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Using a structural root system model for an in-depth assessment of root image analysis pipeline

Root system analysis is a complex task, often performed with fully automated image analysis pipelines. However, the outcome is rarely verified by ground-truth data, which might lead to underestimated biases.\n\nWe have used a root model, ArchiSimple, to create a large and diverse library of ground-truth root system images (10,000). For each image, three levels of noise were created. This library was used to evaluate the accuracy and usefulness of several image descriptors classically used in root image analysis softwares.\n\nOur analysis highlighted that the accuracy of the different traits is strongly dependent on the quality of the images and the type, size and complexity of the root systems analysed. Our study also demonstrated that machine learning algorithms can be trained on a synthetic library to improve the estimation of several root system traits.\n\nOverall, our analysis is a call to caution when using automatic root image analysis tools. If a thorough calibration is not performed on the dataset of interest, unexpected errors might arise, especially for large and complex root images. To facilitate such calibration, both the image library and the different codes used in the study have been made available to the community.

Plant Biology

Host-induced gene silencing compromises Verticillium wilt in tomato and Arabidopsis

Verticillium wilt, caused by soil-borne fungi of the genus Verticillium, is an economically important disease that affects a wide range of host plants. Unfortunately, host resistance against Verticillium wilts is not available for many plant species, and the disease is notoriously difficult to combat. Host-induced gene silencing (HIGS) is an RNA interference (RNAi) based process in which small RNAs are produced by the host plant to target parasite transcripts. HIGS has emerged as a promising strategy for improving plant resistance against pathogens by silencing genes that are essential for these pathogens. Here, we assessed whether HIGS can be utilized to suppress Verticillium wilt disease by silencing previously identified virulence genes of V. dahliae through the host plants tomato and Arabidopsis. In transient assays, tomato plants were agroinfiltrated with Tobacco rattle virus (TRV) constructs to target V. dahliae transcripts. Subsequent V. dahliae inoculation revealed suppression of Verticillium wilt disease in some, but not all, cases. Next, expression of RNAi constructs targeting V. dahliae transcripts was pursued in stable transgenic Arabidopsis thaliana plants. Also in this host, V. dahliae inoculation revealed reduced Verticillium wilt disease in some cases. Thus, our study suggests that, depending on the target gene chosen, HIGS against V. dahliae is operational in tomato and A. thaliana plants and may act as a plant protection approach that may be used in Verticillium wilt-susceptible crops.

Plant Biology

Stomatal and physiological response of contrasting Z. mauritiana (Lamk.) clones to water stress.

Water stress is one of the major limitations to fruit production worldwide. Identifying suitable indicators, screening techniques and quantifiable traits would facilitate the genetic improvement process for water stress tolerance. In the present study, we evaluated the ability of physiological parameters (Transpiration, E; Fv/Fm; leaf water potential, {psi}leaf; leaf temperature, LT; and, leaf relative water content, RWC) to distinguish between contrasting Z. mauritiana clones subjected to a 30-d drought cycle. Four field-grown clones Seb and Gola (tetraploid) and Q 29 and B 5/4 (diploid) were studied. By 30 d after the onset of water stress treatment, the E, Fv/Fm, {psi}leaf and RWC of drought-stressed plants had declined significantly in all genotypes compared to values of well-watered treatments. However, the reductions were more severe in leaves of diploid clones. Under drought stress, the Seb and Gola, maintained higher E (31.5%), Fv/Fm (6.28%), {psi}leaf; (11.2%), and RWC (9.3 %) than Q 29 and B 5/4 clones. In general, LT of drought-stressed plants was higher (~4{degrees}C) than that of well-watered plants but the relative increase was greater among later than former ones. Under maximum drought stress, LT of Seb and Gola clones was on average 3.0{degrees}C lower than that of Q 29 and B 5/4. Former clones yielded 20% more than later ones, mainly reason being (14.8%) less fruit drop as an effect of water stress. The results indicate that presented parameters can be reliable in screening for water stress tolerance ability, with Fv/Fm, {psi}leaf, RWC and LT having the added advantage of being easily and quickly assessed.

