SeedQuant: a deep learning-based tool for assessing stimulant and inhibitor activity on root parasitic seeds.

Witchweeds (Striga spp.) and broomrapes (Orobanchaceae and Phelipanche spp.) are root parasitic plants that infest many crops in warm and temperate zones, causing enormous yield losses and endangering global food security. Seeds of these obligate parasites require rhizospheric, host-released stimulants to germinate, which opens up possibilities for controlling them by applying specific germination inhibitors or synthetic stimulants that induce lethal germination in the host's absence. To determine their effect on germination, root exudates or synthetic stimulants/inhibitors are usually applied to parasitic seeds in in vitro bioassays, followed by assessment of germination ratios. Although these protocols are very sensitive, the germination recording process is laborious, representing a challenge for researchers and impeding high-throughput screens. Here, we developed an automatic seed census tool to count and discriminate germinated seeds (GS) from non-GS. We combined deep learning, a powerful data-driven framework that can accelerate the procedure and increase its accuracy, for object detection with computer vision latest development based on the Faster Region-based Convolutional Neural Network algorithm. Our method showed an accuracy of 94% in counting seeds of Striga hermonthica and reduced the required time from approximately 5 min to 5 s per image. Our proposed software, SeedQuant, will be of great help for seed germination bioassays and enable high-throughput screening for germination stimulants/inhibitors. SeedQuant is an open-source software that can be further trained to count different types of seeds for research purposes.

Integrated analyses of the transcriptome and small RNA of the hemiparasitic plant Monochasma savatieri before and after establishment of parasite-host association.

BACKGROUND: Monochasma savatieri is a medicinal root hemiparasitic herb that extracts water and nutrients from the host plant via a haustorium. M. savatieri exhibits an enhanced growth after the establishment of parasite-host associations, but little is known about the molecular mechanism responsible. In this study, endogenous hormones, RNA sequencing and small RNA sequencing analysis were performed on M. savatieri before and after establishment of parasite-host associations. RESULTS: When grown with the host, decreased contents of jasmonic acid (JA) and indole-3-acetic acid (IAA) and increased abscisic acid (ABA) content were observed in M. savatieri with the established parasitic relationship. When grown with the host, 46,424 differentially expressed genes (DEGs) and 162 differentially expressed miRNAs (DEmiRs) were identified in the comparison between M. savatieri with the established parasitic relationship and without the established parasitic relationship. Analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that these DEGs and targets of DEmiRs mostly participated in plant hormone signal transduction, starch and sucrose metabolism, carbohydrate metabolism, cell growth and death, and transport and catabolism. Furthermore, correlation analysis of mRNA and miRNA revealed that 10 miRNA-target pairs from novel_mir65, novel_mir40, novel_mir80, miR397-5p_1, novel_mir36, novel_mir25 and novel_mir17 may have important roles in regulating the parasitic development of M. savatieri. CONCLUSIONS: Our study not only expands the understanding of enhanced growth in M. savatieri after the establishment of parasite-host associations, but also first provides abundant resources for future molecular and genetic studies in M. savatieri.

Synthesis of Active Strigolactone Analogues Based on Eudesmane- and Guaiane-Type Sesquiterpene Lactones.

Strigolactones are natural products that are exuded by plants and stimulate parasitic weed germination. Their use in herbicides is limited since they are produced in small quantities, but the synthesis of bioactive analogues provides an alternative source. In this work, eleven analogues have been synthesized. Among them, nine compounds belong to a novel family named eudesmanestrigolactones. The procedure is short (3-6 steps), the starting materials are isolated on a multigram scale, and global yields are up to 8%, which significantly enhance isolated yields. In bioassay, the compounds germinated high percentages of Phelipanche ramosa, Orobanche cumana, and Orobanche crenata seeds, even at nanogram doses (100 nM). Bioactivity was stereochemistry-dependent, and it was discussed in terms of the presence and geometry of the enol ether, orientation of the butenolide, and unsaturation of ring A. The reported compounds provide a set of readily obtained allelochemicals with potential applications as preventive herbicides.

