Biology subjects

Kliebenstein, D.

Publications and source records attributed to Kliebenstein, D..

18 recordsLinked to original sources

bioRxiv2026

Gene functional-state covariance reveals modular structure in the Arabidopsis thaliana dispensable genome

Classical multilocus theory predicts that selection acting on combinations of loci can maintain non-random associations among allelic states, causing selection to act on multilocus genotypes rather than individual alleles. Across eukaryotic species, pangenome studies have documented thousands of genes that vary in functional status between individuals, yet this variation is analyzed as if each gene evolves independently. Here we test for non-random association within the dispensable pangenome across 1,012 natural genotypes of Arabidopsis thaliana to better understand the structure and evolution of eukaryotic pangenomes. Genome-wide pairwise association testing of loss-of-function alleles across genotypes identified 150,033 significantly covarying gene pairs among 5,679 unique genes after controlling for kinship and population structure. Most associations were between genes on different chromosomes, and covarying gene pairs showed greater co-expression and functional similarity than expected by chance. Network analysis revealed a non-random higher-order architecture comprising stable functional communities with distinct biological functions and structured connectivity among communities. The enriched functions and connectivity of communities revealed a tight coupling of modules involving plant immunity, environmental response, and specialized metabolism, highlighting how these systems integrate and evolve in response to dynamic ecological pressures. Taken together, these results show that the dispensable genome has a complex higher-order structure driven by functionally interacting genes, and that variation in gene content provides a population-scale resource for investigating the organization and evolution of biological systems.

genomics↗

bioRxiv2026

Strategy Sets the Scene: Genetic architecture of linalool resistance in Botrytis cinerea

Botrytis cinerea is a necrotrophic fungal pathogen that infects thousands of plant species. During infection, these diverse plant hosts produce different specialized metabolites that can inhibit pathogen growth and shape pathogen fitness. However, the genetic architecture of pathogen resistance toward individual host defense metabolites remains poorly understood. To address this question, we exposed 83 B. cinerea isolates to the metabolite linalool and quantified metabolic and structural responses. Exposure revealed extensive phenotypic diversity across isolates. Population structure analysis using genome-wide SNP data showed little genetic subdivision despite diverse hosts and geographic location. Genome-wide association identified 98 genes of interest associated with membrane transport and stress response regulation. Genetic associations were stronger for morphological traits than for metabolic traits, suggesting that hyphal architecture may have a complex genetic architecture contributing to linalool resistance. Together, these results establish natural variation in linalool response and provide candidate loci for understanding how generalist pathogens respond to host-derived chemical defenses. Article SummaryTo understand how a generalist pathogen responds to host defenses, we asked how Botrytis cinerea responds to linalool, a widespread monoterpene involved in plant defense. We exposed 83 B. cinerea isolates to 1000 {micro}M of linalool for 72 hours and quantified metabolic traits (growth curves and growth dynamics over time) and morphological traits (hyphal network features). Using GWA, we linked phenotypic variation to genetic variants. Results indicate substantial natural variation in linalool resistance and distinct genetic architectures across trait classes: metabolic responses are driven by a relatively small number of loci with larger effects, whereas structural/morphological responses appear more polygenic.

genomics↗

bioRxiv2026

Host-Botrytis co-transcriptomics reveals finely tuned interactions with closely related legumes

