Profiling mRNAs of two Cuscuta species reveals possible candidate transcripts shared by parasitic plants

The plant vampire diaries: a historic perspective on Cuscuta research

The angiosperm genus Cuscuta lives as an almost achlorophyllous root- and leafless holoparasite and has therefore occupied scientists for more than a century. The 'evolution' of Cuscuta research started with early studies that established the phylogenetic framework for this unusual genus. It continued to produce groundbreaking cytological, morphological, and physiological insight throughout the second half of the 20th century and culminated in the last two decades in exciting discoveries regarding the molecular basis of Cuscuta parasitism that were facilitated by the modern 'omics' tools and traceable fluorescent marker technologies of the 21st century. This review will show how present activities are inspired by those past breakthroughs. It will describe significant milestones and recurring themes of Cuscuta research and connect these to the remaining as well as newly evolving questions and future directions in this research field that is expected to sustain its strong growth in the future.

Genomic and Epigenomic Mechanisms of the Interaction between Parasitic and Host Plants

Parasitic plants extract nutrients from the other plants to finish their life cycle and reproduce. The control of parasitic weeds is notoriously difficult due to their tight physical association and their close biological relationship to their hosts. Parasitic plants differ in their susceptible host ranges, and the host species differ in their susceptibility to parasitic plants. Current data show that adaptations of parasitic plants to various hosts are largely genetically determined. However, multiple cases of rapid adaptation in genetically homogenous parasitic weed populations to new hosts strongly suggest the involvement of epigenetic mechanisms. Recent progress in genome-wide analyses of gene expression and epigenetic features revealed many new molecular details of the parasitic plants' interactions with their host plants. The experimental data obtained in the last several years show that multiple common features have independently evolved in different lines of the parasitic plants. In this review we discuss the most interesting new details in the interaction between parasitic and host plants.

Metabolomics Analysis Provides New Insights Into the Molecular Mechanisms of Parasitic Plant Dodder Elongation in vitro

Dodder (Cuscuta spp.) species are obligate parasitic flowering plants that totally depend on host plants for growth and reproduction and severely suppress hosts' growth. As a rootless and leafless plant, excised dodder shoots exhibit rapid growth and elongation for several days to hunt for new host stems, and parasitization could be reestablished. This is one unique ability of the dodder to facilitate its success in nature. Clearly, excised dodder stems have to recycle stored nutrients to elongate as much as possible. However, the mechanism of stored nutrient recycling in the in vitro dodder shoots is still poorly understood. Here, we found that dodder is a carbohydrate-rich holoparasitic plant. During the in vitro dodder shoot development, starch was dramatically and thoroughly degraded in the dodder shoots. Sucrose derived from starch degradation in the basal stems was transported to the shoot tips, in which EMP and TCA pathways were activated to compensate for carbon demand for the following elongation according to the variations of sugar content related to the crucial gene expression, and the metabolomics analysis. Additionally, antioxidants were significantly accumulated in the shoot tips in contrast to those in the basal stems. The variations of phytohormones (jasmonic acid, indole-3-acetic acid, and abscisic acid) indicated that they played essential roles in this process. All these data suggested that starch and sucrose degradation, EMP and TCA activation, antioxidants, and phytohormones were crucial and associated with the in vitro dodder shoot elongation.

Investigating Host and Parasitic Plant Interaction by Tissue-Specific Gene Analyses on Tomato and Cuscuta campestris Interface at Three Haustorial Developmental Stages

Parasitic weeds cause billions of dollars in agricultural losses each year worldwide. Cuscuta campestris (C. campestris), one of the most widespread and destructive parasitic plants in the United States, severely reduces yield in tomato plants. Reducing the spread of parasitic weeds requires understanding the interaction between parasites and hosts. Several studies have identified factors needed for parasitic plant germination and haustorium induction, and genes involved in host defense responses. However, knowledge of the mechanisms underlying the interactions between host and parasitic plants, specifically at the interface between the two organisms, is relatively limited. A detailed investigation of the crosstalk between the host and parasite at the tissue-specific level would enable development of effective parasite control strategies. To focus on the haustorial interface, we used laser-capture microdissection (LCM) with RNA-seq on early, intermediate and mature haustorial stages. In addition, the tomato host tissue that immediately surround the haustoria was collected to obtain tissue- resolution RNA-Seq profiles for C. campestris and tomato at the parasitism interface. After conducting RNA-Seq analysis and constructing gene coexpression networks (GCNs), we identified CcHB7, CcPMEI, and CcERF1 as putative key regulators involved in C. campestris haustorium organogenesis, and three potential regulators, SlPR1, SlCuRe1-like, and SlNLR, in tomatoes that are involved in perceiving signals from the parasite. We used host-induced gene silencing (HIGS) transgenic tomatoes to knock-down the candidate genes in C. campestris and produced CRISPR transgenic tomatoes to knock out candidate genes in tomatoes. The interactions of C. campestris with these transgenic lines were tested and compared with that in wild-type tomatoes. The results of this study reveal the tissue-resolution gene regulatory mechanisms at the parasitic plant-host interface and provide the potential of developing a parasite-resistant system in tomatoes.

Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes

Background

The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus.

Results

The mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmF_C gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT.

Conclusions

The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08105-z.

Mechanisms of resistance and virulence in parasitic plant-host interactions

Parasitic plants pose a major biotic threat to plant growth and development and lead to losses in crop productivity of billions of USD annually. By comparison with "normal" autotrophic plants, parasitic plants live a heterotrophic lifestyle and rely on water, solutes and to a greater (holoparasitic plants) or lesser extent (hemiparasitic plants) on sugars from other host plants. Most hosts are unable to detect an infestation by plant parasites or unable to fend off these parasitic invaders. However, a few hosts have evolved defense strategies to avoid infestation or protect themselves actively post-attack often leading to full or partial resistance. Here, we review the current state of our understanding of the defense strategies to plant parasitism used by host plants with emphasis on the active molecular resistance mechanisms. Furthermore, we outline the perspectives and the potential of future studies that will be indispensable to develop and breed resistant crops.

Host-produced ethylene is required for marked cell expansion and endoreduplication in dodder search hyphae

The genus Cuscuta comprises stem holoparasitic plant species with wide geographic distribution. Cuscuta spp. obtain water, nutrients, proteins, and mRNA from their host plants via a parasitic organ called the haustorium. As the haustorium penetrates into the host tissue, search hyphae elongate within the host tissue and finally connect with the host's vascular system. Invasion by Cuscuta spp. evokes various reactions within the host plant's tissues. Here, we show that, when Arabidopsis (Arabidopsis thaliana) is invaded by Cuscuta campestris, ethylene biosynthesis by the host plant promotes elongation of the parasite's search hyphae. The expression of genes encoding 1-aminocylclopropane-1-carboxylic acid (ACC) synthases, ACC SYNTHASE2 (AtACS2) and ACC SYNTHASE6 (AtACS6), was activated in the stem of Arabidopsis plants upon invasion by C. campestris. When the ethylene-deficient Arabidopsis acs octuple mutant was invaded by C. campestris, cell elongation and endoreduplication of the search hyphae were significantly reduced, and the inhibition of search hyphae growth was complemented by exogenous application of ACC. In contrast, in the C. campestris-infected Arabidopsis ethylene-insensitive mutant etr1-3, no growth inhibition of search hyphae was observed, indicating that ETHYLENE RESPONSE1-mediated ethylene signaling in the host plant is not essential for parasitism by C. campestris. Overall, our results suggest that C. campestris recognizes host-produced ethylene as a stimulatory signal for successful invasion.

Efficient carbon recycling and modulation of antioxidants involved in elongation of the parasitic plant dodder (Cuscuta spp.) in vitro

Dodder is a holoparasitic flowering plant that re-establishes parasitism with the host when broken off from the host. However, how in vitro dodder shoots recycle stored nutrients to maintain growth for reparasitizing hosts is not well characterized. Here, the spatial and temporal distribution characteristics of carbohydrates and reactive oxygen species (ROS) were analysed to explore the mechanism of recycling stored nutrients in dodder shoots in vitro. Our results showed that in vitro dodder shoots grew actively for more than 10 d, while dry mass decreased continuously. During this process, the transcript levels and activities of amylases gradually increased until 2 d and then declined in basal stems, which induced starch degradation at the tissue, cellular and subcellular levels. Additionally, the distribution characteristics of H₂O₂ and the activities and transcript levels of antioxidant enzymes indicated that shoot tips exhibited more robust ROS-scavenging capacity, and basal stems maintained higher ROS accumulation. Comparative proteomics analysis revealed that starch in basal stems acted as an energy source, and the glycolysis, TCA cycle and pentose phosphate pathway represented the energy supply for shoot tip elongation with time. These results indicated that efficient nutrient recycling and ROS modulation facilitated the parasitism of dodder grown in vitro by promoting shoot elongation growth to reach the host.

