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Results for “Plant Biology”

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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 37 records · Page 2Linked to original sources

bioRxiv2018

Molecular characterization of beast’s maguey (Agave antillarum Descourt), in the Dominican Republic

BackgroundThis research project was proposed to determine the genetic variability (if any) of beast maguey (Agave antillanarum Decourt) populations, by means of molecular markers of the AFLPs (Amplified Fragment Length Polymorphism) type. For the determination of genetic variability, samples were collected from wild populations of maguey growing in some regions of the Dominican Republic, mainly the north, northwest, south and southwest regions, using statistical techniques already established for these cases. These samples were processed and analyzed in the plant molecular biology laboratory of the Centtro de Biotecnologia Vegetal (CEBIVE) of Instituto de Innovacion en Biotecnologia e Industria (IIBI) in Santo Domingo, Dominican Republic.\n\nResultsAs for the genetic diversity is concerned, it was found that several of the populations studied differ from each other without taking into account the geographic distance where they grow. We concluded that there is a possibility that more than one species of Agave antillarun could be found in the wild in the Dominican Republic.

plant biology↗

bioRxiv2016

Fungal Induced Protein Hyperacetylation Identified by Acetylome Profiling

Lysine acetylation is a key post-translational modification that regulates diverse proteins involved in a range of biological processes. The role of histone acetylation in plant defense is well established and it is known that pathogen effector proteins encoding acetyltransferses can directly acetylate host proteins to alter immunity. However, it is unclear whether endogenous plant enzymes can modulate protein acetylation during an immune response. Here we investigate how the effector molecule HC-toxin, a histone deacetylase inhibitor, produced by Cochliobolus carbonum race 1 promotes pathogen virulence in maize through altering protein acetylation. Using mass spectrometry we globally quantified the abundance of 3,636 proteins and the levels of acetylation at 2,791 sites in maize plants treated with HC-toxin as well as HC-toxin deficient or producing strains of C. carbonum. Analyses of these data demonstrate that acetylation is a widespread post-translational modification impacting proteins encoded by many intensively studied maize genes. Furthermore, the application of exogenous HC-toxin enabled us to show that the activity of plant-encoded enzymes can be modulated to alter acetylation of non-histone proteins during an immune response. Collectively, these results provide a resource for further mechanistic studies examining the regulation of protein function and offer insight into the complex immune response triggered by virulent C. carbonum.

Plant Biology↗

bioRxiv2018

Fragmentation of pooled PCR products for highly multiplexed TILLING

Improvements to massively parallel sequencing have allowed the routine recovery of natural and induced sequence variants. A broad range of biological disciplines have benefited from this, ranging from plant breeding to cancer research. The need for high sequence coverage to accurately recover single nucleotide variants and small insertions and deletions limits the applicability of whole genome approaches. This is especially true in organisms with a large genome size or for applications requiring the screening of thousands of individuals, such as the reverse-genetic technique known as TILLING, where whole genome approaches become cost prohibitive. Using PCR to target and sequence chosen genomic regions provides an attractive alternative as the vast reduction in interrogated bases means that sample size can be dramatically increased through amplicon multiplexing and multidimensional sample pooling while maintaining suitable coverage for recovery of small mutations. Direct sequencing of PCR products is limited, however, due to limitations in read lengths of many next generation sequencers. In the present study we show the optimization and use of ultrasonication for the simultaneous fragmentation of multiplexed PCR amplicons for TILLING highly pooled samples. Thirty-two PCR products were produced from genomic DNA pools representing 265 pooled barley mutant lines. Mutant lines were produced with the chemical mutagen ethyl methanesulfonate. Samples were subjected to 2x300PE illumina sequencing. Evaluation of read coverage and base quality across amplicons suggests this approach is suitable for high-throughput TILLING and other applications employing highly pooled complex sampling schemes. Induced mutations previously identified in a traditional TILLING screen were recovered in this dataset further supporting the efficacy of the approach.

