Uncovering the defence responses of Eucalyptus to pests and pathogens in the genomics age

Construction of Host Plant Insect-Resistance Mutant Library by High-Throughput CRISPR/Cas9 System and Identification of A Broad-Spectrum Insect Resistance Gene

Insects pose significant challenges in cotton-producing regions. Here, they describe a high-throughput CRISPR/Cas9-mediated large-scale mutagenesis library targeting endogenous insect-resistance-related genes in cotton. This library targeted 502 previously identified genes using 968 sgRNAs, generated ≈2000 T0 plants and achieved 97.29% genome editing with efficient heredity, reaching upto 84.78%. Several potential resistance-related mutants (10% of 200 lines) their identified that may contribute to cotton-insect molecular interaction. Among these, they selected 139 and 144 lines showing decreased resistance to pest infestation and targeting major latex-like protein 423 (GhMLP423) for in-depth study. Overexpression of GhMLP423 enhanced insect resistance by activating the plant systemic acquired resistance (SAR) of salicylic acid (SA) and pathogenesis-related (PR) genes. This activation is induced by an elevation of cytosolic calcium [Ca2+ ]cyt flux eliciting reactive oxygen species (ROS), which their demoted in GhMLP423 knockout (CR) plants. Protein-protein interaction assays revealed that GhMLP423 interacted with a human epidermal growth factor receptor substrate15 (EPS15) protein at the cell membrane. Together, they regulated the systemically propagating waves of Ca2+ and ROS, which in turn induced SAR. Collectively, this large-scale mutagenesis library provides an efficient strategy for functional genomics research of polyploid plant species and serves as a solid platform for genetic engineering of insect resistance.

Unraveling the evolutionary dynamics of the TPS gene family in land plants

Terpenes and terpenoids are key natural compounds for plant defense, development, and composition of plant oil. The synthesis and accumulation of a myriad of volatile terpenoid compounds in these plants may dramatically alter the quality and flavor of the oils, which provide great commercial utilization value for oil-producing plants. Terpene synthases (TPSs) are important enzymes responsible for terpenic diversity. Investigating the differentiation of the TPS gene family could provide valuable theoretical support for the genetic improvement of oil-producing plants. While the origin and function of TPS genes have been extensively studied, the exact origin of the initial gene fusion event - it occurred in plants or microbes - remains uncertain. Furthermore, a comprehensive exploration of the TPS gene differentiation is still pending. Here, phylogenetic analysis revealed that the fusion of the TPS gene likely occurred in the ancestor of land plants, following the acquisition of individual C- and N- terminal domains. Potential mutual transfer of TPS genes was observed among microbes and plants. Gene synteny analysis disclosed a differential divergence pattern between TPS-c and TPS-e/f subfamilies involved in primary metabolism and those (TPS-a/b/d/g/h subfamilies) crucial for secondary metabolites. Biosynthetic gene clusters (BGCs) analysis suggested a correlation between lineage divergence and potential natural selection in structuring terpene diversities. This study provides fresh perspectives on the origin and evolution of the TPS gene family.

Correlating Eucalyptus leaf metabolomics with preference of the bronze bug, Thaumastocoris peregrinus

Eucalyptus species are among the most planted trees in forestry production, an ever-increasing commercial activity worldwide. Forestry expansion demands a continuous search for preventive and sanitary measures against pests and diseases. Massive application of phytosanitary products is incompatible with the forestry sector, so forest health management must be based on other principles. In this context, studies on insect plant relationships mediated by plant metabolites may contribute information relevant to plant resistance and genotype selection. In this study, we analyzed the leaf metabolome of four Eucalyptus species commonly planted in southern South America, to correlate this chemical information with feeding preference of Thaumastocoris peregrinus (Hemiptera: Thaumastocoridae), an important pest of eucalypt plantations. Gas chromatography mass spectrometry analyses were performed on polar and non-polar leaf extracts from Eucalyptus globulus, Eucalyptus grandis, Eucalyptus robusta, and Eucalyptus tereticornis (Myrtaceae). Feeding preferences were assessed in two-choice laboratory bioassays resulting in a preference gradient of the four plant species. Moreover, a performance bioassay where we contrasted survival and development time between the most and least preferred plants, showed a clear correlation with preference both in survival and developmental time of the most susceptible nymph instar. We found that species with high or low feeding preferences differ significantly in several foliar metabolites, which may be acting as feeding stimulants or deterrents for T. peregrinus. These findings may provide useful criteria for choosing Eucalyptus genotypes when planting in bronze bug infested areas.