ABA signaling components in Phelipanche aegyptiaca

Obligate root holoparasite Phelipanche aegyptiaca is an agricultural pest, which infests its hosts and feeds on the sap, subsequently damaging crop yield and quality. Its notoriously viable seed bank may serve as an ideal pest control target. The phytohormone abscisic acid (ABA) was shown to regulate P. aegyptiaca seed dormancy following strigolactones germination stimulus. Transcription analysis of signaling components revealed five ABA receptors and two co-receptors (PP2C). Transcription of lower ABA-affinity subfamily III receptors was absent in all tested stages of P. aegyptiaca development and parasitism stages. P. aegyptiaca ABA receptors interacted with the PP2Cs, and inhibited their activity in an ABA-dependent manner. Moreover, sequence analysis revealed multiple alleles in two P. aegyptiaca ABA receptors, with many non-synonymous mutations. Functional analysis of selected receptor alleles identified a variant with substantially decreased inhibitory effect of PP2Cs activity in-vitro. These results provide evidence that P. aegyptiaca is capable of biochemically perceiving ABA. In light of the possible involvement of ABA in parasitic activities, the discovery of active ABA receptors and PP2Cs could provide a new biochemical target for the agricultural management of P. aegyptiaca. Furthermore, the potential genetic loss of subfamily III receptors in this species, could position P. aegyptiaca as a valuable model in the ABA perception research field.

Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris

A parasitic lifestyle, where plants procure some or all of their nutrients from other living plants, has evolved independently in many dicotyledonous plant families and is a major threat for agriculture globally. Nevertheless, no genome sequence of a parasitic plant has been reported to date. Here we describe the genome sequence of the parasitic field dodder, Cuscuta campestris. The genome contains signatures of a fairly recent whole-genome duplication and lacks genes for pathways superfluous to a parasitic lifestyle. Specifically, genes needed for high photosynthetic activity are lost, explaining the low photosynthesis rates displayed by the parasite. Moreover, several genes involved in nutrient uptake processes from the soil are lost. On the other hand, evidence for horizontal gene transfer by way of genomic DNA integration from the parasite's hosts is found. We conclude that the parasitic lifestyle has left characteristic footprints in the C. campestris genome.

Plants under stress by parasitic plants

In addition to other biotic stresses, parasitic plants pose an additional threat to plants and cause crop losses, worldwide. Plant parasites directly connect to the vasculature of host plants thereby stealing water, nutrients, and carbohydrates consequently leading to tremendously reduced biomass and losses in seed yields of the infected host plants. Initial steps to understand the molecular resistance mechanisms and the successes in ancient and recent breeding efforts will provide fundamental knowledge to further generate crop plants that will resist attacks by plant parasites.

Getting ready for host invasion: elevated expression and action of xyloglucan endotransglucosylases/hydrolases in developing haustoria of the holoparasitic angiosperm Cuscuta

Changes in cell walls have been previously observed in the mature infection organ, or haustorium, of the parasitic angiosperm Cuscuta, but are not equally well charted in young haustoria. In this study, we focused on the molecular processes in the early stages of developing haustoria; that is, before the parasite engages in a physiological contact with its host. We describe first the identification of differentially expressed genes in young haustoria whose development was induced by far-red light and tactile stimuli in the absence of a host plant by suppression subtractive hybridization. To improve sequence information and to aid in the identification of the obtained candidates, reference transcriptomes derived from two species of Cuscuta, C. gronovii and C. reflexa, were generated. Subsequent quantitative gene expression analysis with different tissues of C. reflexa revealed that among the genes that were up-regulated in young haustoria, two xyloglucan endotransglucosylase/hydrolase (XTH) genes were highly expressed almost exclusively at the onset of haustorium development. The same expression pattern was also found for the closest XTH homologues from C. gronovii. In situ assays for XTH-specific action suggested that xyloglucan endotransglucosylation was most pronounced in the cell walls of the swelling area of the haustorium facing the host plant, but was also detectable in later stages of haustoriogenesis. We propose that xyloglucan remodelling by Cuscuta XTHs prepares the parasite for host infection and possibly aids the invasive growth of the haustorium.

Macromolecule exchange in Cuscuta-host plant interactions

Cuscuta species (dodders) are parasitic plants that are able to grow on many different host plants and can be destructive to crops. The connections between Cuscuta and its hosts allow movement of not only water and small nutrients, but also macromolecules including mRNA, proteins and viruses. Recent studies show that RNAs move bidirectionally between hosts and parasites and involve a large number of different genes. Although the function of mobile mRNAs has not been demonstrated in this system, small RNAs are also transmitted and a silencing construct expressed in hosts is able to affect expression of the target gene in the parasite. High throughput sequencing of host-parasite associations has the potential to greatly accelerate understanding of this remarkable interaction.