Plant Biology

AGO4 is specifically required for heterochromatic siRNA accumulation at Pol V-dependent loci in Arabidopsis thaliana

Significance statementGenome-wide characterization of AGO4-dependent siRNAs revealed that AGO4 is required for the accumulation of a small subset of heterochromatic siRNAs in Arabidopsis thaliana. These AGO4-depdenent siRNAs are likely secondary het-siRNAs produced by a self-reinforcing loop of RdDM. Slicing-defective AGO4 is unable to fully complement het-siRNA accumulation from an ago4 mutant, demonstrating the critical role of AGO4 catalytic ability in het-siRNA accumulation.\n\nSummary: 152; Introduction: 618; Results: 1291; Discussion: 1013; Experimental procedures: 881; Acknowledgements: 24; Figure legends: 568; Author contribution: 25; Conflict of interest: 13; Funding: 34; References: 1289\n\nSummaryIn plants, 24 nucleotide long heterochromatic siRNAs (het-siRNAs) transcriptionally regulate gene expression by RNA-directed DNA methylation (RdDM). The biogenesis of most het-siRNAs depends on the plant-specific RNA polymerase IV (Pol IV), and ARGONAUTE4 (AGO4) is a major het-siRNA effector protein. Through genome-wide analysis of sRNA-seq data sets, we found that AGO4 is required for the accumulation of a small subset of het-siRNAs. The accumulation of AGO4-dependent het-siRNAs also requires several factors known to participate in the effector portion of the RdDM pathway, including RNA POLYMERASE V (POL V), DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1). Like many AGO proteins, AGO4 is an endonuclease that can slice RNAs. We found that a slicing-defective AGO4 was unable to fully recover AGO4-dependent het-siRNA accumulation from ago4 mutant plants. Collectively, our data suggest that AGO4-dependent siRNAs are secondary siRNAs dependent on the prior activity of the RdDM pathway at certain loci.

Plant Biology

Sequencing of small RNAs of the fern Pleopeltis minima (Polypodiaceae) offers insight into the evolution of the microRNA repertoire in land plants

MicroRNAs (miRNAs) are short, single stranded RNA molecules that regulate the stability and translation of messenger RNAs in diverse eukaryotic groups. Several miRNA genes are of ancient origin and have been maintained in the genomes of animal and plant taxa for hundreds of millions of years, and functional studies indicate that ancient miRNAs play key roles in development and physiology. In the last decade, genome and small RNA (sRNA) sequencing of several plant species have helped unveil the evolutionary history of land plant miRNAs. Land plants are divided into bryophytes (liverworts, mosses), lycopods (clubmosses and spikemosses), monilophytes (ferns and horsetails), gymnosperms (cycads, conifers and allies) and angiosperms (flowering plants). Among these, the fern group occupies a key phylogenetic position, since it represents the closest extant cousin taxon of seed plants, i.e. gymno- and angiosperms. However, in spite of their evolutionary, economic and ecological importance, no fern genome has been sequenced yet and few genomic resources are available for this group. Here, we sequenced the small RNA fraction of an epiphytic South American fern, Pleopeltis minima (Polypodiaceae), and compared it to plant miRNA databases, allowing for the identification of miRNA families that are shared by all land plants, shared by all vascular plants (tracheophytes) or shared by euphyllophytes (ferns and seed plants) only. Using the recently described transcriptome of another fern, Lygodium japonicum, we also estimated the degree of conservation of fern miRNA targets in relation to other plant groups. Our results pinpoint the origin of several miRNA families in the land plant evolutionary tree with more precision and are a resource for future genomic and functional studies of fern miRNAs.