Meloidogyne spp. in Eucalypts - Reproduction and Damage to Seedling Growth

Eucalypts are cultivated worldwide, but little is known about their status as hosts of root-knot nematodes (RKN) (Meloidogyne spp.). Moreover, information is scarce regarding the nature of the damage caused by RKN to eucalypt seedlings and trees. To investigate these aspects, we separately inoculated Meloidogyne enterolobii, M. javanica and M. incognita in seedlings of the world's most cultivated eucalypts: Eucalyptus dunni, E. grandis, E. cloeziana, E. camaldulensis, E. saligna, Corymbia citriodora, and the hybrid E. grandis × E. urophylla. After six months of greenhouse cultivation, we assessed nematode reproduction and variables that expressed the seedlings' shoot and root growth. We observed a diverse pattern of host statuses to RKN among the eucalypts, and all three Meloidogyne species reduced (p < 0.05) the root system mass, volume and length of E. grandis, E. saligna and the hybrid E. grandis × E. urophylla. Our results reaffirm previous reports indicating that RKN can delay the growth of seedlings in nurseries, who should thus adopt appropriate sanitary measures to avoid RKN establishment and spread. Moreover, the damage caused by RKN to eucalypts after just six months of cultivation suggests that the growth of eucalypt trees may be affected over the course of several years of cultivation.

Rapid Detection of Mercury Ions Using Sustainable Natural Gum-Based Silver Nanoparticles

Fabrication of metal nanostructures using natural products has attracted scientists and researchers due to its renewable and environmentally benign availability. This work has prepared an eco-friendly, low-cost, and rapid colorimetric sensor of silver nanoparticles using tree gum as a reducing and stabilizing agent. Several characterization techniques have been exploited to describe the synthesized nanosensor morphology and optical properties. Ultraviolet−Visible (UV−Vis) spectroscopy has been used for monitoring the localized plasmon surface area. High-resolution transmission electron microscopy (HR-TEM) illustrated the size and shape of silver nanoparticles. X-ray diffraction spectra showed the crystallography and purity of the product. Silver nanoparticles decorated with almond gum molecules (AgNPs@AG) demonstrated high sensitivity and colorimetric detection of mercury ions in water samples. The method is based on the aggregation of AgNPs and the disappearing yellow color of AgNPs via a spectrophotometer. The detection limit of this method was reported to be 0.5 mg/L. This work aimed to synthesize a rapid, easy-preparation, eco-friendly, and efficient naked-eye colorimetric sensor to detect toxic pollutants in aqueous samples.

Transcriptome profiling of Toona ciliata young stems in response to Hypsipyla robusta Moore

Toona ciliata is a traditional woody plant that can be used as a medicinal material in China. The extracts of its roots, stems, leaves, and flowers all have a wide range of bioactive compounds. However, T. ciliata has been facing an unresolved pest problem caused by Hypsipyla robusta Moore (HRM), which seriously affects its growth and development. In this study, the expression level of TcMYB3 gene reached the maximum (28-fold) at 12 h and transcriptome sequencing of young stems eaten by HRM for 0, 3, 12, and 21 h were performed. A large number of differentially expressed genes (DEGs) were identified including jointly up-regulated genes (263) and down-regulated genes (378). JA synthesis and signaling transduction, terpene biosynthesis, and MAPKs signaling pathway were analyzed in depth and found that TcOPR3, TcJAR1, TcJAZs, and TcTPS9 genes possessed anti-insect potential. Moreover, MYB and ERF transcription factor (TF) families were significantly strengthened to the point that they may participate in induced defense mechanisms in T. ciliata. These data not only provide insights into the molecular mechanisms in resistance of T. ciliata to HRM but also helps to explore the new biocontrol strategies against insects in eco-friendly woody plants.

