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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2019

Potato genotypes differentially alter the expression of Phytophthora infestans effectors during PAMP-mediated resistance induction

O_LIPathogen recognition by plants via pathogen-associated molecular patterns leads to PAMP-triggered immunity. However, pathogens can modulate it via the secretion of effectors. We hypothesize that in potato, induced defense triggered by a Phytophthora infestans concentrated culture filtrate (CCF) could alter both effector expression and disease severity. C_LIO_LICCF was sprayed onto three potato genotypes with different resistance levels, before inoculation with P. infestans. Symptoms were scored visually at 1-4 dpi, while the expression of defense and effector genes was assessed by qRT-PCR. C_LIO_LICCF induced most defense genes in Desiree (PRs, EIN3) and Bintje (PRs, PAL and POX), but repressed most defense genes in Rosafolia. On the contrary, CCF induced most effector genes in Rosafolia (Pi03192, Avrblb2, Avr3a, EPIC2B and SNE1). INF1 was over-expressed in Bintje, despite its earlier expression in both Desiree and Rosafolia compared to unsprayed controls. Pi03192 was repressed in Desiree, and was expressed earlier in Rosafolia than in controls. However, induced defense responses by CCF significantly reduced lesion areas at 3 dpi only in Desiree. C_LIO_LIThe effectiveness of induced defense thus depends on host genotypes. It results from differential interactions and kinetics of defense and effector genes expressions. C_LI

plant biology↗

bioRxiv2019

Control of Shoot Meristem Size by an Aminoacyl tRNA Synthetase, OKI1, in Arabidopsis

In plants, the stem cells that form the shoot system reside within the shoot apical meristem (SAM), which is regulated by feedback signaling between the WUSCHEL (WUS) homeobox protein and CLAVATA (CLV) peptides and receptors. WUS-CLV feedback signaling can be modulated by various endogenous or exogenous factors such as chromatin state, hormone signaling, reactive oxygen species (ROS) signaling and nutrition, leading to a dynamic control of SAM size corresponding to meristem activity. Despite these insights, however, the knowledge of genes that control stem cell fate is still limited, and in particular the regulation by ROS signaling is only beginning to be comprehended. Here, we report a new regulator of SAM size, OKINA KUKI (OKI1), which is expressed in the SAM and encodes a mitochondrial aspartyl tRNA synthetase (AspRS). oki1 mutants display enlarged SAMs with abnormal expression of WUS and CLV3, and overaccumulation of ROS in the meristem. Our findings support the importance of normal AspRS function in the maintenance of the WUS-CLV3 feedback loop and SAM size.

plant biology↗

bioRxiv2019

HEXOKINASE 1 Glycolytic Action Fuels Post-Germinative Seedling Growth

O_LIIn darkness, PHYTOCHROME INTERACTING FACTOR (PIF)-induced skotomorphogenic seedling growth, is exemplified by increased hypocotyl elongation. HEXOKINASE1 (HXK1), which is also implicated in seedling establishment, can operate as a glycolytic enzyme or as a glucose-activated sensor signalling molecule. Under light and nutrient limiting conditions, the HXK1 sensor-signalling has been shown to control hypocotyl elongation. Little is known of whether HXK1 glycolytic function, or HXK1 and PIF cross-talk, is required to control hypocotyl growth. C_LIO_LIWe demonstrate HXK1 glycolytic activity is critical for cell expansion, and hypocotyl growth, post-germination. Notably, application of glucose-6-phosphate, the HXK1 enzymatic product, can restore short gin2-1/hxk1-1 mutant hypocotyls to wild-type length. Further, HXK1 sensor-signalling complex components, VHA-B1 and RPT5B, do not contribute to this response, for unlike gin2-1/hxk1-1, the vha-B1 and rpt5b alleles only disrupt hypocotyl growth following exogenous glucose application. C_LIO_LImRNA-seq analysis illustrates that HXK1 and PIF signalling converge at genes with known roles in light signalling. HXK1 imposes strong regulation on chloroplast and mitochondrial encoded genes, also branched chain amino acid catabolism pathway genes, which can provide a source of respiratory substrates in starvation conditions. C_LIO_LIOur study establishes the importance of HXK1 enzymatic function in supporting cell expansion and hypocotyl growth. We demonstrate a degree of cross-talk between HXK1 and PIFs through common target gene set. C_LI

plant biology↗

bioRxiv2019

Visible light-triggered NO generation from Naphthalimide-based probe for photoreceptor-mediated plant root growth regulation