plant biology↗

bioRxiv2018

Genome-wide characterization, evolutionary analysis of WRKY genes in Cucurbitaceae species and assessment of its roles in resisting to powdery mildew disease

The WRKY proteins constitute a large family of transcription factors that have been known to play a wide range of regulatory roles in multiple biological processes. Over the past few years, many reports have focused on analysis of evolution and biological function of WRKY genes at the whole genome level in different plant species. However, little information is known about WRKY genes in melon (Cucumis melo L.). In the present study, a total of 56 putative WRKY genes were identified in melon, which were randomly distributed on their respective chromosomes. A multiple sequence alignment and phylogenetic analysis using melon, cucumber and watermelon predicted WRKY domains indicated that melon WRKY proteins could be classified into three main groups (I-III). Our analysis indicated that no recent duplication events of WRKY genes were detected in melon, and strong purifying selection was observed among the 85 orthologous pairs of Cucurbitaceae species. Expression profiles of CmWRKY derived from RNA-seq data and quantitative RT-PCR (qRT-PCR) analyses showed distinct expression patterns in various tissues, and the expression of 16 CmWRKY were altered following powdery mildew infection in melon. Besides, we also found that a total of 24 WRKY genes were co-expressed with 11 VQ family genes in melon. Our comparative genomic analysis provides a foundation for future functional dissection and understanding the evolution of WRKY genes in cucurbitaceae species, and will promote powdery mildew resistance study in melon.

plant biology↗

bioRxiv2017

Dissection of MAPK signaling specificity through protein engineering in a developmental context

Mitogen-activated protein kinases (MAPK) signaling affects many processes, some of which have different outcomes in the same cell. In Arabidopsis, activation of a MAPK cascade consisting of YODA, MKK4/5 and MPK3/6 inhibits early stages of stomatal developmental, but this ability is lost at the latest stage when guard mother cells (GMCs) transition to guard cells (GCs). Rather than downregulating cascade components, stomatal precursors must have a mechanism to prevent late stage inhibition because the same MKKs and MPKs mediate other physiological responses. Here, we artificially activated the MAPK cascade using MKK7, another MKK that can modulate stomatal development, and found that inhibition of stomatal development is still possible in GMCs. This suggests that MKK4/5, but not MKK7, are specifically prevented from inhibiting stomatal development. To identify regions of MKKs responsible for cell-type specific regulation, we used a domain swap approach with MKK7 and a battery of in vitro and in vivo kinase assays. We found that N-terminal regions of MKK5 and MKK7 establish specific signal-to-output connections like they do in other organisms, but they do so in combination with previously undescribed modules in the C-terminus. One of these modules encodes the GMC-specific regulation of MKK5, that when swapped with MKK7s, allows MKK5 to mediate robust inhibition of late stomatal development. Because MKK structure is conserved across species, the identification of new MKK specificity modules and signaling rules furthers our understanding of how eukaryotes create specificity in complex biological systems.

plant biology↗

bioRxiv2017

Wide sampling of natural diversity identifies novel molecular signatures of C4 photosynthesis

Introductory paragraphMuch of biology is associated with convergent traits, and it is challenging to determine the extent to which underlying molecular mechanisms are shared across phylogeny. By analyzing plants representing eighteen independent origins of C4 photosynthesis, we quantified the extent to which this convergent trait utilises identical molecular mechanisms. We demonstrate that biochemical changes that characterise C4 species are recovered by this process, and expand the paradigm by four metabolic pathways not previously associated with C4 photosynthesis. Furthermore, we show that expression of many genes that distinguish C3 and C4 species respond to low CO2, providing molecular evidence that reduction in atmospheric CO2 was a driver for C4 evolution. Thus the origin and architecture of complex traits can be derived from transcriptome comparisons across natural diversity.