Plant Biology

The PhytoClust Tool for Metabolic Gene Clusters Discovery in Plant Genomes

The existence of Metabolic Gene Clusters (MGCs) in plant genomes has recently raised increased interest. Thus far, MGCs were commonly identified for pathways of specialized metabolism, mostly those associated with terpene type products. For efficient identification of novel MGCs computational approaches are essential. Here we present PhytoClust; a tool for the detection of candidate MGCs in plant genomes. The algorithm employs a collection of enzyme families related to plant specialized metabolism, translated into hidden Markov models, to mine given genome sequences for physically co-localized metabolic enzymes. Our tool accurately identifies previously characterized plant MBCs. An exhaustive search of 31 plant genomes detected 1232 and 5531 putative gene cluster types and candidates, respectively. Clustering analysis of putative MGCs types by species reflected plant taxonomy. Furthermore, enrichment analysis revealed taxa- and species-specific enrichment of certain enzyme families in MGCs. When operating through our web-interface, PhytoClust users can mine a genome either based on a list of known cluster types or by defining new cluster rules. Moreover, for selected plant species, the output can be complemented by co-expression analysis. Altogether, we envisage PhytoClust to enhance novel MGCs discovery which will in turn impact the exploration of plant metabolism.

Plant Biology

Linking gene expression to unilateral pollen-pistil reproductive barriers

Unilateral incompatibility (UI) is an asymmetric reproductive barrier that unidirectionally prevents gene flow between species and/or populations. UI is characterized by a compatible interaction between partners in one direction, but in the reciprocal cross fertilization fails, generally due to pollen tube rejection by the pistil. Although UI has long been observed in crosses between different species, the underlying molecular mechanisms are only beginning to be characterized. The wild tomato relative Solanum habrochaites provides a unique study system to investigate the molecular basis of this reproductive barrier, as populations within the species exhibit both interspecific and interpopulation UI. Here we used a transcriptomic approach to identify genes in both pollen and pistil tissues that may be probable key players in UI. We confirmed UI at the pollen-pistil level between a self-incompatible population and a self-compatible population of S. habrochaites. A comparison of gene expression between pollinated styles exhibiting the incompatibility response and unpollinated controls revealed only a small number of differentially expressed transcripts. Many more differences in transcript profiles were identified between UI-competent versus UI-compromised reproductive tissues. A number of intriguing candidate genes were highly differentially expressed, including a putative pollen arabinogalactan protein, a stylar Kunitz family protease inhibitor, and a stylar peptide hormone Rapid Alkalinization Factor. Our data also provide transcriptomic evidence that fundamental processes including reactive oxygen species signaling are likely key in UI pollen-pistil interactions between both populations and species. Our transcriptomic analysis highlighted specific genes, including those in ROS signaling pathways that warrant further study in investigations of UI. To our knowledge, this is the first report to identify candidate genes involved in unilateral barriers between populations of the same species.

plant biology

Artificial Microbiome-Selection to Engineer Microbiomes That Confer Salt-Tolerance to Plants

We develop a method to artificially select for rhizosphere microbiomes that confer salt-tolerance to the model grass Brachypodium distachyon. We differentially propagate microbiomes within the background of a non-evolving, highly-inbred plant population, and therefore only microbiomes evolve in our experiment, but not the plants. To optimize methods, we conceptualize artificial microbiome-selection as a special case of indirect selection: We do not measure microbiome properties directly, but we use host performance (e.g., biomass; seed set) as an indicator to infer association with rhizosphere microbiomes that confer salt-tolerance to a plant. We previously called this indirect-selection scheme host-mediated indirect selection on microbiomes (Mueller & Sachs 2015). Our methods aim to maximize evolutionary changes due to differential microbiome-propagation, while minimizing some (but not all) ecological processes affecting microbiome composition. Specifically, our methods aim to maximize microbiome perpetuation between selection-cycles and maximize response to artificial microbiome-selection by (a) controlling microbiome assembly when inoculating seeds at the beginning of each selection cycle; (b) using low-carbon soil to enhance host-control mediated by carbon secretions of plants during initial microbiome assembly and subsequent microbiome persistence; (c) fractionating microbiomes before transfer between plants to perpetuate and select only on bacterial and viral (but not fungal) microbiome components; and (d) ramping of salt-stress between selection-cycles to minimize the chance of over-stressing plants. Our selection protocol generates microbiomes that enhance plant fitness after only 1-3 rounds of artificial selection on rhizosphere microbiomes. Relative to fallow-soil control treatments, artificially-selected microbiomes increase plant fitness by 75% under sodium-sulfate stress, and by 38% under aluminum-sulfate stress. Relative to null control treatments, artificially-selected microbiomes increase plant fitness by 13% under sodium-sulfate stress, and by 12% under aluminum-sulfate stress. When testing microbiomes after nine rounds of differential microbiome propagation, the effect of bacterial microbiomes selected to confer tolerance to sodium-sulfate stress appears specific (these microbiomes do not confer tolerance to aluminum-sulfate stress), but the effect of microbiomes selected to confer tolerance to aluminum-sulfate stress appears non-specific (selected microbiomes ameliorate both sodium- and aluminum-sulfate stresses). Complementary metagenomic analyses of the artificially selected microbiomes will help elucidate metabolic properties of microbiomes that confer specific versus non-specific salt-tolerance to plants.