An efficient visible light-triggered nitric oxide (NO) releasing fluorescent molecule is designed and synthesized by coupling 2,6-dimethyl nitrobenzene moiety at the peri-position of 1, 8-naphthalimide through an alkene bond. The NO-releasing ability is investigated in details using various spectroscopic techniques, and the photoproduct was also characterized. Further, the photo-generated NO has been employed to examine the effect of photoreceptor-mediated NO uptake on plant root growth regulation.

plant biology↗

bioRxiv2019

Impacts of reduced inorganic N:P ratio on three distinct plankton communities in the Humboldt upwelling system

The ratio of inorganic nitrogen to phosphorus (NP) is projected to decrease in the Eastern Boundary Upwelling Systems (EBUS) due to warming of the surface waters. In an enclosure experiment, we employed two levels of NP ratios (10 and 5) for three distinct plankton communities collected along the coast of central Chile (33{degrees}S). The primary effect of the NP treatment was related to different concentrations of NO3, which directly influenced the biomass of phytoplankton. Additionally, low inorganic NP ratio reduced the seston NP and Chl a-C ratios, and there were some effects on the plankton community composition, e.g. benefitting Synechococcus spp in some communities. One of the communities was clearly top down controlled and trophic transfer to grazers was up to 5.8% during the 12 day experiment. Overall, the initial plankton community composition was more important for seston stoichiometry and trophic transfer than the inorganic NP ratio. Any long term change in the plankton community structure will likely have greater impact than direct effects of a decreasing inorganic NP ratio on the Humboldt Current ecosystem.

plant biology↗

bioRxiv2019

Pathogen-induced pH changes regulate the growth-defense balance of plants

Environmental adaptation of organisms relies on fast perception and response to external signals, which lead to developmental changes. Plant cell growth is strongly dependent on cell wall remodeling. However, little is known about cell wall-related sensing of biotic stimuli and the downstream mechanisms that coordinate growth and defense responses. We generated genetically encoded pH sensors to determine absolute pH changes across the plasma membrane in response to biotic stress. A rapid apoplastic acidification by phosphorylation-based proton pump activation was followed by an acidification of the cortical side of the plasma membrane in response to the fungus Fusarium oxysporum. The proton chemical gradient modulation immediately reduced cellulose synthesis and cell growth and, furthermore, had a direct influence on the pathogenicity of the fungus. All these effects were dependent on the COMPANION OF CELLULOSE SYNTHASE proteins that are thus at the nexus of plant growth and defense. Hence, our discoveries show a remarkable connection between plant biomass production, immunity, and pH control, and advance our ability to investigate the plant growth-defense balance.

plant biology↗

bioRxiv2019

Ancestral and neo-sex chromosomes contribute to population divergence in a dioecious plant

Empirical evidence from several animal groups suggests that sex chromosomes may disproportionately contribute to reproductive isolation. This occurs particularly when sex chromosomes are associated with turnover of sex determination systems resulting from structural rearrangements to the sex chromosomes. We investigated these predictions in the dioecious plant Rumex hastatulus, which is comprised of populations of two sex chromosome cytotypes. Using population genomic analyses, we investigated the demographic history of R. hastatulus and explored the contributions of ancestral and neo-sex chromosomes to population genetic divergence. Our study revealed that the cytotypes represented genetically divergent populations with evidence for historical but not contemporary gene flow between them. In agreement with classical predictions, we found that the ancestral X chromosome was disproportionately divergent compared with the rest of the genome. Excess differentiation was also observed on the Y chromosome, even when using measures of differentiation that control for differences in effective population size. Our estimates of the timing of the origin of the neo-sex chromosomes in R. hastatulus are coincident with cessation of gene flow, suggesting that the chromosomal fusion event that gave rise to the origin of the XYY cytotype may have also been a key driver of reproductive isolation.

plant biology↗

bioRxiv2019

Transcriptional dynamics of bread wheat in response to nitrate and phosphate supply reveal functional divergence of genetic factors involved in nitrate and phosphate signaling