plant biology↗

bioRxiv2018

The draft genome of the invasive walking stick, Medauroidea extradendata, reveals extensive lineage-specific gene family expansions of cell wall degrading enzymes in Phasmatodea

Plant cell wall components are the most abundant macromolecules on Earth. The study of the breakdown of these molecules is thus a central question in biology. Surprisingly, plant cell wall breakdown by herbivores is relatively poorly understood, as nearly all early work focused on the mechanisms used by symbiotic microbes to breakdown plant cell walls in insects such as termites. Recently, however, it has been shown that many organisms make endogenous cellulases. Insects, and other arthropods, in particular have been shown to express a variety of plant cell wall degrading enzymes in many gene families with the ability to break down all the major components of the plant cell wall. Here we report the genome of a walking stick, Medauroidea extradentata, an obligate herbivore that makes uses of endogenously produced plant cell wall degrading enzymes. We present a draft of the 3.3Gbp genome along with an official gene set that contains a diversity of plant cell wall degrading enzymes. We show that at least one of the major families of plant cell wall degrading enzymes, the pectinases, have undergone a striking lineage-specific gene family expansion in the Phasmatodea. This genome will be a useful resource for comparative evolutionary studies with herbivores in many other clades and will help elucidate the mechanisms by which metazoans breakdown plant cell wall components.\n\nData availabilityThe Medauroidea extradentata genome assembly, Med v1.0, is available for download via NCBI (Bioproject: PRJNA369247). The genome, annotation files, and official gene set Mext_OGS_v1.0 are also available at the i5k NAL workspace (https://i5k.nal.usda.gov/medauroidea-extradentata) and at github (https://github.com/pbrec/medauroidea_genome_resources). The genomic raw reads are available via NCBI SRA: SRR6383867 and the raw transcriptomic reads are available at NCBI SRA: SRR6383868, SRR6383869.

genomics↗

bioRxiv2018

A multi-model Framework for the Arabidopsis life cycle

Linking our understanding of biological processes at different scales is a major conceptual challenge in biology, which is aggravated by differences in research methods. Modelling can be a useful approach to consolidating our understanding across traditional research domains. The laboratory model species Arabidopsis thaliana is very widely used to study plant growth processes and has also been tested more recently in eco-physiology and population genetics. However, approaches from crop modelling that might link these domains are rarely applied to Arabidopsis. Here, we combine plant growth models with phenology models from eco-physiology, using the agent-based modelling language Chromar. We introduce a simpler Framework Model of vegetative growth for Arabidopsis, FM-lite. By extending this model to include inflorescence and fruit growth and seed dormancy, we present a whole-life-cycle, multi-model FM-life, which allows us to simulate at the population level in various genotype x environment scenarios. Environmental effects on plant growth distinguish between the simulated life history strategies that were compatible with previously-described Arabidopsis phenology. Our results simulate reproductive success that is founded on the broad range of physiological processes familiar from crop models and suggest an approach to simulate evolution directly in future.\n\nHighlightA whole-life-cycle multi-model for Arabidopsis thaliana combines phenology and physical growth models to explain reproductive success in different genotype x environment scenarios.

plant biology↗

bioRxiv2017

Increased pericarp cell length underlies a major QTL for grain weight in hexaploid wheat

O_LICrop yields must increase to address food insecurity. Grain weight, determined by grain length and width, is an important yield component, but our understanding of the underlying genes and mechanisms is limited.\nC_LIO_LIWe used genetic mapping and near isogenic lines (NILs) to identify, validate and fine map a major quantitative trait loci (QTL) on wheat chromosome 5A associated with grain weight. Detailed phenotypic characterisation of developing and mature grains from the NILs was performed.\nC_LIO_LIWe identified a stable and robust QTL associated with a 6.9 % increase in grain weight. The positive interval leads to 4.0 % longer grains, with differences first visible twelve days post fertilization. This grain length effect was fine-mapped to a 4.3 cM interval. The locus also has a pleiotropic effect on grain width (1.5 %) during late grain development that determines the relative magnitude of the grain weight increase. Positive NILs have increased maternal pericarp cell length, an effect which is independent of absolute grain length.\nC_LIO_LIThese results provide direct genetic evidence that pericarp cell length affects final grain size and weight in polyploid wheat. We propose that combining genes which control distinct biological mechanisms, such as cell expansion and proliferation, will enhance crop yields.\nC_LI