Generalist pathogens infect diverse plant hosts, yet how these interactions differ across hosts is poorly understood. Here, we conduct a molecular analysis of a generalist pathogen interacting with closely related hosts. A co-transcriptomic framework is used to dissect host-pathogen interactions between the generalist necrotroph Botrytis cinerea and two closely related legume hosts, common bean (Phaseolus vulgaris) and cowpea (Vigna unguiculata). Using a diverse set of 72 Botrytis isolates, we quantified lesion development alongside host and pathogen gene expression. Although lesion formation was driven primarily by pathogen genetic variation, transcriptomic responses in both host and pathogen exhibited significant host x isolate interactions. This indicated that extensive, fine-scale transcriptional plasticity created similar disease outcomes. Botrytis genes showing host-specific expression were enriched for cell wall-modifying enzymes and some specialized metabolic genes, indicating greater host responsiveness of these core virulence mechanisms than previously appreciated. Co-expression network analysis in both host and pathogen further showed that in both organisms, gene membership for individual networks are restructured in response to genetic diversity. For example in Botrytis, we identify different sets of genes host-dependently co-expressing with a non-ribosomal peptide synthetase (NRPS) gene cluster, suggesting divergent functional deployment of the same virulence machinery across closely related hosts. Both legume species exhibited extensive isolate-dependent transcriptional reprogramming, with approximately two-thirds of expressed host genes responding to pathogen diversity. While conserved defense pathways such as jasmonate/ethylene signaling and phenylpropanoid metabolism were upregulated in both hosts, the specific genes in the networks differed markedly, highlighting lineage-specific rewiring of defense strategies. These results suggest that generalist pathogen success is underpinned by pervasive gene expression plasticity in both host and pathogen, allowing similar phenotypic outcomes to emerge from highly divergent molecular states. SummaryO_LIGeneralist pathogens infect diverse plant hosts, yet how these interactions differ across hosts is poorly understood. This study investigates how a generalist pathogen achieves successful infection across closely related hosts, and how these hosts respond. C_LIO_LIA co-transcriptomic approach was applied to interactions between 72 genetically diverse isolates of the fungal necrotroph Botrytis cinerea and two legume hosts, common bean and cowpea. Lesion development and host and pathogen gene expression were quantified. C_LIO_LILesion formation was primarily driven by pathogen genetic variation, yet both host and pathogen transcriptomes showed strong host x isolate interactions. Both host and pathogen balance conserved responses with finely tuned, host-specific mechanisms. Further, host-dependent transcriptional responses involve network modulation around a common core of genes in both host and pathogen. C_LIO_LIGeneralist pathogen success is underpinned by pervasive gene expression plasticity in both host and pathogen, allowing similar phenotypic outcomes to emerge from highly divergent molecular states. C_LI

plant biology↗

bioRxiv2025

Evaluating Regulatory Module Function within Mitochondrial Pyruvate Dehydrogenase Complex

Regulatory networks coordinate metabolism to control how plants adapt to biotic and abiotic stresses. This coordination can align transcriptional shifts across metabolic pathways using cis-regulatory elements shared across the enzyme genes within these pathways. While the role of transcription factors (TFs) in controlling this process across pathways is well known, less is known regarding the role of shared cis-regulatory elements across the genes in a pathway. Sharing cis-regulatory elements across the genes in an enzyme complex or pathway, can create coordinated regulation of the pathway by a TF. However, it is unclear if all the genes in a pathway or enzyme complex need to be fully coordinated for maximal function. For example, if one gene in an enzyme complex loses a cis-regulatory element, it may not alter the function of the enzyme complexes function if post-transcriptional or compensatory transcriptional changes are sufficient to balance the complex. To test how cis-modular membership shapes the function of an enzyme complex, we used CRISPR/Cas9 to abolish a common cis-regulatory element across the promoters of nine genes required for the mitochondrial pyruvate dehydrogenase complex (mtPDC). This complex is composed of three apoenzymes and is a central hub coordinating carbon flow between glycolysis and the tricarboxylic acid (TCA) cycle. Different combinations of these cis-element mutations were tested across the genes in the complex in Arabidopsis thaliana and the created genotypes were phenotyped for altered enzyme function using digital growth analysis, disease assays, metabolomics, and transcriptomics. This analysis revealed that mutating cis-element motifs of genes in this enzyme complex produced distinct phenotypes, displaying promoter-specific buffering and modularity.

