Biology subjects

Jander, G.

Publications and source records attributed to Jander, G..

34 records · Page 2Linked to original sources

bioRxiv2021

Rapid screening of pest resistance genes in maize using a sugarcane mosaic virus vector

Spodoptera frugiperda (fall armyworm) is a notorious pest that threatens maize production world-wide. Current control measures involve the use of chemical insecticides and transgenic maize expressing Bacillus thuringiensis (Bt) toxins. Although several additional transgenes have confirmed insecticidal activity in other plants, limited research has been conducted in maize, at least partially due to the technical difficulty of maize transformation. Here, we describe implementation of a sugarcane mosaic virus (SCMV) vector for rapidly testing the efficacy of transgenes for the control of S. frugiperda in maize. Four categories of proteins were tested using the SCMV vector: (i) maize defense signaling proteins: peptide elicitors (Pep1 and Pep3) and jasmonate acid conjugating enzymes (JAR1a and JAR1b); (ii) maize defensive proteins: the previously identified ribosome-inactivating protein (RIP2) and maize proteinase inhibitor (MPI), and two proteins with predicted but unconfirmed anti-insect activities, an antimicrobial peptide (AMP) and a lectin (JAC1); (iii) lectins from other plant species: Allium cepa agglutinin (ACA) and Galanthus nivalis agglutinin (GNA); and (iv) spider and scorpion toxins: peptides from Urodacus yaschenkoi (UyCT3 and UyCT5) and Hadronyche versuta (Hvt). In most cases, S. frugiperda larval growth on maize was reduced by transient SCMV-mediated overexpression of genes encoding these proteins. Additionally, experiments with some of the SCMV-expressed genes showed effectiveness against two aphid species, Rhopalosiphum maidis (corn leaf aphid) and Myzus persicae (green peach aphid). Together, these results demonstrate that SCMV vectors can be exploited as a rapid screening method for testing the efficacy and insecticidal activity of candidate genes in maize.

plant biology↗

bioRxiv2021

Indole-3-glycerolphosphate synthase, a branchpoint for the biosynthesis of tryptophan, indole, and benzoxazinoids in maize

The maize (Zea mays) genome encodes three indole-3-glycerolphosphate synthase enzymes (IGPS1, 2, and 3) catalyzing the conversion of 1-(2-carboxyphenylamino)-l-deoxyribulose-5-phosphate to indole-3-glycerolphosphate. Three further maize enzymes (BX1, benzoxazinoneless 1; TSA, tryptophan synthase subunit; and IGL, indole glycerolphosphate lyase) convert indole-3-glycerolphosphate to indole, which is released as a volatile defense signaling compound and also serves as a precursor for the biosynthesis of tryptophan and defense-related benzoxazinoids. Phylogenetic analyses showed that IGPS2 is similar to enzymes found in both monocots and dicots, whereas maize IGPS1 and IGPS3 are in monocot-specific clades. Fusions of yellow fluorescent protein (YFP) with maize IGPS enzymes and indole-3-glycerolphosphate lyases were all localized in chloroplasts. In bimolecular fluorescence complementation assays, IGPS1 interacted strongly with BX1 and IGL, IGPS2 interacted primarily with TSA, and IGPS3 interacted equally with all three indole-3-glycerolphosphate lyases. Whereas IGPS1 and IGPS3 expression was induced by insect feeding, IGPS2 expression was not. Transposon insertions in IGPS1 and IGPS3 reduced the abundance of both benzoxazinoids and free indole. Spodoptera exigua (beet armyworm) larvae show improved growth on igps1 mutant maize plants. Together, these results suggest that IGPS1 and IGPS3 function mainly in the biosynthesis of defensive metabolites, whereas IGPS2 may be involved in the biosynthesis of tryptophan. This metabolic channeling is similar, though less exclusive than that proposed for the three maize indole-3-glycerolphosphate lyases.