BpEIL1 negatively regulates resistance to Rhizoctonia solani and Alternaria alternata in birch

Pathogen attacks affect tree health, causing considerable economic losses as well as serious damage to the surrounding environment. Understanding the disease resistance mechanisms of trees is important for tree breeding. In previous studies on birch (Betula platyphylla × B. pendula), we identified a lesion mimic mutant called lmd. We found that reduced expression of BpEIL1 was responsible for the phenotype in lmd. Following cloning, we acquired several BpEIL1 overexpression and suppression lines in birch. In this study, we cloned the BpEIL1 promoter and found that BpEIL1 was primarily expressed in leaves, particularly in veins. We further studied the traits of transgenic lines and the function of BpEIL1 in disease resistance in birch using the BpEIL1 overexpression line OE9, the suppression line SE13 and the non-transgenic line NT. We found that hydrogen peroxide accumulated in SE13 leaves. Ascorbate peroxidase and catalase activity significantly increased in SE13. SE13 was more resistant to the fungal pathogens Alternaria alternata and Rhizoctonia solani than were the OE9 and NT lines. RNA-seq indicated that pathways related to signal transduction, disease resistance and plant immunity were enriched in SE13. BpEIL1 is thus a negative regulatory transcription factor for disease resistance in birch. This study provides a reference for disease resistance of birch and other trees.

Susceptibility to the fungal plant pathogen Austropuccinia psidii is related to monoterpene production in Australian Myrtaceae species

In 2010, the fungal plant pathogen that causes Myrtle rust, Austropuccinia psidii, which is native to South America, was first detected in Australia and has since had significant impacts on several Australian Myrtaceae species. Despite this, our understanding of the role secondary metabolites play in plant susceptibility to A. psidii is limited. This study aimed to determine: (1) whether secondary metabolite (phenolics, terpenes) production is induced after A. psidii inoculation and if so, (2) how their production relates to A. psidii susceptibility. To test these aims, we selected seven Myrtaceae species that have a wide range of within-species variability in their susceptibility to A. psidii. We found that five of the study species significantly increased either their phenolic or sesquiterpene production post-inoculation suggesting their pre-inoculation secondary metabolite levels were not sufficient to combat A. psidii infection. The two species (Angophora costata and Corymbia citriodora) that did not increase their secondary metabolite production post-inoculation tended to have the greatest pre-inoculation production levels amongst the species. Interestingly, across all species, monoterpenes were the only secondary metabolite found to reduce plant susceptibility to A. psidii. This study contributes to our limited understanding of the role that secondary metabolites play in plant susceptibility to A. psidii. In light of these findings, future research should aim to identify biomarkers (e.g. individual chemical compounds) that confer resistance to A. psidii, so that individuals with these biomarkers can be utilised in commercial and conservation projects.

Short-term changes related to autotetraploidy in essential oil composition of Eucalyptus benthamii Maiden & Cambage and its applications in different bioassays

Some forest trees have been polyploidized to improve their traits and to supply new germplasms for breeding programs. As trees have a long juvenile stage, the early characterization of the chromosome set doubling effects is crucial for previous selection. Thus, we aimed to characterize the chemical variability of essential oils from diploid and autotetraploid germplasms (autotetraploid A and B) of Eucalyptus benthamii, as well as to evaluate their larvicidal and allelopathic effects. Autotetraploid A showed a higher essential oil yield than diploid and autotetraploid B, which did not differ quantitatively. Aromadendrene, viridiflorol and α-pinene were the major compounds in the diploid essential oil. In contrast, compounds were present in autotetraploids, such as 1,8-cineole, limonene, α-terpineol, and α-terpinyl-acetate. Essential oils from the diploid at 50-200 ppm were twice as larvicidal than those from autotetraploids against Aedes aegypti larvae. Considering the phytotoxicity bioassays using Lactuca sativa, essential oils from both ploidy levels affected root growth. Moreover, the essential oils inhibited shoot growth at all concentrations tested (187.5; 375; 750; 1500; and 3000 ppm). Autotetraploid A and B had the same effect on shoot growth as glyphosate. The essential oils had no cytogenotoxic effect on root meristematic cells of L. sativa, whereas phytotoxic potential was identified mainly in shoot growth. This work demonstrated a dramatic change in secondary metabolism (terpene composition) related to an increase in the ploidy level in Eucalyptus germplasms. In addition, we report the novelty of the chemical composition of essential oils among germplasms and their potential use as larvicidal and post-emergence weed control agents.