molecular biology↗

bioRxiv2025

Evaluating the Effectiveness of Data Reduction Techniques in QTL Mapping

Data reduction methods are frequently employed in large genomics and phenomics studies to extract core patterns, reduce dimensionality, and alleviate multiple testing effects. Principal component analysis (PCA), in particular, identifies the components that capture the most variance within omics datasets. While data reduction can simplify complex datasets, it remains unclear how the use of PCA impacts downstream analyses such as quantitative trait loci (QTL) or genome-wide association (GWA) approaches and their biological interpretation. In QTL studies, an alternative to data reduction is the use of post-hoc data summarization approaches, such as hotspot analysis, which involves mapping individual traits and consolidating results based on shared genomic locations. To evaluate how different analytical approaches may alter the biological insights derived from multi-dimensional QTL datasets, we compared individual trait hotspots with PCA-based QTL mapping using transcriptomic and metabolomic data from a structured recombinant inbred line population. Interestingly, these two approaches identified different genomic regions and genetic architectures. These findings suggest that mapping PCA-reduced data does not merely streamline analyses but may generate a fundamentally different view of the underlying genetic architecture compared to individual trait mapping and hotspot analysis. Thus, the use of PCA and other data reduction techniques prior to QTL or GWAS mapping should be carefully considered to ensure alignment with the specific biological question being addressed.

genetics↗

bioRxiv2024

Molecular evolution of a reproductive barrier in maize and related species

Three cross-incompatibility loci each control a distinct reproductive barrier in both domesticated maize (Zea mays ssp. mays) and its wild teosinte relatives. These three loci, Teosinte crossing barrier1 (Tcb1), Gametophytic factor1 (Ga1), and Ga2, each play a key role in preventing hybridization between incompatible populations and are proposed to maintain the barrier between domesticated and wild subspecies. Each locus encodes both a silk-active and a matching pollen-active pectin methylesterase (PMEs). To investigate the diversity and molecular evolution of these gametophytic factor loci, we identified existing and improved models of the responsible genes in a new genome assembly of maize line P8860 that contains active versions of all three loci. We then examined fifty-two assembled genomes from seventeen species to classify haplotype diversity and identify sites under diversifying selection during the evolution of these genes. We show that Ga2, the oldest of these three loci, was duplicated to form Ga1 at least 12 million years ago. Tcb1, the youngest locus, arose as a duplicate of Ga1 before or around the time of diversification of the Zea genus. We find evidence of positive selection during evolution of the functional genes at an active site in the pollen-expressed PME and predicted surface sites in both the silk- and pollen-expressed PMEs. The most common allele at the Ga1 locus is a conserved ga1 allele (ga1-Off), which is specific haplotype containing three full-length PME gene copies, all of which are non-coding due to conserved stop codons and are between 610 thousand and 1.5 million years old. We show that the ga1-Off allele is associated with and likely generates 24-nt siRNAs in developing pollen-producing tissue, and these siRNAs map to functional Ga1 alleles. In previously-published crosses, the ga1-Off allele was associated with reduced function of the typically dominant functional alleles for the Ga1 and Tcb1 barriers. Taken together, this seems to be an example of a type of epigenetic trans-homolog silencing known as paramutation functioning at a locus controlling a reproductive barrier.

genetics↗

bioRxiv2024

Leaf abaxial and adaxial surfaces differentially affect plant-fungal pathogen interactions

Eudicot plant species have bifacial leaves with each surface varying in a diversity of components, resulting in potentially different microhabitats for pathogens. We tested how Botrytis cinerea, a necrotroph fungal pathogen, interacts with the two different leaf surfaces across 16 crop species and 20 Arabidopsis genotypes. This showed that the abaxial surface is generally more susceptible to the pathogen than the adaxial surface. In Arabidopsis, the differential lesion area between leaf surfaces was associated to jasmonic acid (JA) and salicylic acid (SA) signaling and differential induction of defense chemistry. When infecting the adaxial surface, leaves mounted stronger defenses by producing more glucosinolates and camalexin defense compounds, partially explaining the differential susceptibility across surfaces. Testing a collection of 96 B. cinerea strains showed genetic heterogeneity of growth patterns, with a few strains preferring the adaxial surface while most are more virulent on the abaxial surface. Overall, we show that leaf-Botrytis interactions are complex with host-specific, surface-specific, and strain-specific behaviors. Within Arabidopsis, this mechanistically links to potential variation in JA/SA signaling across the two surfaces.

