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bioRxiv2018

Population genome sequencing of the scab fungal species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata.

The Venturia genus comprises fungal species that are pathogens on Rosaceae host plants, including V. inaequalis and V. asperata on apple, V. aucupariae on sorbus and V. pirina on pear. Although the genetic structure of V. inaequalis populations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood. Here, we report whole genome sequencing of 87 Venturia strains that represent each species and each population within V. inaequalis. We present a PacBio genome assembly for the V. inaequalis EU-B04 reference isolate. The size of selected genomes was determined by flow cytometry, and varied from 45 to 93 Mb. Genome assemblies of V. inaequalis and V. aucupariae contain a high content of transposable elements (TEs), most of which belong to the Gypsy or Copia LTR superfamilies and have been inactivated by Repeat-Induced Point mutations. The reference assembly of V. inaequalis presents a mosaic structure of GC-equilibrated regions that mainly contain predicted genes and AT-rich regions, mainly composed of TEs. Six pairs of strains were identified as clones. Single-Nucleotide Polymorphism (SNP) analysis between these clones revealed a high number of SNPs that are mostly located in AT-rich regions due to misalignments and allowed determining a false discovery rate. The availability of these genome sequences is expected to stimulate genetics and population genomics research of Venturia pathogens. Especially, it will help understanding the evolutionary history of Venturia species that are pathogenic on different hosts, a history that has probably been substantially influenced by TEs.

plant biology↗

bioRxiv2018

β-cyclocitric acid: a new apocarotenoid eliciting drought tolerance in plants

{beta}-Cyclocitral ({beta}-CC) is a volatile compound deriving from 1O2 oxidation of {beta}-carotene in plant leaves. {beta}-CC elicits a retrograde signaling, modulating 1O2-responsive genes and enhancing tolerance to photooxidative stress. Here, we show that {beta}-CC is largely converted into {beta}-cyclocitric acid ({beta}-CCA) in leaves and that this metabolite is a signal involved in stress tolerance. Treatment of Arabidopsis plants with {beta}-CCA markedly enhanced plant tolerance to drought by a mechanism different from known responses such as stomatal closure, changes in osmotic potential and jasmonate signaling. Furthermore, we show that the response to {beta}-CCA does not fully overlap with the {beta}-CC-dependent signaling, indicating that {beta}-CCA induces only a branch of the {beta}-CC signaling pathway. In addition, the protective effect of {beta}-CCA is a conserved mechanism, being observed in a variety of plant species. This study provides a new bioactive agent with promising agronomic applications for protecting plants against drought.

plant biology↗

bioRxiv2018

HNI9 and HY5 maintain ROS homeostasis under high nitrogen provision in Arabidopsis

One sentence summaryExcessive N nutrition leads to ROS accumulation, and requires the function of major transcriptional regulators to maintain plants under physiological conditions.\n\nAuthor contributionsAn.M. and A.G. conceived research plans and supervised the experiments; F.B, Am.M., J.B., L.L., L.B. and An.M performed most of the experiments; F.B, Am.M., J.B., G.K., L.L., L.B. and An.M analyzed the data; An.M. wrote the article with contributions of all the authors.\n\nCompeting interestsThe authors declare no competing financial interests.\n\nSummaryReactive Oxygen Species (ROS) can accumulate in cells at excessive levels, leading to unbalanced redox status and to a potential oxidative stress, which can have damaging effects to the molecular components of plant cells. Several environmental conditions have been described as causing an elevation of ROS production in plants. Consequently, this requires the expression of detoxification responses in order to maintain ROS homeostasis at physiological levels. In case of mis-regulation of the detoxification systems, oxidative stress can lead ultimately to growth retardation and developmental defects. Here, we demonstrate that Arabidopsis plants growing under high nitrogen environment have to express a set of genes involved in detoxification of ROS in order to maintain ROS at physiological levels. We show that the chromatin factor HNI9 is an important actor of this response, required for the expression of these detoxification genes. Mutation in HNI9 leads to elevated ROS levels, and to ROS-dependent phenotypic defects under high but not low N provision. In addition, we identify HY5 as one of the major transcription factors also required for the expression of this detoxification program under high N condition. Our results demonstrate the requirement of a balance between N nutrition and ROS production, and identified the first major regulators required to control ROS homeostasis under excessive N nutrition.