plant biology

Tomographic docking suggests the mechanism of auxin receptor TIR1 selectivity

We study the binding of plant hormone IAA on its receptor TIR1 introducing a novel computa-tional method that we call tomographic docking and that accounts for interactions occurring along the depth of the binding pocket. Our results suggest that selectivity is related to constraints that potential ligands encounter on their way from the surface of the protein to their final position at the pocket bottom. Tomographic docking helps develop specific hypotheses about ligand binding, distinguishing binders from non-binders, and suggests that binding is a three-step mechanism, consisting of engagement with a niche in the back wall of the pocket, interaction with a molecular filter which allows or precludes further descent of ligands, and binding on the pocket base. Only molecules that are able to descend the pocket and bind at its base allow the co-receptor IAA7 to bind on the complex, thus behaving as active auxins. Analyzing the interactions at different depths, our new method helps in identifying critical residues that constitute preferred future study targets and in the quest for safe and effective herbicides. Also, it has the potential to extend the utility of docking from ligand searches to the study of processes contributing to selectivity.

plant biology

Arabidopsis MADS-box transcription factor AGL21 acts as environmental surveillance for seed germination by regulating ABI5

Seed germination is a crucial checkpoint for plant survival under unfavorable environmental conditions. Abscisic acid (ABA) and its signaling play a vital role in integrating environmental information to regulate seed germination. MCM1/AGAMOUS/DEFICIENS/SRF (MADS)-box transcription factors are mainly known as key regulators of seed and flower development in Arabidopsis. However, their functions in seed germination are still poorly understood. Here we report that MADS-box transcription factor AGL21 negatively modulates seed germination and post-germination growth by controlling the expression of ABA-INSENSITIVE 5 (ABI5) in Arabidopsis. AGL21 responds to multiple environmental stresses and plant hormones. The AGL21-overexpressing plants are hypersensitive to ABA, salt and osmotic stresses during seed germination and early post-germination growth, whereas agl21 mutants are less sensitive. AGL21 positively regulates ABI5 expression in seeds. Genetic analyses reveal that AGL21 is epistatic to ABI5 in controlling seed germination. Chromatin immunoprecipitation assays further demonstrate that AGL21 could directly bind to the ABI5 promoter in plant cells. Taken together, our results suggest that AGL21 acts as a surveillance integrator that incorporates environmental cues and endogenous hormonal signals into ABA signaling to regulate seed germination and early post-germination growth.

plant biology

Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria

Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed twelve controlled growth trials of an interspecific Setaria italica x Setaria viridis recombinant inbred line population to assess how the genetic architecture of plant height is influenced by developmental queues, water availability and planting density. The nondestructive nature of plant height measurements has enabled us to monitor vertical growth throughout the plant life cycle in both field and controlled environments. We find that plant height is reduced under water limitation and high density planting and affected by growth environment (field vs. growth chamber). The results support a model where plant height is a heritable, polygenic trait and that the major genetic loci that influence plant height function independent of growth environment. The identity and contribution of loci that influence height changes dynamically throughout development and the reduction of growth observed in water limited environments is a consequence of delayed progression through the genetic program which establishes plant height in Setaria. In this population, alleles inherited from the weedy S. viridis parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated S. italica parent collectively act to increase plant height later in development.

plant biology

The Tension-sensitive Ion Transport Activity of MSL8 is Critical for its Function in Pollen Hydration and Germination