plant biology↗

bioRxiv2021

A Genome-Scale TF-DNA Interaction Network of Transcriptional Regulation of Arabidopsis Primary and Specialized Metabolism

In single-celled microbes, transcriptional regulation by single transcription factors is sufficient to shift primary metabolism. Corresponding genome-level transcriptional regulatory maps of metabolism reveal the underlying design principles responsible for these shifts as a model in which master regulators largely coordinate specific metabolic pathways. Relative to individual microbes, plant metabolism is more complex. Primary and specialized metabolism occur within innumerable cell types, and their reactions shift depending on internal and external cues. Given the importance of plants and their metabolites in providing humanity with food, fiber and medicine, we set out to develop a genome-scale transcriptional regulatory map of Arabidopsis metabolic genes. A comprehensive set of protein-DNA interactions between Arabidopsis thaliana transcription factors and promoters of primary metabolism and specialized metabolism were mapped. To demonstrate the utility of this resource, we identified and functionally validated regulators of the TCA cycle. The resulting network suggests that plant metabolic design principles are distinct from that of microbes. Instead, metabolism appears to be transcriptionally coordinated via developmental- and stress-conditional processes that can coordinate across primary and specialized metabolism. These data represent the most comprehensive resource of interactions between TFs and metabolic genes in plants.

systems biology↗

bioRxiv2020

Fine-mapping identifies NAD-ME1 as a candidate underlying a major locus controlling temporal variation in primary and specialized metabolism in Arabidopsis

Plant metabolism is modulated by a complex interplay between internal signals and external cues. A major goal of all quantitative metabolomic studies is to clone the underlying genes to understand the mechanistic basis of this variation. Using fine-scale genetic mapping, in this work we report the identification and initial characterization of NAD-DEPENDENT MALIC ENZYME 1 (NAD-ME1) as the candidate gene underlying the pleiotropic network Met.II.15 QTL controlling variation in plant metabolism and circadian clock outputs in the Bay x Sha Arabidopsis population. Transcript abundance and promoter analysis in NAD-ME1Bay-0 and NAD-ME1Sha alleles confirmed allele-specific expression that appears to be due a polymorphism disrupting a putative circadian cis-element binding site. Analysis of T-DNA insertion lines and heterogeneous inbred families (HIFs) showed that transcript variation of the NAD-ME1 gene led to temporal shifts of tricarboxylic acid cycle (TCA) intermediates, glucosinolate (GSL) accumulation and altered regulation of several GSL biosynthesis pathway genes. Untargeted metabolomics analyses reveal complex regulatory networks of NAD-ME1 dependent upon the day-time. The mutant lead to shifts in plant primary metabolites, cell-wall components, isoprenoids, fatty acids and plant immunity phytochemicals, among others. Our findings suggest that NAD-ME1 may act as a key component to coordinate plant primary and secondary metabolism in a time-dependent manner.

plant biology↗

bioRxiv2020

Red-light is an environmental effector for mutualism between begomovirus and its vector whitefly