plant biology↗

bioRxiv2018

A SOSEKI-based coordinate system interprets global polarity cues in Arabidopsis

Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division. In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI (SOK) proteins that integrate apical-basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. SOK proteins structurally resemble the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation. Our work identifies a plant compass, interpreted by SOK proteins. Furthermore, despite fundamental differences, polarity in plants and animals converge upon the same protein domain.

plant biology↗

bioRxiv2018

Black pod disease profile: Monitoring its outbreak in Southwest, Nigeria

Black pod disease (BPD) has been and still remains a major threat to cocoa farmers worldwide due to its annual recurrence, fast spread and highly destructive nature. The disease has caused great anxiety in many cocoa producing communities due to the inability of indigenous cocoa farmers to determine when and where BPD outbreak will take place. Twelve (12) stations were structured from four important cocoa-producing States in the Southwestern region of Nigeria. An investigation of BPD outbreak was conducted in 2015/2016 within these regions. Infected cocoa pods and topsoil samples were collected for laboratory analysis. Pests attack, cherelle wilt and BPD outbreak were seasonal with 50% chances of occurrence in all the stations. Black pod diseases outbreak was recorded in all the States (100%) during the rainy season. The disease was at its peak in August 2015 in almost all the stations (station 1 (30.0%), station 3 (23.0%), station 11 (16.0%), station 4 (9.0%), station 5 (7.0%), and station 8 (3.0%). The height of disease severity was in September 2015 (station 1 (100.0%), station 3 (96.7%), station 5 (85.7%), station 11 (84.3%), and station 4 (70.0%), with station 8 reaching the 100% mark in October 2015. Most cocoa farmlands are now being abandoned, unless concerted efforts are made to effectively manage the disease, BPD will greatly reduce cocoa production in Nigeria and around the world.

plant biology↗

bioRxiv2018

Partitioning index and non-structural carbohydrate dynamics among contrasting cassava genotypes under early terminal water stress

Cassava (Manihot esculenta Crantz.) is a storage root crop of importance in tropical regions where periodic dry season and drought affect performance. Cassava genotypes that differ in performance in ecosystems with various water regimes were subjected to water stress during storage-root initiation and early development. Plants were grown in 50 kg pots in a screen house environment under well-watered and water stress for over a 120-day period. Water stress had a significant effect on most traits analyzed. However, relative water content, partitioning index and non-structural carbohydrates were unaffected. Tolerant genotypes had a higher partitioning index than susceptible genotypes during water stress, associated with a larger number of storage roots initiated and larger storage root biomass, while they were shorter and had less fibrous root biomass. Tolerant lines were indistinguishable from susceptible lines in above ground biomass. These findings suggest that early evaluation of storage root number, partitioning index, and associated traits at an early stage of cassava storage-root development could be an effective approach by which cassava genotypes are screened for favorable drought tolerance response.

plant biology↗

bioRxiv2018

Integrated multiomic analysis from chromatin to translation of stimulus-regulated gene activity exposes dominant patterns of nuclear-level control