Integrative Pre-Breeding for Biotic Resistance in Forest Trees

Climate change is unleashing novel biotic antagonistic interactions for forest trees that may jeopardize populations' persistence. Therefore, this review article envisions highlighting major opportunities from ecological evolutionary genomics to assist the identification, conservation, and breeding of biotic resistance in forest tree species. Specifically, we first discuss how assessing the genomic architecture of biotic stress resistance enables us to recognize a more polygenic nature for a trait typically regarded Mendelian, an expectation from the Fisherian runaway pathogen-host concerted arms-race evolutionary model. Secondly, we outline innovative pipelines to capture and harness natural tree pre-adaptations to biotic stresses by merging tools from the ecology, phylo-geography, and omnigenetics fields within a predictive breeding platform. Promoting integrative ecological genomic studies promises a better understanding of antagonistic co-evolutionary interactions, as well as more efficient breeding utilization of resistant phenotypes.

Characterization of terpene biosynthesis in Melaleuca quinquenervia and ecological consequences of terpene accumulation during myrtle rust infection

Plants use a wide array of secondary metabolites including terpenes as defense against herbivore and pathogen attack, which can be constitutively expressed or induced. Here, we investigated aspects of the chemical and molecular basis of resistance against the exotic rust fungus Austropuccinia psidii in Melaleuca quinquenervia, with a focus on terpenes. Foliar terpenes of resistant and susceptible plants were quantified, and we assessed whether chemotypic variation contributed to resistance to infection by A. psidii. We found that chemotypes did not contribute to the resistance and susceptibility of M. quinquenervia. However, in one of the chemotypes (Chemotype 2), susceptible plants showed higher concentrations of several terpenes including α-pinene, limonene, 1,8-cineole, and viridiflorol compared with resistant plants. Transcriptome profiling of these plants showed that several TPS genes were strongly induced in response to infection by A. psidii. Functional characterization of these TPS showed them to be mono- and sesquiterpene synthases producing compounds including 1,8-cineole, β-caryophyllene, viridiflorol and nerolidol. The expression of these TPS genes correlated with metabolite data in a susceptible plant. These results suggest the complexity of resistance mechanism regulated by M. quinquenervia and that modulation of terpenes may be one of the components that contribute to resistance against A. psidii.

The Impacts of Drought Stress and Phytophthora cinnamomi Infection on Short-Term Water Relations in Two Year-Old Eucalyptus obliqua

The effects of drought stress, Phytophthora cinnamomi infection and their interaction on water relations and growth were examined for 28 days on two year-old potted trees of Eucalyptus obliqua (L’Hér.). There were significant effects of drought stress on plant photosynthesis, stomatal conductance, biomass accumulation, plant water potential at turgor loss point and the bulk modulus of elasticity. E. obliqua was successfully infected but the trees showed only mild symptoms. Infection with P. cinnamomi led to a significant reduction in the root biomass and root-to-shoot ratio in well-watered and droughted plants but did not impact water relations. There was no observable cumulative effect of drought and P. cinnamomi infection. There are multiple potential reasons why P. cinnamomi infection did not lead to drought-like symptoms in E. obliqua, including short experimental duration, delayed infection symptoms, potential resistance of E. obliqua and a possible lower aggressiveness of the P. cinnamomi strain. Hence, our results indicate that P. cinnamomi infection will not always lead to immediate short-term symptoms, and that plants that are mildly symptomatic respond very similar to drought stress compared to non-infected trees.

Genomic Breeding for Diameter Growth and Tolerance to Leptocybe Gall Wasp and Botryosphaeria/Teratosphaeria Fungal Disease Complex in Eucalyptus grandis