plant biology↗

bioRxiv2017

Morphometrics Reveals Complex And Heritable Apple Leaf Shapes

Apple (Malus spp.) is a widely grown and valuable fruit crop. Leaf shape and size are important for flowering in apple and may also be early indicators for other agriculturally valuable traits. We examined 9,000 leaves from 869 unique apple accessions using linear measurements and comprehensive morphometric techniques. We identified allometric variation in the length-to-width aspect ratio between accessions and species of apple. The allometric variation was due to variation in the width of the leaf blade, not length. Aspect ratio was highly correlated with the primary axis of morphometric variation (PC1) quantified using elliptical Fourier descriptors (EFDs) and persistent homology (PH). While the primary source of variation was aspect ratio, subsequent PCs corresponded to complex shape variation not captured by linear measurements. After linking the morphometric information with over 122,000 genome-wide SNPs, we found high narrow-sense heritability values even at later PCs, indicating that comprehensive morphometrics can capture complex, heritable phenotypes. Thus, techniques such as EFDs and PH are capturing heritable biological variation that would be missed using linear measurements alone, and which could potentially be used to select for a hidden phenotype only detectable using comprehensive morphometrics.

plant biology↗

bioRxiv2017

CropQuant: An automated and scalable field phenotyping platform for crop monitoring and trait measurements to facilitate breeding and digital agriculture

Automated phenotyping technologies are capable of providing continuous and precise measurements of traits that are key to todays crop research, breeding and agronomic practices. In additional to monitoring developmental changes, high-frequency and high-precision phenotypic analysis can enable both accurate delineation of the genotype-to-phenotype pathway and the identification of genetic variation influencing environmental adaptation and yield potential. Here, we present an automated and scalable field phenotyping platform called CropQuant, designed for easy and cost-effective deployment in different environments. To manage infield experiments and crop-climate data collection, we have also developed a web-based control system called CropMonitor to provide a unified graphical user interface (GUI) to enable realtime interactions between users and their experiments. Furthermore, we established a high-throughput trait analysis pipeline for phenotypic analyses so that lightweight machine-learning modelling can be executed on CropQuant workstations to study the dynamic interactions between genotypes (G), phenotypes (P), and environmental factors (E). We have used these technologies since 2015 and reported results generated in 2015 and 2016 field experiments, including developmental profiles of five wheat genotypes, performance-related traits analyses, and new biological insights emerged from the application of the CropQuant platform.

plant biology↗

bioRxiv2018

Switching toxic protein function in life cells

Toxic proteins are prime targets for molecular farming and efficient tools for targeted cell ablation in genetics, developmental biology, and biotechnology. Achieving conditional activity of cytotoxins and their maintenance in form of stably transformed transgenes is challenging. We demonstrate here a switchable version of the highly cytotoxic bacterial ribonuclease barnase by using efficient temperature-dependent control of protein accumulation in living multicellular organisms. By tuning the levels of the protein, we were able to control the fate of a plant organ in vivo. The on-demand-formation of specialized epidermal cells (trichomes) through manipulating stabilization versus destabilization of barnase is a proof-of-concept for a robust and powerful tool for conditional switchable cell arrest. We present this tool both as a potential novel strategy for the manufacture and accumulation of cytotoxic proteins and toxic high-value products in plants or for conditional genetic cell ablation.