Nitrate (N) and phosphate (P) levels are sensed by plant cells and signaled via local and systemic signaling pathways to modulate plant growth and development. Understanding the genetic basis of these signaling mechanisms is key to future improvement of nutrient use efficiency. While major progress has been made in understanding N and P signaling pathways and their interaction in the model plant Arabidopsis, understanding of transcriptional responses to N and P in a major monocot crop wheat is lacking. Therefore, we investigated gene expression dynamics of wheat roots in response to N and/or P provision using RNA-Seq. We found that nitrate presence is the major trigger for most of the transcriptional response to occur within 24 h, however, we also identified a large array of synergistic transcriptional responses to concomitant supply of N and P. Through gene co-expression analysis, we identified gene co-expression modules prominent in nitrate signaling and metabolism in wheat. Importantly, we identified likely instances of functional divergence in major N-responsive transcription factors families HRS1/HHO and TGA of wheat from their rice/Arabidopsis homologues. Our work broadens the understanding of wheat N and P transcriptional responses and aids in prioritizing gene candidates for production of wheat varieties that are efficient in nitrogen usage.

plant biology↗

bioRxiv2019

Cold Vacuum Extracts of Double Cherry Blossom (Gosen-Sakura) Leaves Show Antitumor Activity

The present research examines the possibility of finding bio-molecular compounds from the double cherry blossom (termed as Gosen-Sakura of Gosen-city, Niigata-prefecture, Japan) leaves, which have been long used in the preparation of the traditional Japanese sweet (wagashi) - sakura-mochi. Based on its indicated anti-microbial properties historically, our study provides a new low temperature vacuum extraction method for extracting near natural form of water soluble leaf (cell) extracts from the Gosen-Sakura, and demonstrates the presence of some novel compound(s) with anti-tumor cell lines proliferation inhibitory affects through the MTT assay. To our knowledge, no reports exist on the sakura tree leaf (cell) extracts inhibiting tumor cell line growth. We further examined and compared the effects of known compounds with anti-tumor activity, coumarin and benzyl alcohol with Gosen-Sakura leaf extract; results lead us to hypothesize that the Gosen-Sakura leaf extract contains substance(s) other than the above 2 known compounds, with antitumor effect. Additionally, we speculate on the underlying mechanism of action of the Gosen-Sakura leaf extract by targeting cell division at the point of DNA synthesis and causing apoptosis. In conclusion, we present scientific evidence on the presence of a certain novel biomolecule(s), with anti-tumor activity, in the Gosen-Sakura leaf which has been long used as a Japanese - the sakura-mochi.

plant biology↗

bioRxiv2019

Honey bees, Apis mellifera, are important pollinators of the highbush blueberry variety Ventura despite the inability to sonicate

Animal-mediated pollination is an essential ecosystem service which over a third of the worlds agricultural crops depend on. Blueberry fruit production is highly dependent on pollinators and in their native range they are pollinated mostly by bumble bees (Bombus spp.). Demand for blueberries has increased in recent years due to their perceived health benefits. Consequently, blueberry cultivation has expanded well beyond their native range, including several regions where bumble bees are not present. In many areas, honey bees may be the only commercially available pollinators of blueberries because many countries ban the importation of bumble bees. This study aimed to determine the benefits of honey bee pollination on blueberry fruit quality and quantity for the variety Ventura by comparing yields of honey-bee-pollinated flowers to flowers where pollinators had been excluded. Honey bees significantly increased berry mass and diameter. Our results suggest that the presence of honey bee pollinators potentially increases revenue by approximately $864 501/ha in areas without bumble bees. We conclude that Ventura is reliably pollinated by honey bees, and that honey bee pollination may be a useful substitute for bumble bees in areas where bumble bees are absent. We also determined the extent to which blueberry yields could still be improved by comparing fruit quality and quantity under honey bee pollination to fruit quality and quantity achieved through ideal hand pollination. We found that blueberry yields may be still be significantly increased relative to ideal hand pollination and we discuss potential ways to improve the efficiency of honeybee pollination in the future. Additional research is required to study how beneficial honey bees are to fruit yield on varieties as the benefits of honey bees are likely to vary across different varieties.

plant biology↗

bioRxiv2019

Cell type specific transcriptional reprogramming of maize leaves during Ustilago maydis induced tumor formation