Eucalyptus grandis is one of the most important species for hardwood plantation forestry around the world. At present, its commercial deployment is in decline because of pests and pathogens such as Leptocybe invasa gall wasp (Lepto), and often co-occurring fungal stem diseases such as Botryosphaeria dothidea and Teratosphaeria zuluensis (BotryoTera). This study analyzed Lepto, BotryoTera, and stem diameter growth in an E. grandis multi-environmental, genetic trial. The study was established in three subtropical environments. Diameter growth and BotryoTera incidence scores were assessed on 3,334 trees, and Lepto incidence was assessed on 4,463 trees from 95 half-sib families. Using the Eucalyptus EUChip60K SNP chip, a subset of 964 trees from 93 half-sib families were genotyped with 14,347 informative SNP markers. We employed single-step genomic BLUP (ssGBLUP) to estimate genetic parameters in the genetic trial. Diameter and Lepto tolerance showed a positive genetic correlation (0.78), while BotryoTera tolerance had a negative genetic correlation with diameter growth (-0.38). The expected genetic gains for diameter growth and Lepto and BotryoTera tolerance were 12.4, 10, and -3.4%, respectively. We propose a genomic selection breeding strategy for E. grandis that addresses some of the present population structure problems.

Transcriptome analysis of Eucalyptus grandis genotypes reveals constitutive overexpression of genes related to rust (Austropuccinia psidii) resistance

Key Message A resistant E. grandis genotype showed a constitutive overexpression of genes related to resistance to myrtle rust caused by A. psidii. Abstract Myrtle rust caused by Austropuccinia psidii is considered one of the most important fungal diseases affecting Eucalyptus spp. plantations in Brazil. Although the selection and planting of resistant eucalypt genotypes have been the major strategies to manage the disease in Brazil, the molecular mechanisms involved in resistance are still unclear. In this study, we evaluated the gene expression profile of two contrasting Eucalyptus grandis genotypes in resistance level to rust by RNA-Seq. The two genotypes showed a very different background gene expression level even without A. psidii infection. The resistant genotype had a constitutive overexpression of a large number of protein-coding genes compared to the susceptible genotype. These genes were mainly associated with signal transduction, photosynthesis, regulation and response to salicylic acid (SA), and protein kinase leucine-rich receptors (PK-LRR). PK-LRR and SA mediated disease resistance are well known to be effective against obligate biotroph pathogens, such as A. psidii. In addition, at 24 h after infection, the susceptible genotype was able to activate some response, however, several resistance-related proteins had their expression level reduced with A. psidii infection. Here, we present the first analysis of E. grandis genotypes transcriptomes infected by A. psidii and it reveals a constitutive overexpression of several resistance-related genes in the resistant genotype compared to the susceptible one. Our findings have the potential to be used as candidate molecular markers for resistance to myrtle rust.

Modern Strategies to Assess and Breed Forest Tree Adaptation to Changing Climate

Studying the genetics of adaptation to new environments in ecologically and industrially important tree species is currently a major research line in the fields of plant science and genetic improvement for tolerance to abiotic stress. Specifically, exploring the genomic basis of local adaptation is imperative for assessing the conditions under which trees will successfully adapt in situ to global climate change. However, this knowledge has scarcely been used in conservation and forest tree improvement because woody perennials face major research limitations such as their outcrossing reproductive systems, long juvenile phase, and huge genome sizes. Therefore, in this review we discuss predictive genomic approaches that promise increasing adaptive selection accuracy and shortening generation intervals. They may also assist the detection of novel allelic variants from tree germplasm, and disclose the genomic potential of adaptation to different environments. For instance, natural populations of tree species invite using tools from the population genomics field to study the signatures of local adaptation. Conventional genetic markers and whole genome sequencing both help identifying genes and markers that diverge between local populations more than expected under neutrality, and that exhibit unique signatures of diversity indicative of "selective sweeps." Ultimately, these efforts inform the conservation and breeding status capable of pivoting forest health, ecosystem services, and sustainable production. Key long-term perspectives include understanding how trees' phylogeographic history may affect the adaptive relevant genetic variation available for adaptation to environmental change. Encouraging "big data" approaches (machine learning-ML) capable of comprehensively merging heterogeneous genomic and ecological datasets is becoming imperative, too.

The Road to Resistance in Forest Trees

In recent years, forests have been exposed to an unprecedented rise in pests and pathogens. This, coupled with the added challenge of climate change, renders forest plantation stock vulnerable to attack and severely limits productivity. Genotypes resistant to such biotic challenges are desired in plantation forestry to reduce losses. Conventional breeding has been a main avenue to obtain resistant genotypes. More recently, genetic engineering has become a viable approach to develop resistance against pests and pathogens in forest trees. Tree genomic resources have contributed to advancements in both these approaches. Genome-wide association studies and genomic selection in tree populations have accelerated breeding tools while integration of various levels of omics information facilitates the selection of candidate genes for genetic engineering. Furthermore, tree associations with non-pathogenic endophytic and subterranean microbes play a critical role in plant health and may be engineered in forest trees to improve resistance in the future. We look at recent studies in forest trees describing defense mechanisms using such approaches and propose the way forward to developing superior genotypes with enhanced resistance against biotic stress.