Gene regulation is modulated from chromatin to translation. To better understand the integration of nuclear and cytoplasmic gene regulatory dynamics, we performed a multi-omic survey of the epigenome through the translatome of the response of Arabidopsis seedlings to hypoxia and reoxygenation. This included eight assays of chromatin (histones, accessibility, RNAPII and transcription factor binding) and three assays of RNA (nuclear, polyadenylated, and ribosome-associated). Dynamic patterns of nuclear regulation distinguished stress-induced and growth-associated mRNAs. The rapid upregulation of hypoxia-responsive gene transcripts and their preferential translation was accompanied by increased chromatin accessibility, RNAPII engagement and reduced Histone 2A.Z association. The more progressive upregulation of heat stress gene transcripts was characterized by early engagement of RNAPII and elevation of nuclear over polyadenylated RNA. Promoters of the rapidly versus progressively upregulated gene cohorts were enriched for cis-elements of ethylene-responsive and heat shock factor transcription factor families, respectively. By contrast, genes associated with growth including ribosomal proteins underwent distinct histone modifications, yet retained RNAPII engagement and accumulated nuclear transcripts during the stress. Upon reaeration, many of the progressively upregulated and growth-associated gene transcripts were mobilized to ribosomes. Thus, multi-level nuclear regulation distinguishes transcript synthesis, accumulation and translation in response to a transient stress.

plant biology↗

bioRxiv2018

Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor

Gibberellins (GA) are key positive regulators of seed germination. Although the GA effects on seed germination have been studied in a number of species, little is known about the transcriptional reprogramming modulated by GA during this phase in species other than Arabidopsis thaliana. Here we report the transcriptome analysis of soybean embryonic axes during germination in the presence of paclobutrazol (PBZ), a GA biosynthesis inhibitor. We found a number of differentially expressed cell wall metabolism genes, supporting their roles in cell expansion during germination. Several genes involved in the biosynthesis and signaling of other phytohormones were also modulated, indicating an intensive hormonal crosstalk at the embryonic axis. We have also found 26 photosynthesis genes that are up-regulated by PBZ at 24 hours of imbibition (HAI) and down-regulated at 36 HAI, which led us to suggest that this is part of a strategy to implement an autotrophic growth program in the absence of GA-driven mobilization of reserves. Finally, 30 transcription factors (mostly from the MYB, bHLH and bZIP families) that are down-regulated by PBZ and are likely downstream GA targets that will drive transcriptional changes during germination.

plant biology↗

bioRxiv2018

Determining targeting specificity of nuclear-encoded organelle proteins with the self-assembling split fluorescent protein toolkit

A large number of nuclear-encoded proteins are targeted to the organelles of endosymbiotic origin, namely mitochondria and plastids. To determine the targeting specificity of these proteins, fluorescent protein tagging is a popular approach. However, ectopic expression of fluorescent protein fusions commonly results in considerable background signals and often suffers from the large size and robust folding of the reporter protein, which may perturb membrane transport. Among the alternative approaches that have been developed in recent years, the self-assembling split-fluorescent protein (sasplit-FP) technology appears particularly promising to analyze protein targeting specificity in vivo. Here, we have improved this technology with respect to sensitivity and systematically evaluated its utilization to determine protein targeting to plastids and mitochondria. Furthermore, to facilitate high throughput screening of candidate proteins we have developed a Golden Gate-based vector toolkit, named PlaMiNGo (Plastid and/or Mitochondria targeted proteins N-terminally fused to GFP11 tags via Golden Gate cloning). As a result of these improvements, dual targeting could be detected for a number of proteins, which had earlier been characterized as being targeted to a single organelle only. These results were independently confirmed with a plant phenotype complementation approach thus demonstrating the sensitivity and robustness of the sasplit-FP-based method to analyze the targeting specificity of nuclear-encoded proteins. HighlightSeveral mono-specific proteins showed dual targeting to plastids and mitochondria with the self-assembling split-GFP system. A Golden Gate-based vector toolkit was constructed to facilitate easy cloning and subsequent determination of protein targeting specificity.

plant biology↗

bioRxiv2018

PARbars: cheap, easy to build ceptometers for continuous measurement of light interception in plant canopies