plant biology↗

bioRxiv2020

An improved Nicotiana benthamiana strain for aphid and whitefly research

Nicotiana benthamiana is used extensively as a platform for transient gene expression and as a model system for studying plant-virus interactions. However, many tobacco-feeding generalist herbivores, including Myzus persicae (green peach aphid), Bemisia tabaci (whitefly), Macrosiphum euphorbiae (potato aphid), Heliothis virescens (tobacco budworm), Trichoplusia ni (cabbage looper), and Helicoverpa zea (corn earworm), grow poorly on N. benthamiana, limiting its utility for research on plant-insect interactions. Using CRISPR/Cas9, we generated knockout mutations in two N. benthamiana acylsugar acyltransferases, ASAT1 and ASAT2, which contribute to the biosynthesis of insect-deterrent acylsucroses. Whereas asat1 mutations reduced the abundance of two predominant acylsucroses, asat2 mutations caused almost complete depletion of foliar acylsucroses. The tested hemipteran and lepidopteran species survived, gained weight, and/or reproduced significantly better on asat2 mutant plants than on wildtype N. benthamiana. Furthermore, both asat1 and asat2 mutations reduced the water content and increased the temperature of leaves, indicating that foliar acylsucroses can protect against desiccation. Two experiments demonstrated the utility of the N. benthamiana asat2 mutant line for insect bioassays. Transmission of turnip mosaic virus by M. persicae was significantly improved by an asat2 mutation. Tobacco rattle virus constructs were used for virus-induced gene silencing of acetylcholinesterase, squalene synthase, toll-like receptor 7, and tubulin-specific chaperon D genes in B. tabaci, an experiment that would have been difficult with wild-type N. benthamiana due to high insect mortality. Additionally, the absence of acylsugars in asat2 mutant lines will simplify transient expression assays for the functional analysis of acylsugar biosynthesis genes from other Solanaceae.

plant biology↗

bioRxiv2020

Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field

BackgroundPlants influence their root and rhizosphere microbial communities through the secretion of root exudates. However, how specific classes of root exudate compounds impact the assembly of these root-associated microbiotas is not well understood. Maize roots secrete benzoxazinoids (BXs), a class of indole-derived defense compounds, and thereby impact the assembly of their microbiota. Here, we investigated the broader impacts of BX exudation on root and rhizosphere microbiotas of adult maize plants grown under natural conditions at different field locations in Europe and the US. We examined the microbiotas of BX-producing and multiple BX-defective lines in two genetic backgrounds across three soil types. ResultsOur analysis showed that the secretion of BXs affected community composition of rhizosphere and root microbiota, with the most pronounced effects observed for root fungi. The impact of the two genetic backgrounds was weaker than that of the presence or absence of BXs, suggesting that BX exudation is a key trait by which maize structures its associated microbiota. BX-producing plants were not consistently enriching microbial lineages across the three soil types. Instead, BX exudation consistently depleted Flavobacteriaceae and Comamonadaceae, and enriched various plant pathogenic fungi in the roots. ConclusionsThese findings reveal that BXs have a selective impact on root and rhizosphere microbiota composition across different field locations. Taken together, this study identifies the BX pathway as an interesting breeding target to manipulate plant-microbiome interactions.

plant biology↗

bioRxiv2020

Less Is More: A Mutation in the Chemical Defense Pathway of Erysimum cheiranthoides (Brassicaceae) Reduces Total Cardenolide Abundance but Increases Resistance to Insect Herbivores