Ustilago maydis is a biotrophic pathogen and well-established genetic model to understand the molecular basis of biotrophic interactions. U. maydis suppresses plant defense and induces tumors on all aerial parts of its host plant maize. In a previous study we found that U. maydis induced leaf tumor formation builds on two major processes: the induction of hypertrophy in the mesophyll and the induction of cell division (hyperplasia) in the bundle sheath. In this study we analyzed the cell-type specific transcriptome of maize leaves 4 days post infection. This analysis allowed identification of key features underlying the hypertrophic and hyperplasic cell identities derived from mesophyll and bundle sheath cells, respectively. We examined the differentially expressed (DE) genes with particular focus on maize cell cycle genes and found that three A-type cyclins, one B-, D- and T-type are upregulated in the hyperplasic tumorous cells, in which the U. maydis effector protein See1 promotes cell division. Additionally, most of the proteins involved in the formation of the pre-replication complex (pre-RC, that assure that each daughter cell receives identic DNA copies), the transcription factors E2Fand DPa as well as several D-type cyclins are deregulated in the hypertrophic cells.

plant biology↗

bioRxiv2019

Functional characterization of genes mediating cell wall metabolism and responses to plant cell wall integrity impairment

Plant cell walls participate in all plant-environment interactions. Maintaining cell wall integrity (CWI) during these interactions is essential. This realization led to increased interest in CWI and resulted in knowledge regarding early perception and signalling mechanisms active during CWI maintenance. By contrast, knowledge regarding processes mediating changes in cell wall metabolism upon CWI impairment is very limited. To identify genes involved and to investigate their contributions to the processes we selected 23 genes with altered expression in response to CWI impairment and characterized the impact of T-DNA insertions in these genes on cell wall composition using Fourier-Transform Infrared Spectroscopy (FTIR) in Arabidopsis thaliana seedlings. Insertions in 14 genes led to cell wall phenotypes detectable by FTIR. A detailed analysis of four genes found that their altered expression upon CWI impairment is dependent on THE1 activity, a key component of CWI maintenance. Phenotypic characterizations of insertion lines suggest that the four genes are required for particular aspects of CWI maintenance, cell wall composition or resistance to Plectosphaerella cucumerina infection in adult plants. Taken together, the results implicate the genes in responses to CWI impairment, cell wall metabolism and/or pathogen defence, thus identifying new molecular components and processes relevant for CWI maintenance.

plant biology↗

bioRxiv2019

A paper-filter system to investigate the real micro-environment circuiting plant roots

The micro-environment circling the plant root is an interesting topic for many researchers. Until now there is not an approach to investigate the exact density of chemicals surrounding the plant roots. here we use a simple paper filter system and gas chromatography to quantify the exact density of chemicals surrounding the plant roots. this can help solve a long-existing doubt about the real micro-environment surrounding the plant roots.

plant biology↗

bioRxiv2019

Calcium-dependent protein kinase 5 links calcium-signaling with SARD1-dependent immune memory in systemic acquired resistance

- Systemic acquired resistance (SAR) prepares infected plants for faster and stronger defense activation upon subsequent attacks. SAR requires an information relay from primary infection to distal tissue and the initiation and maintenance of a self-maintaining phytohormone salicylic acid (SA)-defense loop. - In spatial and temporal resolution we show that calcium-dependent protein kinase CPK5 contributes to immunity and SAR. In local basal resistance CPK5 functions upstream of SA-synthesis, -perception, and -signaling. In systemic tissue, enhanced CPK5 signaling leads to an accumulation of SAR marker genes including transcription factor Systemic Acquired Resistance Deficient 1 (SARD1). - Plants of enhanced CPK5-, but not CPK6-, signaling display a super-priming phenotype of enhanced resistance toward a secondary bacterial infection. In sard1 background, CPK5-mediated basal resistance is still mounted but systemic super-priming is lost. - The biochemical analysis determines CPK5 half maximal kinase activity for calcium K50 [Ca2+] to [~]100 nM close to the cytoplasmic resting level. This low activation threshold uniquely qualifies CPK5 to decode subtle changes in calcium prerequisite to immune signal relay and to onset and maintenance of priming at later time points in distal tissue. Our data explain why CPK5 functions as a hub in basal and systemic plant immunity.

plant biology↗

bioRxiv2019

Application of seaweed organic components increases tolerance to Fe deficiency in tomato plants