Environments such as light condition influence the spread of infectious diseases by affecting insect vector behavior. However, whether and how light affects the host defense which further affect insect preference and performance, remains unclear, nor has been demonstrated how pathogens co-adapt light condition to facilitate vector transmission. We previously showed that begomoviral βC1 inhibits MYC2-mediated jasmonate signaling to establish plant-dependent mutualism with its insect vector. Here we show red-light as an environmental catalyzer to promote mutualism of whitefly-begomovirus by stabilizing βC1, which interacts with PHYTOCHROME-INTERACTING FACTORS (PIFs) transcription factors. PIFs positively control plant defenses against whitefly by directly binding to the promoter of terpene synthase genes and promoting their transcription. Moreover, PIFs integrates light and jasmonate signaling by interaction with MYC2, and co-regulation the transcription of terpene synthase genes. However, begomovirus encoded βC1 inhibit PIFs’ and MYC2’ transcriptional activity via disturbing their dimerization, thereby impairing plant defenses against whitefly-transmitted begomoviruses. Our results thus describe how a viral pathogen hijacks host light signaling to enhance the mutualistic relationship with its insect vector.Author summary Climate change is driving disease rapidly spread, esp. for global distribution of insect-borne diseases. This paper reports red-light as an environmental factor to promote insect vector olfactory orientation behavior and increase viral disease transmission. Plant virus adapts the supplemental red lighting practice in modern agricultural greenhouse production under protection, therefore enhancing disease spreading globally.View Full Text

plant biology↗

bioRxiv2019

Epistatic Transcription Factor Networks Differentially Modulate Arabidopsis Growth and Defense

Plants integrate internal and external signals to finely coordinate growth and defense allowing for maximal fitness within a complex environment. One common model for the relationship between growth and defense is a trade-off model in which there is a simple negative interaction between growth and defense theoretically driven by energy costs. However, there is a developing consensus that the coordination of growth and defense likely involves a more conditional and intricate connection. To explore how a transcription factor network may coordinate growth and defense, we used high-throughput phenotyping to measure growth and flowering in a set of single and pairwise mutants previously linked to the aliphatic glucosinolate defense pathway. Showing the link between growth and aliphatic glucosinolate defense, 17 of the 20 tested TFs significantly influence plant growth and/or flowering time. These effects were conditional upon the environment, age of the plant and more critically varied amongst the phenotypes when using the same genotype. The phenotypic effects of the TF mutants on SC GLS accumulation and on growth did not display a simple correlation, supporting the coordination model. We propose that large transcription factor networks create a system to integrate internal and external signals and separately modulate growth and the accumulation of the defensive aliphatic GLS.

plant biology↗

bioRxiv2019

Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels

A detailed understanding of abiotic stress tolerance in plants is essential to provide food security in the face of increasingly harsh climatic conditions. Glucosinolates (GLSs) are secondary metabolites found in the Brassicaceae that protect plants from herbivory and pathogen attack. Here we report that in Arabidopsis, aliphatic GLS levels are regulated by the auxin-sensitive Aux/IAA repressors IAA5, IAA6, and IAA19. These proteins act in a transcriptional cascade that maintains expression of GLS levels when plants are exposed to drought conditions. Loss of IAA5/6/19 results in reduced GLS levels and decreased drought tolerance. Further, we show that this phenotype is associated with a defect in stomatal regulation. Application of GLS to the iaa5,6,19 mutants restores stomatal regulation and normal drought tolerance. GLS action is dependent on the receptor kinase GHR1, suggesting that GLS may signal via reactive oxygen species. These results provide a novel connection between auxin signaling, GLS levels and drought response.\n\nOne Sentence SummaryAux/IAA proteins promote drought tolerance by regulating glucosinolate levels.

plant biology↗

bioRxiv2018

A generalist pathogen view of plant evolution

Botrytis cinerea is a polyphagous fungal pathogen that causes necrotic disease on more than a thousand known hosts widely spread across the plant kingdom. While it is known that quantitative resistance in the host and quantitative virulence in the pathogen largely mediate this pathosystem, how this pathogen interacts with the extensive host diversity is unknown. Does this pathogen have quantitative virulence efficiency on all hosts or individual solutions for each host? To address this question, we generated an infectivity matrix of 98 strains of Botrytis cinerea on 90 genotypes representing eight host plants. This experimental infectivity matrix showed that the predominant sources of quantitative variation are between host species and among pathogen strains. Furthermore, the eight eudicot hosts interacted individually with Botrytis cinerea strains independently of the evolutionary relatedness between hosts. An additive quantitative model can explain the complexity of these interactions in which Botrytis host specificity and general virulence have distinct polygenic architectures.