plant biology↗

bioRxiv2018

Widespread inter-individual gene expression variability in Arabidopsis thaliana

A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered and could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform and this has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about transcriptional variability in plants. Using transcriptomic approaches, we analysed gene expression variability between individual Arabidopsis thaliana plants growing in identical conditions over a 24 hour time-course. We identified hundreds of genes that exhibit high inter-individual variability and found that many are involved in environmental responses. We also identified factors that might facilitate gene expression variability, such as gene length, the number of transcription factors regulating the genes and the chromatin environment. These results shed new light on the impact of transcriptional variability in gene expression regulation in plants.

plant biology↗

bioRxiv2017

Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

BackgroundThere is an urgent need to increase global crop production. Identifying and combining genes controlling indidviual yield components, such as grain weight, holds the potential to enhance crop yields. Transcriptomics is a powerful tool to gain insights into the complex gene regulatory networks that underlie such traits, but relies on the availability of a high-quality reference sequence and accurate gene models. Previously, we identified a grain weight QTL on wheat chromosome 5A (5A QTL) which acts during early grain development to increase grain length through cell expansion in the pericarp. In this study, we performed RNA-sequencing on near isogenic lines (NILs) segregating for the 5A QTL and used the latest gene models to identify differentially expressed (DE) genes and pathways that potentially influence pericarp cell size and grain weight in wheat.\n\nResultsWe sampled grains at four and eight days post anthesis and found genes associated with metabolism, biosynthesis, proteoloysis and defence response to be upregulated during this stage of grain development in both NILs. We identified a specific set of 112 transcripts DE between 5A NILs at either time point, including seven potential candidates for the causal gene underlying the 5A QTL. The 112 DE transcripts had functional annotations including non-coding RNA, transpon-associated, cell-cycle control, and ubiquitin-related processes. Many of the wheat genes identified belong to families that have been previously associated with seed/grain development in other species. However, few of these wheat genes are the direct orthologs and none have been previously characterised in wheat. Notably, we identified DE transcripts at almost all steps of the pathway associated with ubiquitin-mediated protein degradation. In the promoters of a subset of DE transcripts we identified enrichment of binding sites associated with C2H2, MYB/SANT, YABBY, AT HOOK and Trihelix transcription factor families.\n\nConclusionsIn this study, we identified DE transcripts with a diverse range of predicted biological functions, reflecting the complex nature of the pathways that control early grain development. Further functional characterisation of these candidates and how they interact could provide new insights into the control of grain size in cereals, ultimately improving crop yield.

plant biology↗

bioRxiv2018

Transcriptome analysis of mycorrhizal and non-mycorrhizal soybean plantlets upon infection with Fusarium virguliforme, one causal agent of sudden death syndrome

Soilborne pathogens represent a threat to agriculture causing important yield losses. The \"Sudden Death Syndrome\" (SDS), a severe disease in soybean is caused by a complex of Fusarium species. This pathosystem has been widely investigated and several strategies were proposed to manage SDS. Although a decrease in symptoms and in the level of root tissue infection particularly by F. virguliforme was observed in presence of arbuscular mycorrhizal fungi (AMF), biological control based on AMF has received less attention. Here we report the results, under strict in vitro culture experimental conditions, a transcriptional analysis in mycorrhizal versus non-mycorrhizal soybean plantlets upon infection by F. virguliforme. An important transcriptional reprogramming was detected following infection by the pathogen. Results revealed 1768 and 967 differentially expressed genes in the AMF-colonized (+AMF+Fv) and non-colonized (-AMF+Fv) plants, respectively. Major transcriptional changes, corresponded to defence response related genes belonging to secondary metabolism, stress and signalling categories. The +AMF+Fv treatment showed the largest number of upregulated genes related to defence, as those encoding for disease resistance proteins, WRKY transcription factors, auxins, receptors kinases, and proteases. Only few genes had primed expression in +AMF+Fv treatment, as those coding for a thaumatin-like protein (TLP) and a pleiotropic drug resistance (PDR) protein. Moreover, +AMF+Fv showed a significant number of downregulated genes related to cell wall modification and peroxidases than - AMF+Fv treatment. This detailed insight increases our knowledge on the transcriptional changes and the potential metabolic pathways involved in the enhanced resistance/tolerance of mycorrhizal plants upon infection with F. virguliforme.

