturb epigenetic control of transposable elements, resulting in their proliferation. Understanding the mechanisms that maintain genomic integrity after hybridization is often confounded by changes in ploidy that occur in hybrid plant species. Homoploid hybrid species, which have no change in chromosome number relative to their parents, offer an opportunity to study the genomic consequences of hybridization in the absence of change in ploidy. Yucca gloriosa (Asparagaceae) is a young homoploid hybrid species, resulting from a cross between Yucca aloifolia and Yucca filamentosa. Previous analyses of ~11kb of the chloroplast genome and nuclear-encoded microsatellites implicated a single Y. aloifolia genotype as the maternal parent of Y. gloriosa. Using whole genome resequencing, we assembled chloroplast genomes from multiple accessions of all three species to re-assess the hybrid origins of Y. gloriosa. We further used re-sequencing data to annotate transposon abundance in the three species and mRNA-seq to analyze transcription of transposons. The chloroplast phylogeny and haplotype analysis suggest multiple hybridization events contributing to the origin of Y. gloriosa, with both parental species acting as the maternal donor. Transposon abundance at the superfamily level was significantly different between the three species; the hybrid was frequently intermediate to the parental species in TE superfamily abundance or appeared more similar to one or the other parent. In only one case - Copia LTR transposons - did Y. gloriosa have a significantly higher abundance relative to either parent. Expression patterns across the three species showed little increased transcriptional activity of transposons, suggesting that either no transposon release occurred in Y. gloriosa upon hybridization, or that any transposons that were activated via hybridization were rapidly silenced. Further work will assess the degree to which transposon abundance and location has affected the epigenomic landscape, gene expression, and ecophysiology in Y. gloriosa.

plant biology↗

bioRxiv2019

Leaf anatomy is not correlated to CAM function in a C3+CAM hybrid species, Yucca gloriosa

Background and AimsCAM photosynthesis is often considered to be a complex trait, requiring orchestration of leaf anatomy and physiology for optimal performance. But the observation of trait correlations is based largely on comparisons between C3 and strong CAM species, resulting in a lack of understanding as to how such traits evolve and the level of intraspecific variability for CAM and associated traits.\n\nMethodsTo understand intraspecific variation for traits underlying CAM and how these traits might assemble over evolutionary time, we conducted detailed time course physiological screens and measured aspects of leaf anatomy in 24 genotypes of a C3+CAM hybrid species, Yucca gloriosa (Asparagaceae). Comparisons were made to Y. gloriosas progenitor species, Y. filamentosa (C3) and Y. aloifolia (CAM).\n\nKey resultsBased on gas exchange and measurement of leaf acids, Y. gloriosa appears to use both C3 and CAM, and varies across genotypes in the degree to which CAM can be upregulated under drought stress. While correlations between leaf anatomy and physiology exist when testing across all three Yucca species, such correlations break down at the species level in Y. gloriosa.\n\nConclusionsThe variation in CAM upregulation in Y. gloriosa is a result of its relatively recent hybrid origin. The lack of trait correlations between anatomy and physiology within Y. gloriosa indicate that the evolution of CAM, at least initially, can proceed through a wide combination of traits, and more favorable combinations are eventually selected for in strong CAM plants.

plant biology↗

bioRxiv2018

Altered Gene Regulatory Networks are Associated with the Transition from C3 to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae)

Crassulacean acid metabolism (CAM) photosynthesis is a modification of the core C3 photosynthetic pathway that improves the ability of plants to assimilate carbon in water-limited environments. CAM plants fix CO2 mostly at night, when transpiration rates are low. All of the CAM pathway genes exist in ancestral C3 species, but the timing and magnitude of expression are greatly altered between C3 and CAM species. Understanding these regulatory changes is key to elucidating the mechanism by which CAM evolved from C3. Here we use two closely related species in the Orchidaceae, Erycina pusilla (CAM) and Erycina crista-galli (C3), to conduct comparative transcriptomic analyses across multiple time points. Clustering of genes with expression variation across the diel cycle revealed some canonical CAM pathway genes similarly expressed in both species, regardless of photosynthetic pathway. However, gene network construction indicated that 149 gene families had significant differences in network connectivity and were further explored for these functional enrichments. Genes involved in light sensing and ABA signaling were some of the most differently connected genes between the C3 and CAM Erycina species, in agreement with the contrasting diel patterns of stomatal conductance in C3 and CAM plants. Our results suggest changes to transcriptional cascades are important for the transition from C3 to CAM photosynthesis in Erycina.

plant biology↗

bioRxiv2018

Nocturnal expression of Crassulacean acid metabolism (CAM) genes predates the origin of CAM in the genus Yucca.

HighlightAlthough large differences in metabolism exist between C3 and CAM species, we find that many CAM genes have shared expression patterns regardless of photosynthetic pathway, suggesting ancestral propensity for CAM.\n\nAbstractCrassulacean acid metabolism (CAM) is a carbon-concentrating mechanism that has evolved numerous times across flowering plants and is thought to be an adaptation to water limited environments. CAM has been investigated from physiological and biochemical perspectives, but little is known about how plants evolve from C3 to CAM at the genetic or metabolic level. Here we take a comparative approach in analyzing time-course data of C3, CAM, and C3+CAM intermediate Yucca (Asparagaceae) species. RNA samples were collected over a 24-hour period from both well-watered and drought-stressed plants and were clustered based on time-dependent expression patterns. Metabolomic data reveals differences in carbohydrate metabolism and antioxidant response between the CAM and C3 species, suggesting changes to metabolic pathways are important for CAM evolution and function. However, all three species share expression profiles of canonical CAM pathway genes, regardless of photosynthetic pathway. Despite differences in transcript and metabolite profiles between the C3 and CAM species, shared time-structured expression of CAM genes in both CAM and C3 Yucca species suggests ancestral expression patterns required for CAM may have predated its origin in Yucca.

plant biology↗