Transcriptomics exposes the uniqueness of parasitic plants

Parasitic plants have the ability to obtain nutrients directly from other plants, and several species are serious biological threats to agriculture by parasitizing crops of high economic importance. The uniqueness of parasitic plants is characterized by the presence of a multicellular organ called a haustorium, which facilitates plant-plant interactions, and shutting down or reducing their own photosynthesis. Current technical advances in next-generation sequencing and bioinformatics have allowed us to dissect the molecular mechanisms behind the uniqueness of parasitic plants at the genome-wide level. In this review, we summarize recent key findings mainly in transcriptomics that will give us insights into the future direction of parasitic plant research.

Parasitic plants of the genus Cuscuta and their interaction with susceptible and resistant host plants

By comparison with plant-microbe interaction, little is known about the interaction of parasitic plants with their hosts. Plants of the genus Cuscuta belong to the family of Cuscutaceae and comprise about 200 species, all of which live as stem holoparasites on other plants. Cuscuta spp. possess no roots nor fully expanded leaves and the vegetative portion appears to be a stem only. The parasite winds around plants and penetrates the host stems via haustoria, forming direct connections to the vascular bundles of their hosts to withdraw water, carbohydrates, and other solutes. Besides susceptible hosts, a few plants exist that exhibit an active resistance against infestation by Cuscuta spp. For example, cultivated tomato (Solanum lycopersicum) fends off Cuscuta reflexa by means of a hypersensitive-type response occurring in the early penetration phase. This report on the plant-plant dialog between Cuscuta spp. and its host plants focuses on the incompatible interaction of C. reflexa with tomato.

A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads

BACKGROUND

The genus Cuscuta is a group of parasitic plants that are distributed world-wide. The process of parasitization starts with a Cuscuta plant coiling around the host stem. The parasite's haustorial organs then establish a vascular connection allowing for access to the phloem content. The host and the parasite form new cellular connections, suggesting coordination of developmental and biochemical processes. Simultaneous monitoring of gene expression in the parasite's and host's tissues may shed light on the complex events occurring between the parasitic and host cells and may help to overcome experimental limitations (i.e. how to separate host tissue from Cuscuta tissue at the haustorial connection). A novel approach is to use bioinformatic analysis to classify sequencing reads as either belonging to the host or to the parasite and to characterize the expression patterns. Owing to the lack of a comprehensive genomic dataset from Cuscuta spp., such a classification has not been performed previously.

RESULTS

We first classified RNA-Seq reads from an interface region between the non-model parasitic plant Cuscuta japonica and the non-model host plant Impatiens balsamina. Without established reference sequences, we classified reads as originating from either of the plants by stepwise similarity search against de novo assembled transcript sets of C. japonica and I. balsamina, unigene sets of the same genus, and cDNA sequences of the same family. We then assembled de novo transcriptomes from the classified read sets. We assessed the quality of the classification by mapping reads to contigs of both plants, achieving a misclassification rate low enough (0.22-0.39%) to be used reliably for differential gene expression analysis. Finally, we applied our read classification method to RNA-Seq data from the interface between the non-model parasitic plant C. japonica and the model host plant Glycine max. Analysis of gene expression profiles at 5 parasitizing stages revealed differentially expressed genes from both C. japonica and G. max, and uncovered the coordination of cellular processes between the two plants.

CONCLUSIONS

We demonstrated that reliable identification of differentially expressed transcripts in undissected interface region of the parasite-host association is feasible and informative with respect to differential-expression patterns.

Plant science. Genomic-scale exchange of mRNA between a parasitic plant and its hosts

Movement of RNAs between cells of a single plant is well documented, but cross-species RNA transfer is largely unexplored. Cuscuta pentagona (dodder) is a parasitic plant that forms symplastic connections with its hosts and takes up host messenger RNAs (mRNAs). We sequenced transcriptomes of Cuscuta growing on Arabidopsis and tomato hosts to characterize mRNA transfer between species and found that mRNAs move in high numbers and in a bidirectional manner. The mobile transcripts represented thousands of different genes, and nearly half the expressed transcriptome of Arabidopsis was identified in Cuscuta. These findings demonstrate that parasitic plants can exchange large proportions of their transcriptomes with hosts, providing potential mechanisms for RNA-based interactions between species and horizontal gene transfer.