plant biology↗

bioRxiv2018

Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of Arabidopsis originome

Eukaryotic genome replication depends on thousands of DNA replication origins (ORIs) that constitute the originome. A major challenge is to learn ORI biology in multicellular organisms in the context of growing organs to understand their developmental plasticity. We have determined the originome and chromatin landscape of Arabidopsis thaliana at two stages of postembryonic development. ORIs associate with multiple chromatin signatures including TSS but also regulatory regions and heterochromatin, where ORIs colocalize with retrotransposons. In addition, quantitative analysis of ORI activity led us to conclude that strong ORIs have high GC content and clusters of GGN trinucleotides. Development primarily influences ORI firing strength rather than ORI location. ORIs that preferentially fire at early developmental stages colocalize with GC-rich heterochromatin whereas at later stages with transcribed genes, perhaps as a consequence of changes in chromatin features associated with developmental processes. Our study provides the originome of an organism at the postembryo stage that should allow us to study ORI biology in response to development, environment and mutations with a quantitative approach. In a wider scope, the computational strategies developed here can be transferred to other eukaryotic systems.

plant biology↗

bioRxiv2014

Mesoscale analyses of fungal networks as an approach for quantifying phenotypic traits

We investigate the application of mesoscopic response functions (MRFs) to characterize a large set of networks of fungi and slime moulds grown under a wide variety of different experimental treatments, including inter-species competition and attack by fungivores. We construct structural networks by estimating cord conductances (which yield edge weights) from the experimental data, and we construct functional networks by calculating edge weights based on how much nutrient traffic is predicted to occur along each edge. Both types of networks have the same topology, and we compute MRFs for both families of networks to illustrate two different ways of constructing taxonomies to group the networks into clusters of related fungi and slime moulds. Although both network taxonomies generate intuitively sensible groupings of networks across species, treatments, and laboratories, we find that clustering using the functional-network measure appears to give groups with lower intra-group variation in species or treatments. We argue that MRFs provide a useful quantitative analysis of network behaviour that can (1) help summarize an expanding set of increasingly complex biological networks and (2) help extract information that captures subtle changes in intra-specific and inter-specific phenotypic traits that are integral to a mechanistic understanding of fungal behaviour and ecology. As an accompaniment to our paper, we also make a large data set of fungal networks available in the public domain.

Plant Biology↗

bioRxiv2015

Phenotypic and genomic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian alps

Altitudinal gradients represent short-range clines of environmental parameters like temperature, radiation, seasonality and pathogen abundance, which allows to study the foot-prints of natural selection in geographically close populations. We investigated phenotypic variation for frost resistance and light response in five Arabidopsis thaliana populations ranging from 580 to 2,350 meters altitude at two different valleys in the North Italian Alps. All populations were resequenced as pools and we used a Bayesian method to detect correlations between allele frequencies and altitude while accounting for sampling, pooled sequencing and the expected amount of shared drift among populations. The among population variation to frost resistance was not correlated with altitude. An anthocyanin deficiency causing a high leaf mortality was present in the highest population, which may be non-adaptive and potentially deleterious phenotypic variation. The genomic analysis revealed that the two high-altitude populations are more closely related than the geographically close low-altitude populations. A correlation of genetic variation with altitude revealed an enrichment of highly differentiated SNPs located in genes that are associated with biological processes like response to stress and light. We further identified regions with long blocks of presence absence variation suggesting a sweep-like pattern across populations. Our analysis indicate a complex interplay of local adaptation and a demographic history that was influenced by glaciation cycles and/or rapid seed dispersal by animals or other forces.

Plant Biology↗