Short AbstractDetailed instructions on how to build, calibrate and collect research quality data from PARbar ceptometers are presented.\n\nLong AbstractCeptometry is a technique used to measure the transmittance of photosynthetically active radiation through a plant canopy using multiple light sensors connected in parallel on a long bar. Ceptometry is often used to infer properties of canopy structure and light interception, notably leaf area index (LAI) and effective plant area index (PAIeff). Due to the high cost of commercially available ceptometers, the number of measurements that can be taken is often limited in space and time. This limits the usefulness of ceptometry for studying genetic variability in light interception, and precludes thorough analysis of, and correction for, biases that can skew measurements depending on the time of day. We developed continuously logging ceptometers (called PARbars) that can be produced for USD $75 each and yield high quality data comparable to commercially available alternatives. Here we provide detailed instruction on how to build and calibrate PARbars, how to deploy them in the field and how to estimate PAI from collected transmittance data. We provide representative results from wheat canopies and discuss further considerations that should be made when using PARbars.

plant biology↗

bioRxiv2018

High-throughput genotyping of the spelt gene pool reveals patterns of agricultural history in Europe

Spelt, a close relative of hexaploid bread wheat and a dominant wheat subspecies cultivated in Europe before the 20th century, still plays an important role as a high-value niche product today. Compared to most other cereals, spelt has not been subjected to intensive breeding in the 20th century. Even today, mostly traditional landraces are cultivated on a regional scale. The traditional way of spelt cultivation has limited the extensive exchange of germ plasm and intermixing of genetic material, which makes spelt an ideal crop to study the early agricultural history of cereals in Europe. Here, we unraveled the population structure and agricultural history of spelt based on 22,999 high-quality SNPs obtained by genotyping-by-sequencing on 267 spelt accessions covering the entire cultivation range. SNP markers were aligned to the high-quality bread wheat reference genome, which allowed us to analyze individual subgenomes. Our analyses of genetic variation revealed that bread wheat and spelt are most likely of monophyletic origin, but that European spelt diverged from bread wheat by hybridization with tetraploid emmer wheats. Interestingly, spelt accessions from the Iberian Peninsula formed a separate clade that was distinct from the Central European accessions for all three subgenomes. Demographic modelling indicated that Iberian spelt was introduced into Europe independently from Central European spelt. Our analysis provides a comprehensive assessment of spelt diversity and history. The separate introduction of Iberian spelt is supported by recent molecular evidence of two independent prehistoric migrations of ancient farmers from the Near East into Europe.

plant biology↗

bioRxiv2018

Epigenetics of floral homeotic genes in relation to sexual dimorphism in the dioecious plant Mercurialis annua

In plants, dioecy characterizes species carrying male and female flowers on separate plants and occurs in about 6% of angiosperms. To date, the molecular mechanism(s) underlying sexual dimorphism is essentially unknown. The ability of gender-reversal by hormone application suggests that epigenetics might play an important role in sexual dimorphism. Proteome analysis of nuclei derived from flower buds of females, males and feminized males of the dioecious plant Mercurialis annua revealed differentially expressed proteins related to nucleic acid binding proteins, hydrolases and transcription factors, including floral homeotic genes. Further analysis showed that class B genes are mainly expressed in male flowers, while class D genes, as well as SUPERMAN-like genes, were mainly expressed in female flowers. Cytokinin-induced feminization of male plants was associated with down-regulation of male-specific genes concomitantly with up-regulation of female-specific genes. No correlation could be found between the expression of class B and D genes and their DNA methylation or chromatin conformation. Thus, our results ruled out epigenetic control over floral identity genes as the major determinants regulating sexual dimorphisms. Rather, determination of sex in M. annua might be controlled upstream of floral identity genes by a gender-specific factor that affects hormonal homeostasis.\n\nHighlightsSex determination in Mercurialis annua is not related to epigenetics of floral homeotic genes but appears to be modulated by an unknown gender-specific regulator(s) that affects hormonal homeostasis.

plant biology↗

bioRxiv2018

Development of a New Method for the Highly Effective Identification of Cold Resistance in Living Avocado Varieties