Many plants produce structurally related defensive metabolites with the same target sites in insect herbivores. Two possible drivers of this chemical diversity are: (i) interacting effects of structurally related compounds increase resistance against individual herbivores, and (ii) variants of the same chemical structures differentially affect diverse herbivore species or feeding guilds. Erysimum cheiranthoides L (Brassicaceae; wormseed wallflower) produces abundant and diverse cardenolide toxins, which are derived from digitoxigenin, cannogenol, and strophanthidin, all of which inhibit Na+/K+-ATPases in animal cells. Here we describe an E. cheiranthoides mutant with 66% lower cardenolide content, resulting from greatly decreased cannogenol- and strophanthidin-derived cardenolides, partially compensated for by increases in digitoxigenin-derived cardenolides. This compositional change created a more even cardenolide distribution, decreased the average cardenolide polarity, but did not impact glucosinolates, a different class of chemical defenses. Growth of generalist herbivores from two feeding guilds, Myzus persicae Sulzer (Hemiptera: Aphididae; green peach aphid) and Trichoplusia ni Hubner (Lepidoptera: Noctuidae; cabbage looper), was decreased on the mutant line compared to wildtype. Both herbivores accumulated cardenolides in proportion to plant content, with T. ni accumulating higher total concentrations than M. persicae. Helveticoside, an abundant cardenolide in E. cheiranthoides, was absent in M. persicae, suggesting that this compound is not present in the phloem. Our results support the hypothesis that cardenolide diversity protects plants against different herbivores, with digitoxigenin-derived compounds providing better protection against insects like M. persicae and T. ni, whereas cannogenol and strophanthidin provide better protection against other herbivores of E. cheiranthoides. FundingThis research was funded by US National Science Foundation awards 1907491 to AAA and 1645256 to GJ and AAA, Swiss National Science Foundation grant PZ00P3-161472 to TZ, and a Triad Foundation grant to GJ.

ecology↗

bioRxiv2019

Comparison of in vitro and in planta toxicity of Vip3A for lepidopteran herbivores

Agricultural pest infestation is as old as domestication of food crops and contributes a major share to the cost of crop production. Transgenic production of Vip3A, an insecticidal protein from Bacillus thuringiensis, effectively controls lepidopteran pests. A synthetic vip3A gene was evaluated its efficacy against Spodoptera litura (cotton leafworm), Spodoptera exigua (beet armyworm), Spodoptera frugiperda (fall armyworm), Helicoverpa armigera (cotton bollworm), Helicoverpa zea (corn earworm), Heliothis virescens (tobacco budworm), and Manduca sexta (tobacco hornworm). In artificial diet assays, the Vip3A concentration causing 50% mortality was H. zea > H. virescens > S. exigua > H. armigera > M. sexta > S. frugiperda > S. litura. In contrast, on vip3A transgenic tobacco the order of resistance (time until 50% lethality) was M. sexta > H. virescens > S. litura > H. zea > H. armigera > S. exigua > S. frugiperda. There was no significant correlation between the artificial diet and transgenic tobacco effects. Notably, the two insect species that are best-adapted for growth on tobacco, M. sexta and H. virescens, showed the greatest tolerance of vip3A-transgenic tobacco. This may indicate synergistic effects of Vip3A and endogenous plant defense mechanisms, e.g. nicotine, to which M. sexta and H. virescens would have greater resistance. Together, our results show that artificial diet assays are a poor predictor of Vip3A efficacy in transgenic plants, lepidopteran species vary in their sensitivity to Vip3A in diet-dependent manner, and that host plant adaptation of the targeted herbivores should be considered when designing transgenic plants for pest control.

molecular biology↗

bioRxiv2019

Rapid and independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae)

Phytochemical diversity is thought to result from coevolutionary cycles as specialization in herbivores imposes diversifying selection on plant chemical defenses. Plants in the speciose genus Erysimum (Brassicaceae) produce both ancestral glucosinolates and evolutionarily novel cardenolides as defenses. Here we test macroevolutionary hypotheses on co-expression, co-regulation, and diversification of these potentially redundant defenses across this genus. We sequenced and assembled the genome of E. cheiranthoides and foliar transcriptomes of 47 additional Erysimum species to construct a highly resolved phylogeny, revealing that cardenolide diversity increased rapidly rather than gradually over evolutionary time. Concentrations, inducibility, and diversity of the two defenses varied independently among species, with no evidence for trade-offs. Closely related species shared similar cardenolide traits, but not glucosinolate traits, likely as a result of specific selective pressures acting on distinct molecular diversification mechanisms. Ancestral and novel chemical defenses in Erysimum thus appear to provide complementary rather than redundant functions.

plant biology↗

bioRxiv2019

Cytokinin promotes jasmonic acid accumulation in the control of maize leaf growth.