All cells respond to osmotic challenges, including those imposed during normal growth and development. Mechanosensitive (MS) ion channels provide a conserved mechanism for regulating osmotic forces by conducting ions in response to increased membrane tension. We previously demonstrated that the MS ion channel MscS-Like 8 (MSL8) is required for pollen to survive multiple osmotic challenges that occur during the normal process of fertilization, and that it can inhibit pollen germination. However, it remained unclear whether these physiological functions required ion flux through a mechanically gated channel provided by MSL8. We introduced two point mutations into the predicted pore-lining domain of MSL8 that disrupted normal channel function in different ways. The Ile711Ser mutation increased the tension threshold of the MSL8 channel while leaving conductance unchanged, and the Phe720Leu mutation severely disrupted the MSL8 channel. Both of these mutations impaired the ability of MSL8 to preserve pollen viability during hydration and to maintain the integrity of the pollen tube when expressed at endogenous levels. When overexpressed in a msl8-4 null background, MSL8I711S could partially rescue loss-of-function phenotypes, while MSL8F720L could not. When overexpressed in the wild type Ler background, MSL8I711S suppressed pollen germination, similar to wild type MSL8. In contrast, MSL8F720L failed to suppress pollen germination and increased pollen bursting, thereby phenocopying the msl8-4 mutant. Thus, an intact MSL8 channel is required to for normal pollen function during hydration and germination. These data establish MSL8 as the first plant MS channel to fulfill previously established criteria for assignment as a mechanotransducer.

plant biology

tRNA-derived small RNAs target transposable element transcripts

tRNA-derived RNA fragments (tRFs) are 18-26 nucleotide small RNAs that are not random degradation products, but are rather specifically cleaved from mature tRNA transcripts. Abundant in stressed or viral-infected cells, the function and potential targets of tRFs are not known. We identified that in the unstressed wild-type male gamete containing pollen of flowering plants, and analogous reproductive structure in non-flowering plant species, tRFs accumulate to high levels. In the reference plant Arabidopsis thaliana, tRFs are cleaved by Dicer-like 1 and incorporated into Argonaute1 (AGO1), akin to a microRNA. We utilized the fact that many plant small RNAs direct cleavage of their target transcripts to demonstrate that where the tRF-AGO1 complex acts to specifically target and cleave endogenous transposable element (TE) mRNAs produced from transcriptionally active TEs. The data presented here demonstrate that tRFs are bona-fide regulatory microRNA-like small RNAs involved in the regulation of genome stability through the targeting of TE transcripts.

plant biology

Dynamical modelling of the heat shock response in Chlamydomonas reinhardtii

Global warming is exposing plants to more frequent heat stress, with consequent crop yield reduction. Organisms exposed to large temperature increases protect themselves typically with a heat shock response (HSR). To study the HSR in photosynthetic organisms we present here a data driven mathematical model describing the dynamics of the HSR in the model organism Chlamydomonas reinhartii. Temperature variations are sensed by the accumulation of unfolded proteins, which activates the synthesis of heat shock proteins (HSP) mediated by the heat shock transcription factor HSF1. Our dynamical model employs a system of ordinary differential equations mostly based on mass-action kinetics to study the time evolution of the involved species. The signalling network is inferred from data in the literature, and the multiple experimental data-sets available are used to calibrate the model, which allows to reproduce their qualitative behaviour. With this model we show the ability of the system to adapt to temperatures higher than usual during heat shocks longer than three hours by shifting to a new steady state. We study how the steady state concentrations depend on the temperature at which the steady state is reached. We systematically investigate how the accumulation of HSPs depends on the combination of temperature and duration of the heat shock. We finally investigate the system response to a smooth variation in temperature simulating a hot day.

plant biology

Ancient coding sequences underpin the spatial patterning of gene expression in C4 leaves

Photosynthesis is compromised in most plants because an enzymatic side-reaction fixes O2 instead of CO2. The energetic cost of oxygenation led to the evolution of C4 photosynthesis. In almost all C4 leaves compartmentation of photosynthesis between cells reduces oxygenation and so increases photosynthetic efficiency. Here we report that spatial expression of most C4 genes is controlled by intragenic cis-elements rather than promoter sequence. Two DNA motifs that cooperatively specify the patterning of genes required for C4 photosynthesis are identified. They are conserved in plants and algae that use the ancestral C3 pathway. As these motifs are located in exons they represent duons determining both gene expression and amino acid sequence. Our findings provide functional evidence for the importance of transcription factors recognising coding sequence as previously defined by genome-wide binding studies. Furthermore, they indicate that C4 evolution is based on ancient DNA motifs found in exonic sequence.