An auxin transport network underlies xylem bridge formation between the hemi-parasitic plant Phtheirospermum japonicum and host Arabidopsis.

Parasitic plants form vascular connections with host plants for efficient material transport. The haustorium is the responsible organ for host invasion and subsequent vascular connection. After invasion of host tissues, vascular meristem-like cells emerge in the central region of the haustorium, differentiate into tracheary elements and establish a connection, known as a xylem bridge, between parasite and host xylem systems. Despite the importance of this parasitic connection, the regulatory mechanisms of xylem bridge formation are unknown. Here, we show the role of auxin and auxin transporters during the process of xylem bridge formation using an Orobanchaceae hemiparasitic plant, Phtheirospermum japonicum The auxin response marker DR5 has a similar expression pattern to tracheary element differentiation genes in haustoria. Auxin transport inhibitors alter tracheary element differentiation in haustoria, but biosynthesis inhibitors do not, demonstrating the importance of auxin transport during xylem bridge formation. The expression patterns and subcellular localization of PIN family auxin efflux carriers and AUX1/LAX influx carriers correlate with DR5 expression patterns. The cooperative action of auxin transporters is therefore responsible for controlling xylem vessel connections between parasite and host.

Broomrape infestation in carrot (Daucus carota): Changes in carotenoid gene expression and carotenoid accumulation in the parasitic weed Phelipanche aegyptiaca and its host.

Carotenogenesis has been intensively studied in carrot roots, and transcriptional regulation is thought to be the major factor in carotenoid accumulation in these organs. However, little is known about the transcriptional regulation of carotenoid biosynthetic genes concerning carotenoid accumulation during infestation by the obligate parasite Phelipanche aegyptiaca. HPLC analysis revealed a decrease in carotenoid levels of the different carrot cultivars when parasitized by P. aegyptiaca. Besides, we isolated and analyzed P. aegyptiaca tubercles parasitizing the various carrot root cultivars and show that they accumulate different carotenoids compared to those in non-infested carrot roots. Expression analysis of PHYTOENE SYNTHASE (PSY1) and CAROTENOID ISOMERASE (CRTISO) as well as the strigolactone apocarotenoid biosynthetic genes DWARF27 (D27), CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7) and CCD8 revealed that their transcript levels showed significant variation in P. aegyptiaca infested carrot roots. After parasite infestation, the expression of these genes was strongly reduced, as were the carotenoid levels and this was more pronounced in the uncommon non-orange varieties. We also analyzed the parasite genes encoding D27, CCD7 and CCD8 and show that they are expressed in tubercles. This raises important questions of whether the parasite produces its carotenoids and apocarotenoids including strigolactones and whether the latter might have a role in tubercle development.

Easy Access to Alkoxy, Amino, Carbamoyl, Hydroxy, and Thiol Derivatives of Sesquiterpene Lactones and Evaluation of Their Bioactivity on Parasitic Weeds.

It has been hypothesized that the α-methylene-γ-lactone moiety of sesquiterpene lactones is a key unit for their bioactivity. As a consequence, modifications of these compounds have been focused on this fragment. In the work reported here, two sesquiterpene lactones, namely, dehydrocostuslactone and ß-cyclocostunolide, a eudesmanolide obtained by controlled cyclization of costunolide, were chosen for modification by Michael addition at C-13. On applying this reaction to both compounds, it was possible to introduce the functional groups alkoxy, amino, carbamoyl, hydroxy, and thiol to give products in good to high yields, depending on the base and solvent employed. In particular, the introduction of a thiol group at C-13 in both compounds was achieved with outstanding yields (>90%) and this is unprecedented for these sesquiterpene lactones. The bioactivities of the products were evaluated on etiolated wheat coleoptile elongation and germination of seeds of parasitic weeds, with significant activity observed on Orobanche cumana and Phelipanche ramosa. The structure-activity relationships are discussed.