Tree host-pathogen interactions as influenced by drought timing: linking physiological performance, biochemical defence and disease severity

There is increasing concern about tree mortality around the world due to climatic extremes and associated shifts in pest and pathogen dynamics. Yet, empirical studies addressing the interactive effect of biotic and abiotic stress on plants are very rare. Therefore, in this study, we examined the interaction between drought stress and a canker pathogen, Quambalaria coyrecup, on the eucalypt - Corymbia calophylla (marri), which is experiencing increasing drought stress. We hypothesized that drought stress would increase marri's susceptibility to canker disease, and cankers would have the largest negative effect on plants that are already drought stressed before pathogen inoculation. To test the hypotheses, in a glasshouse, marri saplings were exposed to drought either before or after pathogen inoculation, or were well-watered or droughted throughout the experiment either with or without inoculation. Canker development was greater in well-watered saplings than in droughted saplings, with the fastest development occurring in well-watered saplings that had experienced drought stress before inoculation. Irrespective of water treatments, marri saplings employed phenol-based localized biochemical defence against the pathogen. Drought reduced photosynthesis and growth, however, a negative effect of canker disease on saplings' physiological performance was only observed in well-watered saplings. In well-watered saplings, canker-induced loss of sapwood function contributed to reduced whole-plant hydraulic conductance, photosynthesis and growth. The results provide evidence that timing of drought stress influences host physiology, and host condition influences canker disease susceptibility through differences in induced biochemical defence mechanisms. The observations highlight the importance of explicitly incorporating abiotic and biotic stress, as well as their interactions, in future studies of tree mortality in drought-prone regions worldwide.

Breeding and Engineering Trees to Accumulate High Levels of Terpene Metabolites for Plant Defense and Renewable Chemicals

Plants evolved the capacity to synthesize highly diverse sets of secondary metabolites which are important for plant adaptation and health. In forest trees, many classes of compounds, particularly ones related to defense against insects, fungi, and bacteria accumulate to levels that enable their recovery and commercial use. One of the oldest examples is conifer terpenes, but terpenes are important secondary products from other tree species including eucalypts. Because terpenes, latex, and natural gums are synthesized and stored in specialized secretory glands, ducts, and laticifers in mostly pure forms they can be collected from live trees in addition to being extracted during industrial processing of wood. This minireview describes the potential of breeding and genetic engineering approaches to increase the quantities of terpene secondary metabolites to increase the amount of secondary products and thereby increasing the value of planted and managed forest trees. I advance the view that breeding and genetic engineering of metabolic pathways and specialized cell secretory structures can dramatically increase tissue terpene content.

Transcriptome Profiling of Melaleuca quinquenervia Challenged by Myrtle Rust Reveals Differences in Defense Responses Among Resistant Individuals

Plants have developed complex defense mechanisms to protect themselves against pathogens. A wide-host-range fungus, Austropuccinia psidii, which has caused severe damage to ecosystems and plantations worldwide, is a major threat to Australian ecosystems dominated by members of the family Myrtaceae. In particular, the east coast wetland foundation tree species Melaleuca quinquenervia, appears to be variably susceptible to this pathogen. Understanding the molecular basis of host resistance would enable better management of this rust disease. We identified resistant and susceptible individuals of M. quinquenervia and explored their differential gene expression in order to discover the molecular basis of resistance against A. psidii. Rust screening of germplasm showed a varying degree of response, with fully resistant to highly susceptible individuals. We used transcriptome profiling in samples collected before and at 5 days postinoculation (dpi). Differential gene expression analysis showed that numerous defense-related genes were induced in susceptible plants at 5 dpi. Mapping reads against the A. psidii genome showed that only susceptible plants contained fungal-derived transcripts. Resistant plants exhibited an overexpression of candidate A. psidii resistance-related genes such as receptor-like kinases, nucleotide-binding site leucine-rich repeat proteins, glutathione S-transferases, WRKY transcriptional regulators, and pathogenesis-related proteins. We identified large differences in the expression of defense-related genes among resistant individuals.