This paper first identified the cold resistance of 38 varieties of avocado by determining the semi-lethal low temperature (LT50) of the leaves using an electrical conductivity method in combination with a logistic function, and then analyzed the correlation between the LT50 of 27 varieties and the capacitance measured 9 different parts of the leaves in vivo, to explore the relationship between the cold resistance of various avocado varieties and the capacitance of different parts of avocado leaves, so as to develop a new method for highly effective identification of cold resistance of living avocado varieties. The results showed that various avocado varieties LT50 was significantly positively correlated with the capacitance of some parts of leaves, showing that the cold resistance of various avocado varieties was negatively correlated with the capacitance of various leaf parts. The results of mango variety trials conducted for comparison is coincident with the theoretical conclusion reached in the identification of the cold resistance of the avocado. So as to the study of the cold resistance of avocado and mango varieties, the capacitance of live mature leaves measured in the field can be used as a new method for the judgment of cold resistance.\n\nHighlightA new method for identification of avocado cold resistance through measuring the capacitance of different parts of leaves was developed. This method are simple, quick and efficient.

plant biology↗

bioRxiv2018

Vulnerability to climate change for narrowly ranged species: the case of Ecuadorian endemic Magnolia mercedesiarum

Species vulnerability to climate change has been inferred using species distribution models from an example of the recently discovered Magnolia mercedesiarum (sect. Talauma, Magnoliaceae), a narrowly ranged species endemic to moist tropical forests in the eastern Ecuadorian Andes. The environmental conditions within the current species distribution area has been compared with conditions projected to 2050 and 2070, using data from the HadGEM2-ES model in two CO2 emission scenarios: RCP4.5 and RCP8.5. The ecological niche modelling allowed determination of parameters of climatic environmental conditions that control current species distribution to produce a hypothesis on probable changes in spatial pattern of suitable habitats in future scenarios. Within the current species distribution area of M. mercedesiarum, significant reduction of habitat suitability was projected for both emission scenarios, combined with a lack of nearby areas with adequate environmental conditions. Several disjunct sites of high habitat suitability were found to emerge in the Colombian Andes, but they seem unreachable by this tree species in the scope of a few decades, due to intrinsic dispersal limitations. The reduction of habitat suitability and improbability of distribution area shift to adjacent geographic locations could mean a high species vulnerability to climate change. The species could be at risk of extinction if it does not possess hidden phenotypical plasticity and potential for fast adaptation to climate change.

plant biology↗

bioRxiv2018

Subtilase-mediated activation of CLEL peptides involves several processing events in consecutive compartments of the secretory pathway

Post-translationally modified peptides are involved in many aspects of plant growth and development. The maturation of these peptides from their larger precursors is still poorly understood. We show here that the biogenesis of CLEL6 and CLEL9 peptides in Arabidopsis thaliana requires a series of processing events in consecutive compartments of the secretory pathway. Following cleavage of the signal peptide upon entry into the endoplasmic reticulum (ER), the peptide precursors are processed in the cis-Golgi by the subtilase SBT6.1. SBT6.1-mediated cleavage within the variable domain allows for continued passage of the partially processed precursors through the secretory pathway, and is a prerequisite for subsequent post-translational modifications including tyrosine sulfation and proline hydroxylation within, and proteolytic maturation after exit from the Golgi. Activation by subtilase SBT3.8 in post-Golgi compartments depends on the N-terminal aspartate of the mature peptides. Our work highlights the complexity of post-translational precursor maturation allowing for stringent control of peptide biogenesis.

plant biology↗

bioRxiv2018

Effects of FLOWERING LOCUS T on FD during the transition to flowering at the shoot apical meristem of Arabidopsis thaliana

The transition to flowering is a crucial step in the plant life cycle that is controlled by multiple endogenous and environmental cues, including hormones, sugars, temperature, and photoperiod. Permissive photoperiod induces FLOWERING LOCUS T (FT) in the phloem companion cells of leaves. The FT protein then acts as a florigen that is transported to the shoot apical meristem (SAM) where it physically interacts with the bZIP transcription factor FD and 14-3-3 proteins. However, despite the importance of FD for promoting flowering, its direct transcriptional targets are largely unknown. Here we combined ChIP-seq and RNA-seq to identify targets of FD at the genome-wide scale and assess the contribution of FT to binding DNA. We further investigated the ability of FD to form protein complexes with FT and TFL1 through the interaction with 14-3-3 proteins. Importantly, we observe direct binding of FD to targets involved in several aspects of the plant development not directly related to the regulation of flowering time. Our results confirm FD as central regulator of the floral transition at the shoot meristem and provides evidence for crosstalk between the regulation of flowering and other signaling pathways.\n\nMaterial DistributionThe author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.cell.com/molecular-plant/authors): Markus Schmid (markus.schmid@umu.se).\n\nContact InformationUme[a] Plant Science Centre (UPSC), Dept. of Plant Physiology Ume[a] University, SE-901 87 Ume[a], SWEDEN