Seed germination in parasitic plants: what insights can we expect from strigolactone research?

Obligate root-parasitic plants belonging to the Orobanchaceae family are deadly pests for major crops all over the world. Because these heterotrophic plants severely damage their hosts even before emerging from the soil, there is an unequivocal need to design early and efficient methods for their control. The germination process of these species has probably undergone numerous selective pressure events in the course of evolution, in that the perception of host-derived molecules is a necessary condition for seeds to germinate. Although most of these molecules belong to the strigolactones, structurally different molecules have been identified. Since strigolactones are also classified as novel plant hormones that regulate several physiological processes other than germination, the use of autotrophic model plant species has allowed the identification of many actors involved in the strigolactone biosynthesis, perception, and signal transduction pathways. Nevertheless, many questions remain to be answered regarding the germination process of parasitic plants. For instance, how did parasitic plants evolve to germinate in response to a wide variety of molecules, while autotrophic plants do not? What particular features are associated with their lack of spontaneous germination? In this review, we attempt to illustrate to what extent conclusions from research into strigolactones could be applied to better understand the biology of parasitic plants.

Is induction ability of seed germination of Phelipanche ramosa phylogenetically structured among hosts? A case study on Fabaceae species.

Phelipanche ramosa is a major root-holoparasitic damaging weed characterized by a broad host range, including numerous Fabaceae species. In France, the agricultural threat posed by P. ramosa has increased over two decades due to the appearance of a genetically differentiated pathovar presenting a clear host specificity for oilseed rape. The new pathovar has led to a massive expansion of P. ramosa in oilseed rape fields. The germination rate of P. ramosa seeds is currently known to vary among P. ramosa pathovars and host species. However, only a few studies have investigated whether phylogenetic relatedness among potential host species is a predictor of the ability of these species to induce the seed germination of parasitic weeds by testing for phylogenetic signal. We focused on a set of 12 Fabaceae species and we assessed the rate of induction of seed germination by these species for two pathovars based on in vitro co-cultivation experiments. All Fabaceae species tested induced the germination of P. ramosa seeds. The germination rate of P. ramosa seeds varied between Fabaceae species and tribes studied, while pathovars appeared non-influential. Considering oilseed rape as a reference species, we also highlighted a significant phylogenetic signal. Phylogenetically related species therefore showed more similar rates of induction of seed germination than species drawn at random from a phylogenetic tree. In in vitro conditions, only Lotus corniculatus induced a significantly higher germination rate than oilseed rape, and could potentially be used as a catch crop after confirmation of these results under field conditions.

New Strigolactone Mimics as Exogenous Signals for Rhizosphere Organisms.

The importance of strigolactones in plant biology prompted us to synthesize simplified strigolactone mimics effective as exogenous signals for rhizosphere organisms. New strigolactone mimics easily derived from simple and available starting materials in significant amounts were prepared and fully characterized. These compounds contain an aromatic or heterocyclic ring, usually present in various bioactive molecules, connected by an ether link to a furan-2-one moiety. The new synthesized strigolactone mimics were confirmed to be active on plant pathogenic fungi and parasitic weed seeds.

Quinone oxidoreductase 2 is involved in haustorium development of the parasitic plant Phtheirospermum japonicum.

The family Orobanchaceae includes many parasitic plant species. Parasitic plants invade host vascular tissues and form organs called haustoria, which are used to obtain water and nutrients. Haustorium formation is initiated by host-derived chemicals including quinones and flavonoids. Two types of quinone oxidoreductase (QR) are involved in signal transduction leading to haustorium formation; QR1 mediates single-electron transfers and QR2 mediates 2-electron transfers. In the facultative parasite Triphysaria versicolor, QR1 is involved in haustorium induction signaling, while this role is played by QR2 in the model plant Phtheirospermum japonicum. Our results suggest that there is functional diversification in haustorium signaling molecules among different species of the Orobanchaceae.