plant biology

Verticillium dahliae LysM effectors differentially contribute to virulence on plant hosts

Chitin-binding LysM effectors contribute to virulence of various plant pathogenic fungi that are causal agents of foliar diseases. Here, we report on LysM effectors of the soil-borne fungal vascular wilt pathogen Verticillium dahliae. Comparative genomics revealed three core LysM effectors that are conserved in a collection of V. dahliae strains. Remarkably, and in contrast to the previously studied LysM effectors of other plant pathogens, no expression of core LysM effectors was monitored in planta in a taxonomically diverse panel of host plants. Moreover, targeted deletion of the individual LysM effector genes in V. dahliae strain JR2 did not compromise virulence in infections on Arabidopsis, tomato or Nicotiana benthamiana. Interestingly, an additional lineage-specific LysM effector is encoded in the genome of V. dahliae strain VdLs17 but not in any other V. dahliae strain sequenced to date. Remarkably, this lineage-specific effector is expressed in planta and contributes to virulence of V. dahliae strain VdLs17 on tomato, but not on Arabidopsis or on N. benthamiana. Functional analysis revealed that this LysM effector binds chitin, is able to suppress chitin-induced immune responses, and protects fungal hyphae against hydrolysis by plant hydrolytic enzymes. Thus, in contrast to the core LysM effectors of V. dahliae, this lineage-specific LysM effector of strain VdLs17 contributes to virulence in planta.

plant biology

Shared characteristics underpinning C4 leaf maturation derived from analysis of multiple C3 and C4 species of Flaveria

Most terrestrial plants use C3 photosynthesis to fix carbon. In multiple plant lineages a modified system known as C4 photosynthesis has evolved. To better understand the molecular patterns associated with induction of C4 photosynthesis the genus Flaveria that contains C3 and C4 species was used. A base to tip maturation gradient of leaf anatomy was defined, and RNA sequencing was undertaken along this gradient for two C3 and two C4 Flaveria species. Key C4 traits including vein density, mesophyll and bundle sheath cross-sectional area, chloroplast ultrastructure, and abundance of transcripts encoding proteins of C4 photosynthesis were quantified. Candidate genes underlying each of these C4 characteristics were identified. Principal Components Analysis indicated that leaf maturation and then photosynthetic pathway were responsible for the greatest amount of variation in transcript abundance. Photosynthesis genes were over-represented for a prolonged period in the C4 species. Through comparison with publically available datasets we identify a small number of transcriptional regulators that have been up-regulated in diverse C4 species. The analysis identifies similar patterns of expression in independent C4 lineages and so indicates that the complex C4 pathway is associated with parallel as well as convergent evolution.\n\nHighlightWe identify transcription factors that show conserved patterns of expression in multiple 29 C4 species, both within the Flaveria genus, but also in more distantly related C4 plants.

plant biology

Plant growth regulators ameliorate or exacerbate abiotic and biotic stress effects on Zea mays kernel weight in a genotype-specific manner

Plant growth regulators have documented roles in plant responses to single stresses. In combined-stress environments, plants display novel genetic architecture for growth traits and the response to growth regulators is unclear. We investigated the role of plant growth regulators in combined-stress responses in Zea mays. Twelve maize inbreds were exposed to all combinations of the following stressors: drought, nitrogen, and density stress. Chemical treatments were utilized to alter balances of the hormones abscisic acid, gibberellic acid, and brassinosteroids. We found a significant difference between the seed weights of plants given different chemical treatments after accounting for differences in genotype and stress environments. We conclude that plant growth regulators have targets in combined-stress response pathways in Zea mays.\n\nHIGHLIGHTPlant growth regulators can ameliorate effects of combinations of abiotic and biotic stress in maize, in certain genotypes and under specific stress conditions.

plant biology