Growth of plant organs results from the combined activity of cell division and cell expansion. The coordination of these two processes depends on the interplay between multiple hormones that determine final organ size. Using the semidominant Hairy Sheath Frayed1 (Hsf1) maize mutant, that hypersignals the perception of cytokinin (CK), we show that CK can reduce leaf size and growth rate by decreasing cell division. Linked to CK hypersignaling, the Hsf1 mutant has increased jasmonic acid (JA) content, a hormone that can inhibit cell division. Treatment of wild type seedlings with exogenous JA reduces maize leaf size and growth rate, while JA deficient maize mutants have increased leaf size and growth rate. Expression analysis revealed increased transcript accumulation of several JA pathway genes in the Hsf1 leaf growth zone. A transient treatment of growing wild type maize shoots with exogenous CK also induced JA pathway gene expression, although this effect was blocked by co-treatment with cycloheximide. Together our results suggest that CK can promote JA accumulation possibly through increased expression of specific JA pathway genes.\n\nOne sentence summaryCytokinin-signaling upregulates the jasmonate biosynthesis pathway, resulting in jasmonate accumulation and influences on maize leaf growth.

plant biology↗

bioRxiv2019

Characterizing the serotonin biosynthesis pathway upon aphid infestation in Setaria viridis leaves

Setaria viridis (green foxtail millet), a short life-cycle C4 plant in the Gramineae, serves as a resilient crop that provides good yield even in dry and marginal land. Although S. viridis has been studied extensively in the last decade, its defense responses, in particular the chemical defensive metabolites that protect it against insect herbivory, are unstudied. To characterize S. viridis defense responses, we conducted transcriptomic and metabolomic assays of plants infested with aphids and caterpillars. Pathway enrichment analysis indicated massive transcriptomic changes that involve genes from amino acid biosynthesis and degradation, secondary metabolites and phytohormone biosynthesis. The Trp-derived metabolite serotonin was notably induced by insect feeding. Through comparisons with known rice serotonin biosynthetic genes, we identified several predicted S. viridis Trp decarboxylases and cytochrome P450 genes that were up-regulated in response to insect feeding. The function of one Trp decarboxylase was validated by ectopic expression and detection of tryptamine accumulation in Nicotiana tabacum. To validate the defensive properties of serotonin, we used an artificial diet assay to show reduced Rhopalosiphum padi aphid survival with increasing serotonin concentrations. This demonstrated that serotonin is a defensive metabolite in S. viridis and is fundamental for understanding the adaptation of it to biotic stresses.\n\nHIGHLIGHTA combined transcriptomic and metabolomic profiling of Setaria viridis leaves response to aphid and caterpillar infestation identifies the genes related to the biosynthesis of serotonin and their function in defense.

plant biology↗

bioRxiv2018

Silencing cathepsin L expression reduces Myzus persicae protein content and the nutritional value as prey for Coccinella septempunctata

Gut-expressed aphid genes, which may be more easily inhibited by RNA interference (RNAi) constructs, are attractive targets for pest control efforts involving transgenic plants. Here we show that expression of cathepsin L, a cysteine protease that functions in aphid guts, can be reduced by expression of an RNAi construct in transgenic tobacco. The effectiveness of this approach is demonstrated by up to 80% adult mortality, reduced fecundity, and delayed nymph production of Myzus persicae (green peach aphids) when cathepsin L expression was reduced by plant-mediated RNAi. Consistent with the function of cathepsin L as a gut protease, M. persicae fed on the RNAi plants had a lower protein content in their bodies and excreted more protein in their honeydew. Larvae of Coccinella septempunctata (seven-spotted ladybugs) grew more slowly on aphids having reduced cathepsin L expression, suggesting that prey insect nutritive value, and not just direct negative effects of the RNAi construct, needs to be considered when producing transgenic plants for RNAi-mediated pest control.\n\nHighlightsO_LISilencing expression of cathepsin L by RNA interference reduces protein content of Myzus persicae (green peach aphid) bodies.\nC_LIO_LIHoneydew of aphids with cathepsin L silenced contains elevated protein.\nC_LIO_LICathepsin L is required for efficient protein uptake from phloem sap.\nC_LIO_LIAphids with cathepsin L expression silenced have increased mortality and fewer offspring.\nC_LIO_LICoccinella septempunctata (seven-spotted ladybugs) grow more slowly on aphids with expression of cathepsin L silenced.\nC_LI\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=173 SRC=\"FIGDIR/small/451211_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@5ee6d7org.highwire.dtl.DTLVardef@853fe8org.highwire.dtl.DTLVardef@26c2aborg.highwire.dtl.DTLVardef@b67e2b_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2018

Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch)

BackgroundThe corn leaf aphid (Rhopalosiphum maidis Fitch) is the most economically damaging aphid pest on maize (Zea mays), one of the worlds most important grain crops. In addition to causing direct damage due to the removal of photoassimilates, R. maidis transmits several destructive maize viruses, including Maize yellow dwarf virus, Barley yellow dwarf virus, Sugarcane mosaic virus, and Cucumber mosaic virus.\n\nFindingsA 326-Mb genome assembly of BTI-1, a parthenogenetically reproducing R. maidis clone, was generated with a combination of PacBio (208-fold coverage) and Illumina sequencing (80-fold coverage), which contains a total of 689 contigs with an N50 size of 9.0 Mb. The contigs were further clustered into four scaffolds using the Phase Genomics Hi-C interaction maps, consistent with the commonly observed 2n = 8 karyotype of R. maidis. Most of the assembled contigs (473 spanning 321 Mb) were successfully orientated in the four scaffolds. The R. maidis genome assembly captured the full length of 95.8% of the core eukaryotic genes, suggesting that it is highly complete. Repetitive sequences accounted for 21.2% of the assembly, and a total of 17,647 protein-coding genes were predicted in the R. maidis genome with integrated evidence from ab initio and homology-based gene predictions and transcriptome sequences generated with both PacBio and Illumina. An analysis of likely horizontally transferred genes identified two from bacteria, seven from fungi, two from protozoa, and nine from algae.\n\nConclusionsA high-quality R. maidis genome was assembled at the chromosome level. This genome sequence will enable further research related to ecological interactions, virus transmission, pesticide resistance, and other aspects of R. maidis biology. It also serves as a valuable resource for comparative investigation of other aphid species.

genomics↗

bioRxiv2018

Metabolome-scale genome-wide association studies reveal chemical diversity and genetic control of maize specialized metabolites

One Sentence SummaryHPLC-MS metabolite profiling of maize seedlings, in combination with genome-wide association studies, identifies numerous quantitative trait loci that influence the accumulation of foliar metabolites.\n\nAbstractCultivated maize (Zea mays) retains much of the genetic and metabolic diversity of its wild ancestors. Non-targeted HPLC-MS metabolomics using a diverse panel of 264 maize inbred lines identified a bimodal distribution in the prevalence of foliar metabolites. Although 15% of the detected mass features were present in >90% of the inbred lines, the majority were found in <50% of the samples. Whereas leaf bases and tips were differentiated primarily by flavonoid abundance, maize varieties (stiff-stalk, non-stiff-stalk, tropical, sweet corn, and popcorn) were differentiated predominantly by benzoxazinoid metabolites. Genome-wide association studies (GWAS), performed for 3,991 mass features from the leaf tips and leaf bases, showed that 90% have multiple significantly associated loci scattered across the genome. Several quantitative trait locus hotspots in the maize genome regulate the abundance of multiple, often metabolically related mass features. The utility of maize metabolite GWAS was demonstrated by confirming known benzoxazinoid biosynthesis genes, as well as by mapping isomeric variation in the accumulation of phenylpropanoid hydroxycitric acid esters to a single linkage block in a citrate synthase-like gene. Similar to gene expression databases, this metabolomic GWAS dataset constitutes an important public resource for linking maize metabolites with biosynthetic and regulatory genes.

genetics↗

bioRxiv2018

Ethylene signaling regulates natural variation in the abundance of antifungal acetylated diferuloylsucroses and Fusarium graminearum resistance in maize seedling roots