The beneficial effects of seaweed extracts have been related to plant growth regulators present in seaweeds. However, algae extracts comprise other organic compounds such as phenols, mannitol, alginates, laminarins and fucoidans that may have a relevant role regarding abiotic stress tolerance due to Fe deficiency. Therefore, we evaluated the individual effect of these organic compounds on the mitigation of Fe deficiency applying a range of concentrations (x1/10, x1, x10) in agar Petri dishes (in tomato seeds) and in the nutrient solution of a hydroponic system (tomato plants). Germination and plant growth promotion, root morphology, chlorophyll content and antioxidant activity were determined. Results showed that the lowest concentration x1/10 and phenolics, laminarin and fucose compounds contributed to increase the tolerance to Fe deficiency in tomato plants.

plant biology↗

bioRxiv2019

QTL and genetic analysis controlling fiber quality traits using paternal backcross population in Upland cotton

In present study, F14 recombinant inbred line (RIL) population was backcrossed to paternal parent for a paternal backcross (BC/P) population, deriving from one Upland cotton hybrid. Three repetitive BC/P field trials and one BC/M field trial were performed including both two BC populations and the original RIL population. Totally, for fiber quality traits, 24 novel QTLs were detected and 13 QTLs validated previous results. And 19 quantitative trait loci (QTL) in BC/P populations explained 5.01% - 22.09% of phenotype variation (PV). Among the 19 QTLs, three QTLs were detected simultaneously in BC/M population. The present study provided novel alleles of male parent for fiber quality traits with positive genetic effects. Particularly, qFS-Chr3-1 controlling fiber strength explained 22.09% of PV in BC/P population, which increased 0.48 cN/tex for fiber strength. A total of seven, two, eight, two and six QTLs explained over 10.00% of PV for fiber length, fiber uniformity, fiber strength, fiber elongation and fiber micronaire, respectively. In the RIL population, six common QTLs detected in more than one environment such as qFL-Chr1-2, qFS-Chr5-1, qFS-Chr9-1, qFS-Chr21-1, qFM-Chr9-1 and qFM-Chr9-2. Two common QTLs of qFE-Chr2-2 (TMB2386-SWU12343) and qFM-Chr9-1 (NAU2873-CGR6771) explained 22.42% and 21.91% of PV. In addition, a total of 142 and 46 epistatic QTLs and QTL x environments (E-QTLs and QQEs) were identified in RIL-P and BC/P populations, respectively.

plant biology↗

bioRxiv2019

Elevated CO2 induces age-dependent restoration of growth and metabolism in gibberellin-deficient plants

Main conclusion The effect of elevated [CO2] on the growth of tomato plants with reduced GA content is influenced by developmental stage. The increase of carbon dioxide (CO2) in the atmosphere during the last decades has aroused interest in the function of this gas in the growth and development of plants. Despite the known association between elevated CO2 concentration ([CO2]) and plant growth, its effects in association with gibberellin (GA), plant hormone that regulates de major aspects of plant growth, are still poorly understood. Therefore, we evaluated the effect of elevated [CO2] on growth and primary metabolism in tomato plants with drastic reduction in GA content (gib-1) at two different growth stages (21 and 35 days after germination, dag). Disruption on growth, photosynthetic parameters and primary metabolism were restored when gib-1 plants were transferred to elevated [CO2] at 21 dag. Elevated [CO2] also stimulated growth and photosynthetic parameters in Wild type (WT) plants at 21 dag, however, minor changes were observed in the level of primary metabolites. At 35 dag, elevated [CO2] did not stimulate growth in WT plants and gib-1 mutants showed their characteristic stunted growth phenotype.

plant biology↗

bioRxiv2019

An evolutionarily conserved mechanism for production of secondary meristems in land plants

A variety of plants in diverse taxa can reproduce asexually via vegetative propagation, in which clonal propagules with new meristem(s) are generated directly from vegetative organs. A basal land plant, Marchantia polymorpha, develops clonal propagules, gemmae, in a specialized receptacle, gemma cup. Here we report an R2R3-MYB transcription factor, designated GEMMA CUP-ASSOCIATED MYB 1 (GCAM1), which is an essential regulator of gemma cup development in M. polymorpha. Although gemma cups are a characteristic gametophyte organ for vegetative reproduction in a taxonomically restricted group of liverwort species, phylogenetic and interspecific complementation analyses supported the orthologous relationship of GCAM1 to regulatory factors for axillary meristem formation, e.g. Arabidopsis RAXs and tomato Blind, in angiosperm sporophytes. The present findings in M. polymorpha suggest an ancient acquisition of a regulatory mechanism for production of secondary meristems, and the use of the mechanism for diverse developmental programs during land plant evolution.

plant biology↗