Interactions of inbreeding and stress by poor host quality in a root hemiparasite.

BACKGROUND AND AIMS: Populations of many hemiparasitic plants are fragmented and threatened by inbreeding depression (ID). In addition, they may also be strongly affected by a lack of suitable host species. However, nothing is known about possible interactive effects of inbreeding and host quality for parasitic plants. Poor host quality represents a special type of biotic stress and the magnitude of ID is often expected to be higher in more stressful environments. METHODS: We studied the effects of inbreeding and the quality of host species for the declining root hemiparasite Rhinanthus alectorolophus Selfed and open-pollinated parasites from two natural populations were grown (1) with 13 potential host species and (2) with 15 four-species mixtures. KEY RESULTS: ID differed among host species and mixtures. In the first experiment, ID was highest in parasites grown with good hosts and declined with stress intensity. In the second experiment, ID was not influenced by stress intensity, but was highest in mixtures of hosts from only one functional group and lowest in mixtures containing three functional groups. Both parasite performance with individual host species and the damage to these host species differed between parasites from the two study populations. CONCLUSIONS: Our results contradict the common assumption that ID is generally higher in more stressful environments. In addition, they support the importance of diverse host communities for hemiparasitic plants. The differences in host quality between the two parasite populations indicate genetic variation in the adaptation to individual hosts and in host-specific virulence. However, inbreeding did not affect specific host-parasite interactions.

Mechanism of glyphosate control of Phelipanche aegyptiaca.

MAIN CONCLUSION: Despite its total reliance on its host plant, the holoparasite Phelipanche aegyptiaca suffers from a deficiency of aromatic amino acids upon exposure to glyphosate. The herbicide glyphosate inhibits 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), a key enzyme in the biosynthesis of aromatic amino acids. However, the functionality of the EPSPS pathway in the obligate root holoparasite Phelipanche aegyptiaca is not straightforward because of the parasite's total dependence on the host plant. Despite the importance of glyphosate as a means of controlling P. aegyptiaca, the mechanism of action of the herbicide in this parasite is not clearly understood. We characterized glyphosate control of P. aegyptiaca by using a glyphosate-resistant tomato (GRT) genotype as the host plant and evaluating the activity of EPSPS and the levels of free aromatic amino acids in the parasite. The viability of the parasite's tissues deteriorated within the first 40 h after treatment (HAT) with glyphosate. In parallel, shikimate accumulation in the parasite was first detected at 24 HAT and increased over time. However, shikimate levels in the GRT host did not increase, indicating that the host was indeed glyphosate tolerant. Free phenylalanine and tyrosine levels decreased by 48 HAT in the parasite, indicating a deficiency of aromatic amino acids. The use of GRT as the host enabled us to observe, in an in situ experimental system, both endogenous EPSPS inhibition and a deficiency of aromatic amino acids in the parasite. We thus provided evidence for the presence of an active EPSPS and aromatic amino acid biosynthesis pathway in P. aegyptiaca and pinpointed this pathway as the target of glyphosate action in this parasite.

The Haustorium, a Specialized Invasive Organ in Parasitic Plants.

Parasitic plants thrive by infecting other plants. Flowering plants evolved parasitism independently at least 12 times, in all cases developing a unique multicellular organ called the haustorium that forms upon detection of haustorium-inducing factors derived from the host plant. This organ penetrates into the host stem or root and connects to its vasculature, allowing exchange of materials such as water, nutrients, proteins, nucleotides, pathogens, and retrotransposons between the host and the parasite. In this review, we focus on the formation and function of the haustorium in parasitic plants, with a specific emphasis on recent advances in molecular studies of root parasites in the Orobanchaceae and stem parasites in the Convolvulaceae.

PLANT EVOLUTION. Convergent evolution of strigolactone perception enabled host detection in parasitic plants.