Botryosphaeria dothidea: a latent pathogen of global importance to woody plant health

Botryosphaeria dothidea is the type species of Botryosphaeria (Botryosphaeriaceae, Botryosphaeriales). Fungi residing in this order are amongst the most widespread and important canker and dieback pathogens of trees worldwide, with B. dothidea one of the most common species on a large number of hosts. Its taxonomic circumscription has undergone substantial change in the past decade, making it difficult to interpret the large volume of literature linked to the name B. dothidea. This pathogen profile synthesizes the current understanding of B. dothidea pertaining to its distribution, host associations and role as a pathogen in managed and natural woody environments. The prolonged latent infection or endophytic phase is of particular importance, as it implies that the fungus can easily pass undetected by quarantine systems in traded living plants, fruits and other plant parts. Infections typically become obvious only under conditions of host stress, when disease symptoms develop. This study also considers the knowledge emerging from the recently sequenced B. dothidea genome, elucidating previously unknown aspects of the species, including mating and host infection strategies. Despite more than 150 years of research on B. dothidea, there is clearly much to be learned regarding this global tree pathogen. This is increasingly important given the stresses imposed on various woody hosts as a result of climate change.

TAXONOMY

Botryosphaeria dothidea (Moug. ex Fr) Ces. & De Not, 1863. Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Botryosphaeriales, Family Botryosphaeriaceae, Genus Botryosphaeria, Species dothidea.

HOST RANGE

Confirmed on more than 24 host genera, including woody plants, such as Acacia (= Vachellia), Eucalyptus, Vitis and Pistachio.

DISEASE SYMPTOMS

Associated with twig, branch and stem cankers, tip and branch dieback, fruit rot, blue stain and plant death.

USEFUL WEBSITES

The Botryosphaeria site for detailed morphological descriptions (http://www.crem.fct.unl.pt/botryosphaeria_site/); Systematic Mycology and Microbiology Laboratory Fungal Database for all literature and associated hosts (https://nt.ars-grin.gov/fungaldatabases/); TreeBASE link for the combined ITS and TEF-1α tree (http://purl.org/phylo/treebase/phylows/study/TB2:S18906); DOE Joint Genome Institute, JGI Mycocosm for the Botryosphaeria dothidea genome (http://genome.jgi.doe.gov/Botdo1_1/Botdo1_1.home.html).

Identification of the Eucalyptus grandis chitinase gene family and expression characterization under different biotic stress challenges

Eucalyptus grandis (W. Hill ex Maiden) is an Australian Myrtaceae tree grown for timber in many parts of the world and for which the annotated genome sequence is available. Known to be susceptible to a number of pests and diseases, E. grandis is a useful study organism for investigating defense responses in woody plants. Chitinases are widespread in plants and cleave glycosidic bonds of chitin, the major structural component of fungal cell walls and arthropod exoskeletons. They are encoded by an important class of genes known to be up-regulated in plants in response to pathogens. The current study identified 67 chitinase gene models from two families known as glycosyl hydrolase 18 and 19 (36 GH18 and 31 GH19) within the E. grandis genome assembly (v1.1), indicating a recent gene expansion. Sequences were aligned and analyzed as conforming to currently recognized plant chitinase classes (I-V). Unlike other woody species investigated to date, E. grandis has a single gene encoding a putative vacuolar targeted Class I chitinase. In response to Leptocybe invasa (Fisher & La Salle) (the eucalypt gall wasp) and Chrysoporthe austroafricana (Gryzenhout & M.J. Wingf. 2004) (causal agent of fungal stem canker), this Class IA chitinase is strongly up-regulated in both resistant and susceptible plants. Resistant plants, however, indicate greater constitutive expression and increased up-regulation than susceptible plants following fungal challenge. Up-regulation within fungal resistant clones was further confirmed with protein data. Clusters of putative chitinase genes, particularly on chromosomes 3 and 8, are significantly up-regulated in response to fungal challenge, while a cluster on chromosome 1 is significantly down-regulated in response to gall wasp. The results of this study show that the E. grandis genome has an expanded group of chitinase genes, compared with other plants. Despite this expansion, only a single Class I chitinase is present and this gene is highly up-regulated within diverse biotic stress conditions. Our research provides insight into a major class of defense genes within E. grandis and indicates the importance of the Class I chitinase.