plant biology↗

bioRxiv2018

GONST2 transports GDP-Mannose for sphingolipid glycosylation in the Golgi apparatus of Arabidopsis

The Golgi lumen is the site of many different glycosylation events, including cell wall polysaccharide biosynthesis and lipid glycosylation. Transporters are necessary for the import of the substrates required for glycosylation (nucleotide sugars) from the cytosol where they are synthesized. Plants use four GDP-linked sugars to glycosylate macromolecules: GDP-L-Fucose, GDP-D-Mannose, GDP-L-Galactose and GDP-D-Glucose. Of the predicted fifty-one members of the nucleotide sugar transporter/triose phosphate transporter family in Arabidopsis, only four appear to contain the conserved motif needed for the transport of GDP-linked sugars, GOLGI LOCALIZED NUCLEOTIDE SUGAR TRANSPORTER (GONST) 1-4. Previously, we have demonstrated that GONST1 provides GDP-D-Mannose for glycosylation of a class of sphingolipids, the glycosylinositolphosphorylceramides (GIPCs). Here, we characterize its closest homologue, GONST2, and conclude that it also specifically provides substrate for GIPC glycosylation. Expression of GONST2 driven by the GONST1 promoter is able to rescue the severe growth phenotype of gonst1. Loss of GONST2 exacerbates the gonst1 constitutive hypersensitive response, as well as the reduced cell wall cellulose content. The gonst2 mutant grows normally under standard conditions, but has enhanced resistance to the powdery mildew-causing fungus Golovinomyces orontii.

plant biology↗

bioRxiv2018

Rhizosphere microbes and host plant genotype influence the plant metabolome and reduce insect herbivory

O_LIRhizosphere microbes affect plant performance, including plant resistance against insect herbivores; yet, the relative influence of rhizosphere microbes vs. plant genotype on herbivory levels and on metabolites related to defense remains unclear.\nC_LIO_LIIn Boechera stricta, we tested the effects of rhizosphere microbes and plant genotype on herbivore resistance, the primary metabolome, and select secondary metabolites.\nC_LIO_LIPlant populations differed significantly in the concentrations of 6 glucosinolates (GLS), secondary metabolites known to provide herbivore resistance in the Brassicaceae, and the population with lower GLS levels experienced ~60% higher levels of aphid (Aphis spp.) attack; no effect was observed of GLS on damage by a second herbivore, flea beetles (Altica spp.). Rhizosphere microbiome (intact vs. disrupted) had no effect on plant GLS concentrations. However, aphid number and flea beetle damage were respectively ~3-fold and 7-fold higher among plants grown in the disrupted rhizosphere microbiome treatment, and distinct (as estimated from 16s rRNA amplicon sequencing) intact native microbiomes also differed in their effects on herbivore damage. These differences may be attributable to shifts in primary metabolic pathways.\nC_LIO_LIThe findings suggest that rhizosphere microbes can play a greater role than plant genotype in defense against insect herbivores, and act through mechanisms independent of plant genotype.\nC_LI

plant biology↗

bioRxiv2018

Combining Digital Imaging and Genome Wide Association Mapping to Dissect Uncharacterized Traits in Plant/Pathogen Interactions