Obligate parasitic plants in the Orobanchaceae germinate after sensing plant hormones, strigolactones, exuded from host roots. In Arabidopsis thaliana, the α/ß-hydrolase D14 acts as a strigolactone receptor that controls shoot branching, whereas its ancestral paralog, KAI2, mediates karrikin-specific germination responses. We observed that KAI2, but not D14, is present at higher copy numbers in parasitic species than in nonparasitic relatives. KAI2 paralogs in parasites are distributed into three phylogenetic clades. The fastest-evolving clade, KAI2d, contains the majority of KAI2 paralogs. Homology models predict that the ligand-binding pockets of KAI2d resemble D14. KAI2d transgenes confer strigolactone-specific germination responses to Arabidopsis thaliana. Thus, the KAI2 paralogs D14 and KAI2d underwent convergent evolution of strigolactone recognition, respectively enabling developmental responses to strigolactones in angiosperms and host detection in parasites.

PrCYP707A1, an ABA catabolic gene, is a key component of Phelipanche ramosa seed germination in response to the strigolactone analogue GR24.

After a conditioning period, seed dormancy in obligate root parasitic plants is released by a chemical stimulus secreted by the roots of host plants. Using Phelipanche ramosa as the model, experiments conducted in this study showed that seeds require a conditioning period of at least 4 d to be receptive to the synthetic germination stimulant GR24. A cDNA-AFLP procedure on seeds revealed 58 transcript-derived fragments (TDFs) whose expression pattern changed upon GR24 treatment. Among the isolated TDFs, two up-regulated sequences corresponded to an abscisic acid (ABA) catabolic gene, PrCYP707A1, encoding an ABA 8'-hydroxylase. Using the rapid amplification of cDNA ends method, two full-length cDNAs, PrCYP707A1 and PrCYP707A2, were isolated from seeds. Both genes were always expressed at low levels during conditioning during which an initial decline in ABA levels was recorded. GR24 application after conditioning triggered a strong up-regulation of PrCYP707A1 during the first 18 h, followed by an 8-fold decrease in ABA levels detectable 3 d after treatment. In situ hybridization experiments on GR24-treated seeds revealed a specific PrCYP707A1 mRNA accumulation in the cells located between the embryo and the micropyle. Abz-E2B, a specific inhibitor of CYP707A enzymes, significantly impeded seed germination, proving to be a non-competitive antagonist of GR24 with reversible inhibitory activity. These results demonstrate that P. ramosa seed dormancy release relies on ABA catabolism mediated by the GR24-dependent activation of PrCYP707A1. In addition, in situ hybridization corroborates the putative location of cells receptive to the germination stimulants in seeds.

Role of the sucrose synthase encoding PrSus1 gene in the development of the parasitic plant Phelipanche ramosa L. (Pomel).

Phelipanche ramosa L. (Pomel) is a major root-parasitic weed attacking many important crops. Success in controlling this parasite is rare and a better understanding of its unique biology is needed to develop new specific control strategies. In the present study, quantitative polymerase chain reaction experiments showed that sucrose synthase encoding PrSus1 transcripts accumulate at their highest level once the parasite is connected to the host (tomato) vascular system, mainly in the parasite tubercles, which bear numerous adventitious roots. In situ hybridization experiments revealed strong PrSus1 expression in both shoot and root apices, especially in shoot apical meristems and in the vascular tissues of scale leaves and stems, and in the apical meristems and developing xylem in roots. In addition, immunolocalization experiments showed that a sucrose synthase protein co-localized with cell-wall thickening in xylem elements. These findings highlight the role of PrSus1 in the utilization of host-derived sucrose in meristematic areas and in cellulose biosynthesis in differentiating vascular elements. We also demonstrate that PrSus1 is downregulated in response to 2,3,5-triiodobenzoic acid-induced inhibition of polar auxin transport in the host stem, suggesting that PrSus1 activity in xylem maturation is controlled by host-derived auxin.