plant biology↗

bioRxiv2018

Engineering a decoy substrate in soybean to enable recognition of the Soybean Mosaic Virus NIa protease

In Arabidopsis, recognition of the AvrPphB effector protease from Pseudomonas syringae is mediated by the disease resistance (R) protein RPS5, which is activated by AvrPphB-induced cleavage of the Arabidopsis protein kinase PBS1. The recognition specificity of RPS5 can be altered by substituting the AvrPphB cleavage site within PBS1 with cleavage sequences for other proteases, including proteases from viruses. AvrPphB also activates defense responses in soybean (Glycine max), suggesting that soybean may contain an R protein analogous to RPS5. It was unknown, however, whether this response is mediated by cleavage of a soybean PBS1-like protein. Here we show that soybean contains three PBS1 orthologs and that their products are cleaved by AvrPphB. Further, transient expression of soybean PBS1 derivatives containing a five-alanine insertion at their AvrPphB cleavage sites activated cell death in soybean protoplasts, demonstrating that soybean likely contains an AvrPphB-specific resistance protein that is activated by a conformational change in soybean PBS1 proteins. Significantly, we show that a soybean PBS1 decoy protein modified to contain a cleavage site for the Soybean mosaic virus (SMV) NIa protease triggers cell death in soybean protoplasts when cleaved by this protease, indicating that the PBS1 decoy approach will work in soybean using endogenous PBS1 genes. Lastly, we show that activation of the AvrPphB-dependent cell death response effectively inhibits systemic spread of SMV in soybean. These data also indicate that decoy engineering may be feasible in other crop plant species that recognize AvrPphB protease activity.

plant biology↗

bioRxiv2018

Arbuscular cotton-associated mycorrhizal fungi in Yeola region of Maharashtra, India

Mycorrhizae are a mutual symbiotic link between the plant root and a fungus that colonizes the cortical tissue of the roots during active plant growth periods. Both the host plant and the fungus have the potential to benefit. Mycorrhizae are ubiquitous throughout the world in terrestrial ecosystems. The purpose of this study is to evaluate the association of arbuscular mycorrhizal fungi in cotton crops with AM fungal population density in rhizosphere soils, investigate the qualitative composition of AM fungal species and the percentage of root colonization. The results showed that the number of AM fungal propagules collected from different locations in cotton crops ranged from 235 to 1580 spores per 100 g of soil. Due to the widespread nature of AM fungi, they occurred in almost all soil samples, but the number and type of spores and sporocarps varied. In total, 41 AM fungal species belonging to the genera Glomus, Acaulospora and Scutellospora were isolated. Glomus was found to be predominantly followed by Scutellospora in cotton soils in the rhizosphere. The distribution of spores, density and composition of AM fungi are observed to be influenced by environmental and physicochemical factors. The AM spore number, root colonization percentage and distribution vary depending on the seasonal fluctuations in moisture, temperature, pH and soil mineral nutrient status such as OC, P2O5, K2O, Zn, Cu, Fe, Mn, etc. The obtained data shows that nitrogen-deficient soils had more AM fungal propagules. The soils with a high concentration of phosphorus and potassium had the least AM fungal spores. Depleted zinc, copper and manganese levels have also been positive for more fungal occurrence and distribution. The presence of high iron levels in the soil, however, encourages more AM spores and a percentage of root colonisation.

plant biology↗