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The titan arum (Amorphophallus titanum), commonly known as the corpse flower, produces the largest unbranched inflorescence in the world. Its rare blooms last only a few days and are notable both for their burst of thermogenic activity and for the odor of rotting flesh by which they attract pollinators. Studies on the titan arum can therefor lend insight into the mechanisms underlying thermogenesis as well as the production of sulfur-based volatiles, about which little is known in plants. Here, we made use of transcriptome and metabolite analyses to uncover underlying mechanisms that enable thermogenesis and volatile production in the titan arum. The ability to perform thermogenesis correlated with the expression of genes involved in bypass steps for the mitochondrial electron transport chain, in particular alternative oxidase expression, and through our analysis is placed within the context of sugar transport and metabolism. The major odorants produced by the titan arum are dimethyl disulfide and dimethyl trisulfide, and we identified pathways for sulfur transport and metabolism that culminate in the production of methionine, which our analysis identifies as the amino acid substrate for production of these odorants. Putrescine, derived from arginine, was identified as an additional and previously unrecognized component of the titan arum's odor. Levels of free methionine and putrescine were rapidly depleted during thermogenesis, consistent with roles in production of the titan arum's odor. Models for how tissues of the titan arum contribute to thermogenesis and volatile production are proposed. 

Summary Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. However, harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and utilize genetic diversity.Here, we explore seven complete genomes of the emerging biofuel crop pennycress (Thlaspi arvense) drawn from across the species’s current genetic diversity to catalogue variation in genome structure and content.Across this new pangenome resource, we find contrasting evolutionary modes in different genomic regions. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. In contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions, even in fast-evolving immune genes where microsynteny breaks down across species but the macrosynteny of gene cluster positioning is maintained.Our findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows rearrangement and presence-absence variation on a local scale. This diversity is invisible to classical reference-based approaches and highlights the strength and utility of pangenomic resources. These results provide a valuable case study of rapid genomic structural evolution within a species and powerful resources for crop development in an emerging biofuel crop. 

Abstract Background Non-invasive reporter systems are powerful tools to query physiological and transcriptional responses in organisms. For example, fluorescent and bioluminescent reporters have revolutionized cellular and organismal assays and have been used to study plant responses to abiotic and biotic stressors. Integrated, cooled charge-coupled device (CCD) camera systems have been developed to image bioluminescent and fluorescent signals in a variety of organisms; however, these integrated long-term imaging systems are expensive. Results We have developed self-assembled systems for both growing and monitoring plant fluorescence and bioluminescence for long-term experiments under controlled environmental conditions. This system combines environmental growth chambers with high-sensitivity CCD cameras, multi-wavelength LEDs, open-source software, and several options for coordinating lights with imaging. This easy-to-assemble system can be used for short and long-term imaging of bioluminescent reporters, acute light-response, circadian rhythms, delayed fluorescence, and fluorescent-protein-based assays in vivo. Conclusions We have developed two self-assembled imaging systems that will be useful to researchers interested in continuously monitoring in vivo reporter systems in various plant species. 

Abstract The plant circadian clock coordinates developmental, physiological, and metabolic processes with diel changes in light and temperature throughout the year. The balance between the persistence and plasticity of the clock in response to predictable and unpredictable environmental changes may be key to the clock’s adaptive nature across temporal and spatial scales. Studies under controlled conditions have uncovered critical signaling pathways involved in light and temperature perception by the clock; however, they don’t account for the natural lag of temperature behind photoperiod. Studies in natural environments provide key insights into the clock’s adaptive advantage under more complex natural settings. Here, we discuss the role of the circadian clock in light and temperature perception and signaling, how the clock integrates these signals for a coordinated and adaptive response, and the adaptive advantage conferred by the clock across time and space in natural environments. 

Abstract Motivation Clustering spatial-resolved gene expression is an essential analysis to reveal gene activities in the underlying morphological context by their functional roles. However, conventional clustering analysis does not consider gene expression co-localizations in tissue for detecting spatial expression patterns or functional relationships among the genes for biological interpretation in the spatial context. In this article, we present a convolutional neural network (CNN) regularized by the graph of protein–protein interaction (PPI) network to cluster spatially resolved gene expression. This method improves the coherence of spatial patterns and provides biological interpretation of the gene clusters in the spatial context by exploiting the spatial localization by convolution and gene functional relationships by graph-Laplacian regularization. Results In this study, we tested clustering the spatially variable genes or all expressed genes in the transcriptome in 22 Visium spatial transcriptomics datasets of different tissue sections publicly available from 10× Genomics and spatialLIBD. The results demonstrate that the PPI-regularized CNN constantly detects gene clusters with coherent spatial patterns and significantly enriched by gene functions with the state-of-the-art performance. Additional case studies on mouse kidney tissue and human breast cancer tissue suggest that the PPI-regularized CNN also detects spatially co-expressed genes to define the corresponding morphological context in the tissue with valuable insights. Availability and implementation Source code is available at https://github.com/kuanglab/CNN-PReg. Supplementary information Supplementary data are available at Bioinformatics online. 