O_LIThe production and regulation of defensive specialized metabolites plays a central role in pathogen resistance in maize (Zea mays) and other plants. Therefore, identification of genes involved in plant specialized metabolism can contribute to improved disease resistance.\nC_LIO_LIWe used comparative metabolomics to identify previously unknown antifungal metabolites in maize seedling roots, and investigated the genetic and physiological mechanisms underlying their natural variation using quantitative trait locus (QTL) mapping and comparative transcriptomics approaches.\nC_LIO_LITwo maize metabolites, smilaside A (3,6-diferuloyl-3',6'-diacetylsucrose) and smiglaside C (3,6-diferuloyl-2',3',6'-triacetylsucrose), that may contribute to maize resistance against Fusarium graminearum and other fungal pathogens were identified. Elevated expression of an ethylene receptor gene, ETHYLENE INSENSITIVE 2 (ZmEIN2), co-segregated with decreased smilaside A/smiglaside C ratio. Pharmacological and genetic manipulation of ethylene availability and sensitivity in vivo indicated that, whereas ethylene was required for the production of both metabolites, the smilaside A/smiglaside C ratio was negatively regulated by ethylene sensitivity. This ratio, rather than the absolute abundance of these two metabolites, was important for maize seedling root defense against F. graminearum.\nC_LIO_LIEthylene signaling regulates the relative abundance of the two F. graminearum-resistance-related metabolites and affects resistance against F. graminearum in maize seedling roots.\nC_LI

plant biology↗

bioRxiv2018

Fusarium graminearum-Induced Shoot Elongation and Root Reduction in Maize Seedlings Correlate with Later Seedling Blight Severity

Fusarium graminearum seedling blight is a common disease of maize (Zea mays). Development of genetic resistance to seedling blight in maize germplasm requires efficient and accurate quantitative assessment of disease severity. Through artificial inoculation experiments under controlled growth conditions, we determined that host genotype, pathogen genotype, and infection dose influence the extent to which F. graminearum induces shoot elongation and inhibits root growth in maize seedlings. A comparison of fifteen maize inbred lines showed independent variation of these two fungus-induced effects on seedling growth. In a broader survey with nine commercial maize hybrids and three field-collected fungal isolates, there was significant correlation between these seedling growth responses, as well as with later seedling blight severity. Analysis of variance suggested that this variation and the observed correlative relationships were primarily driven by differing pathogenicity of the three fungal isolates. Together, our results indicate that F. graminearum-induced shoot elongation and root reduction in maize seedlings have distinct underlying physiological mechanisms, and that early observations of seedling growth responses can serve as a proxy for investigating natural variation in host resistance and pathogen aggressiveness at later growth stages.

plant biology↗

bioRxiv2017

Spodoptera exigua caterpillar feeding induces rapid defense responses in maize leaves

Insects such as beet armyworm caterpillars (Spodoptera exigua) cause extensive damage to maize (Zea mays) by consuming foliar tissue. Maize plants respond to such insect attack by triggering defense mechanisms that involve large changes in gene expression and the biosynthesis of specialized metabolites and defense signaling molecules. To investigate dynamic maize responses to herbivore feeding, leaves of maize inbred line B73 were infested with S. exigua caterpillars for 1 to 24 hours, followed by comprehensive transcriptomic and metabolomic characterization. Our results show that the most significant gene expression responses of maize to S. exigua feeding occur at early time points, within 4 to 6 hours after caterpillar infestation. However, both gene expression and metabolite profiles continued changing during the entire 24-hour experiment while photosynthesis genes were gradually decreased. The primary and specilaze metabolism shift maught be temporal and dynamic processes in the infested leaf tissue. We analyzed the effects of mutating genes in two major defense-related pathways, benzoxazinoids (Bx1 and Bx2) and jasmonic acid (Lox8), using Dissociation (Ds) transposon insertions in maize inbred line W22. Together, these results show that maize leaves shift to implementation of chemical defenses within one hour after the initiation of caterpillar attack. Thus, the induced biosynthesis of specialized metabolites can have major effects in maize-caterpillar interactions.\n\nHIGHLIGHTA comprehensive transcriptic and metabolomic profiling time course of maize foliar responses to caterpillar feeding identifies genes for the synthesis of benzoxazinoids and phytohormones.

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↗