Plant resistance to generalist pathogens with broad host ranges, such as Botrytis cinerea, is typically quantitative and highly polygenic. Recent studies have begun to elucidate the molecular genetic basis underpinning plant-pathogen interactions using commonly measured traits including lesion size and/or pathogen biomass. Yet with the advent of digital imaging and phenomics, there are a large number of additional resistance traits available to study quantitative resistance. In this study, we used high-throughput digital imaging analysis to investigate previously uncharacterized visual traits of plant-pathogen interactions related disease resistance using the Arabidopsis thaliana/Botrytis cinerea pathosystem. Using a large collection of 75 visual traits collected from every lesion, we focused on lesion color, lesion shape, and lesion size, to test how these aspects of the interaction are genetically related. Using genome wide association (GWA) mapping in A. thaliana, we show that lesion color and shape are genetically separable traits associated with plant-disease resistance. Using defined mutants in 23 candidate genes from the GWA mapping, we could identify and show that novel loci associated with each different plant-pathogen interaction trait, which expands our understanding of the functional mechanisms driving plant disease resistance.\n\nSummaryDigital imaging allows the identification of genes controlling novel lesion traits.

plant biology↗

bioRxiv2018

Crop domestication and pathogen virulence: Interactions of tomato and Botrytis genetic diversity

Human selection during crop domestication alters numerous traits, including disease resistance. Studies of qualitative resistance to specialist pathogens typically find decreased resistance in domesticated crops in comparison to their wild relatives. However, less is known about how crop domestication affects quantitative interactions with generalist pathogens. To study how crop domestication impacts plant resistance to generalist pathogens, and correspondingly how this interacts with the pathogens genetics, we infected a collection of wild and domesticated tomato accessions with a genetically diverse population of the generalist pathogen Botrytis cinerea. We quantified variation in lesion size of 97 B. cinerea genotypes (isolates) on 6 domesticated Solanum lycopersicum and 6 wild S. pimpinellifolium genotypes. This showed that lesion size was significantly controlled by plant domestication, plant genetic variation, and the pathogens genotype. Overall, resistance was slightly elevated in the wild germplasm in comparison to domesticated tomato accessions. Genome-wide association (GWA) mapping in B. cinerea identified a highly polygenic collection of genes. This suggests that breeding against this pathogen would need to utilize a diversity of isolates to capture all possible mechanisms. Critically, we identified a discrete subset of B. cinerea genes where the allelic variation was linked to altered virulence against the wild versus domesticated tomato accessions. This indicates that this generalist pathogen already has the necessary allelic variation in place to handle the introgression of wild resistance mechanisms into the domesticated crop. Future studies are needed to assess how these observations extend to other domesticated crops and other generalist pathogens.

plant biology↗

bioRxiv2016

A global co-expression network approach for connecting genes to specialized metabolic pathways in plants

Plants produce a tremendous diversity of specialized metabolites (SMs) to interact with and manage their environment. A major challenge hindering efforts to tap this seemingly boundless source of pharmacopeia is the identification of SM pathways and their constituent genes. Given the well-established observation that the genes comprising a SM pathway are co-regulated in response to specific environmental conditions, we hypothesized that genes from a given SM pathway would form tight associations (modules) with each other in gene co-expression networks, facilitating their identification. To evaluate this hypothesis, we used 10 global co-expression datasets--each a meta-analysis of hundreds to thousands of expression experiments--across eight plant model organisms to identify hundreds of modules of co-expressed genes for each species. In support of our hypothesis, 15.3-52.6% of modules contained two or more known SM biosynthetic genes (e.g., cytochrome P450s, terpene synthases, and chalcone synthases), and module genes were enriched in SM functions (e.g., glucoside and flavonoid biosynthesis). Moreover, modules recovered many experimentally validated SM pathways in these plants, including all six known to form biosynthetic gene clusters (BGCs). In contrast, genes predicted based on physical proximity on a chromosome to form plant BGCs were no more co-expressed than the null distribution for neighboring genes. These results not only suggest that most predicted plant BGCs do not represent genuine SM pathways but also argue that BGCs are unlikely to be a hallmark of plant specialized metabolism. We submit that global gene co-expression is a rich, but largely untapped, data source for discovering the genetic basis and architecture of plant natural products, which can be applied even without knowledge of the genome sequence.

plant biology↗