Effects of ozone on species composition in an upland grassland.

Northern hemispheric background concentrations of ozone are increasing, but few studies have assessed the ecological significance of these changes for grasslands of high conservation value under field conditions. We carried out a 3-year field experiment in which ozone was released at a controlled rate over three experimental transects to produce concentration gradients over the field site, an upland mesotrophic grassland located in the UK. We measured individual species biomass in an annual hay cut in plots receiving ambient ozone, and ambient ozone elevated by mean concentrations of approximately 4 ppb and 10 ppb in the growing seasons of 2008 and 2009. There was a significant negative effect of ozone exposure on herb biomass, but not total grass or legume biomass, in 2008 and 2009. Within the herb fraction, ozone exposure significantly decreased the biomass of Ranunculus species and that of the hemi-parasitic species Rhinanthus minor. Multivariate analysis of species composition, taking into account spatial variation in soil conditions and ozone exposure, showed no significant ozone effect on the grass component. In contrast, by 2009, ozone had become the dominant factor influencing species composition within the combined herb and legume component. Our results suggest that elevated ozone concentrations may be a significant barrier to achieving increased species diversity in managed grasslands.

Agrobacterium rhizogenes-mediated transformation of the parasitic plant Phtheirospermum japonicum.

BACKGROUND: Plants within the Orobanchaceae are an agriculturally important group of parasites that attack economically important crops to obtain water and nutrients from their hosts. Despite their agricultural importance, molecular mechanisms of the parasitism are poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: We developed transient and stable transformation systems for Phtheirospermum japonicum, a facultative parasitic plant in the Orobanchaceae. The transformation protocol was established by a combination of sonication and acetosyringone treatments using the hairy-root-inducing bacterium, Agrobacterium rhizogenes and young seedlings. Transgenic hairy roots of P. japonicum were obtained from cotyledons 2 to 3 weeks after A. rhizogenes inoculation. The presence and the expression of transgenes in P. japonicum were verified by genomic PCR, Southern blot and RT-PCR methods. Transgenic roots derived from A. rhizogenes-mediated transformation were able to develop haustoria on rice and maize roots. Transgenic roots also formed apparently competent haustoria in response to 2,6-dimethoxy-1,4-benzoquinone (DMBQ), a haustorium-inducing chemical. Using this system, we introduced a reporter gene with a Cyclin B1 promoter into P. japonicum, and visualized cell division during haustorium formation. CONCLUSIONS: We provide an easy and efficient method for hairy-root transformation of P. japonicum. Transgenic marker analysis revealed that cell divisions during haustorium development occur 24 h after DMBQ treatment. The protocols described here will allow functional analysis of genes involved in plant parasitism.

The role of heterotrophic carbon acquisition by the hemiparasitic plant Rhinanthus alectorolophus in seedling establishment in natural communities: a physiological perspective.

• Heterotrophic acquisition of substantial amounts of organic carbon by hemiparasitic plants was clearly demonstrated by numerous studies. Many hemiparasites are, however, also limited by competition for light preventing the establishment of their populations on highly productive sites. • In a growth-chamber experiment, we investigated the effects of competition for light, simulated by shading, on growth and heterotrophic carbon acquisition by the hemiparasite Rhinanthus alectorolophus attached to C(3) and C(4) hosts using analyses of biomass production and stable isotopes of carbon. • Shading had a detrimental effect on biomass production and vertical growth of the hemiparasites shaded from when they were seedlings, while shading imposed later caused only a moderate decrease of biomass production and had no effect on the height. Moreover, shading increased the proportion of host-derived carbon in hemiparasite biomass (up to 50% in shaded seedlings). • These results demonstrate that host-derived carbon can play a crucial role in carbon budget of hemiparasites, especially if they grow in a productive environment with intense competition for light. The heterotrophic carbon acquisition can allow hemiparasite establishment in communities of moderate productivity, helping well-attached hemiparasites to escape from the critical seedling stage.