Abstract Changes in gene expression are important for responses to abiotic stress. Transcriptome profiling of heat- or cold-stressed maize genotypes identifies many changes in transcript abundance. We used comparisons of expression responses in multiple genotypes to identify alleles with variable responses to heat or cold stress and to distinguish examples of cis- or trans-regulatory variation for stress-responsive expression changes. We used motifs enriched near the transcription start sites (TSSs) for thermal stress-responsive genes to develop predictive models of gene expression responses. Prediction accuracies can be improved by focusing only on motifs within unmethylated regions near the TSS and vary for genes with different dynamic responses to stress. Models trained on expression responses in a single genotype and promoter sequences provided lower performance when applied to other genotypes but this could be improved by using models trained on data from all three genotypes tested. The analysis of genes with cis-regulatory variation provides evidence for structural variants that result in presence/absence of transcription factor binding sites in creating variable responses. This study provides insights into cis-regulatory motifs for heat- and cold-responsive gene expression and defines a framework for developing models to predict expression responses across multiple genotypes. 

Like animals, plants have internal biological clocks that allow them to adapt to daily and yearly changes, such as day-night cycles or seasons turning. Unlike animals, however, plants cannot move when their environment becomes different, so they need to be able to weather these changes by adjusting which genes they switch on and off. To do this, plants keep track of how long days are using external cues such as light or temperature. One of the effects of climate change is that these cues become less reliable, making it harder for plants to adapt to their environment and survive. This is a potential problem for crop species, like Brassica rapa . This plant has many edible forms, including Chinese cabbage, oilseed, pak choi, and turnip. It is also a close relative of the well-studied model plant, Arabidopsis . Since evolving away from Arabidopsis , the genome of B. rapa tripled, meaning it has one, two, or three copies of each gene. This has allowed the extra gene copies to mutate and adapt to different purposes. The question is, what impact has this genome expansion had on the plant's biological clock? One way to find out is to perform RNA-sequencing experiments, which record the genes a plant is using at any one time. Here, Greenham, Sartor et al. report the results of a series of RNA-sequencing experiments performed every two hours across two days. Plants were first exposed to light-dark or temperature cycles and then samples were taken when the plants were in constant light and temperature. This revealed which genes B. rapa turned on and off in response to signals from the internal biological clock. It turns out that the biological clock of B. rapa controls close to three quarters of its genes. These genes showed distinct phases, increasing or decreasing in regular patterns. But the different copies of duplicated and triplicated genes did not necessarily all behave in the same way. Many of the copies had different rhythms, and some increased and decreased in patterns totally opposite to their counterparts. Not only did the daily patterns differ, but responses to stressors like drought were also altered. Comparing these patterns to the patterns seen in Arabidopsis revealed that often, one B. rapa gene behaved just like its Arabidopsis equivalent, while its copies had evolved new behaviors. The different behaviors of the copies of each gene in B. rapa relative to its biological clock allow this plant to grow in different environments with varying temperatures and day lengths. Understanding how these adaptations work opens new avenues of research into how plants detect and respond to environmental signals. This could help to guide future work into targeting genes to improve crop growth and stress resilience. 

SUMMARY The demand for agricultural production is becoming more challenging as climate change increases global temperature and the frequency of extreme weather events. This study examines the phenotypic variation of 149 accessions ofBrachypodium distachyonunder drought, heat, and the combination of stresses. Heat alone causes the largest amounts of tissue damage while the combination of stresses causes the largest decrease in biomass compared to other treatments. Notably, Bd21‐0, the reference line forB. distachyon, did not have robust growth under stress conditions, especially the heat and combined drought and heat treatments. The climate of origin was significantly associated withB. distachyonresponses to the assessed stress conditions. Additionally, a GWAS found loci associated with changes in plant height and the amount of damaged tissue under stress. Some of these SNPs were closely located to genes known to be involved in responses to abiotic stresses and point to potential causative loci in plant stress response. However, SNPs found to be significantly associated with a response to heat or drought individually are not also significantly associated with the combination of stresses. This, with the phenotypic data, suggests that the effects of these abiotic stresses are not simply additive, and the responses to the combined stresses differ from drought and heat alone. 

SUMMARY As sessile organisms, plants are finely tuned to respond dynamically to developmental, circadian and environmental cues. Genome‐wide studies investigating these types of cues have uncovered the intrinsically different ways they can impact gene expression over time. Recent advances in single‐cell sequencing and time‐based bioinformatic algorithms are now beginning to reveal the dynamics of these time‐based responses within individual cells and plant tissues. Here, we review what these techniques have revealed about the spatiotemporal nature of gene regulation, paying particular attention to the three distinct ways in which plant tissues are time sensitive. (i) First, we discuss how studying plant cell identity can reveal developmental trajectories hidden in pseudotime. (ii) Next, we present evidence that indicates that plant cell types keep their own local time through tissue‐specific regulation of the circadian clock. (iii) Finally, we review what determines the speed of environmental signaling responses, and how they can be contingent on developmental and circadian time. By these means, this review sheds light on how these different scales of time‐based responses can act with tissue and cell‐type specificity to elicit changes in whole plant systems.