Dual RNA-Sequencing of Eucalyptus nitens during Phytophthora cinnamomi Challenge Reveals Pathogen and Host Factors Influencing Compatibility

Damage caused by Phytophthora cinnamomi Rands remains an important concern on forest tree species. The pathogen causes root and collar rot, stem cankers, and dieback of various economically important Eucalyptus spp. In South Africa, susceptible cold tolerant Eucalyptus plantations have been affected by various Phytophthora spp. with P. cinnamomi considered one of the most virulent. The molecular basis of this compatible interaction is poorly understood. In this study, susceptible Eucalyptus nitens plants were stem inoculated with P. cinnamomi and tissue was harvested five days post inoculation. Dual RNA-sequencing, a technique which allows the concurrent detection of both pathogen and host transcripts during infection, was performed. Approximately 1% of the reads mapped to the draft genome of P. cinnamomi while 78% of the reads mapped to the Eucalyptus grandis genome. The highest expressed P. cinnamomi gene in planta was a putative crinkler effector (CRN1). Phylogenetic analysis indicated the high similarity of this P. cinnamomi CRN1 to that of Phytophthora infestans. Some CRN effectors are known to target host nuclei to suppress defense. In the host, over 1400 genes were significantly differentially expressed in comparison to mock inoculated trees, including suites of pathogenesis related (PR) genes. In particular, a PR-9 peroxidase gene with a high similarity to a Carica papaya PR-9 ortholog previously shown to be suppressed upon infection by Phytophthora palmivora was down-regulated two-fold. This PR-9 gene may represent a cross-species effector target during P. cinnamomi infection. This study identified pathogenicity factors, potential manipulation targets, and attempted host defense mechanisms activated by E. nitens that contributed to the susceptible outcome of the interaction.

The Eucalyptus grandis NBS-LRR Gene Family: Physical Clustering and Expression Hotspots

Eucalyptus grandis is a commercially important hardwood species and is known to be susceptible to a number of pests and pathogens. Determining mechanisms of defense is therefore a research priority. The published genome for E. grandis has aided the identification of one important class of resistance (R) genes that incorporate nucleotide binding sites and leucine-rich repeat domains (NBS-LRR). Using an iterative search process we identified NBS-LRR gene models within the E. grandis genome. We characterized the gene models and identified their genomic arrangement. The gene expression patterns were examined in E. grandis clones, challenged with a fungal pathogen (Chrysoporthe austroafricana) and insect pest (Leptocybe invasa). One thousand two hundred and fifteen putative NBS-LRR coding sequences were located which aligned into two large classes, Toll or interleukin-1 receptor (TIR) and coiled-coil (CC) based on NB-ARC domains. NBS-LRR gene-rich regions were identified with 76% organized in clusters of three or more genes. A further 272 putative incomplete resistance genes were also identified. We determined that E. grandis has a higher ratio of TIR to CC classed genes compared to other woody plant species as well as a smaller percentage of single NBS-LRR genes. Transcriptome profiles indicated expression hotspots, within physical clusters, including expression of many incomplete genes. The clustering of putative NBS-LRR genes correlates with differential expression responses in resistant and susceptible plants indicating functional relevance for the physical arrangement of this gene family. This analysis of the repertoire and expression of E. grandis putative NBS-LRR genes provides an important resource for the identification of novel and functional R-genes; a key objective for strategies to enhance resilience.

Transcriptome and hormone profiling reveals Eucalyptus grandis defence responses against Chrysoporthe austroafricana

BACKGROUND

Eucalyptus species and interspecific hybrids exhibit valuable growth and wood properties that make them a highly desirable commodity. However, these trees are challenged by a wide array of biotic stresses during their lifetimes. The Eucalyptus grandis reference genome sequence provides a resource to study pest and pathogen defence mechanisms in long-lived woody plants. E. grandis trees are generally susceptible to Chrysoporthe austroafricana, a causal agent of stem cankers on eucalypts. The aim of this study was to characterize the defence response of E. grandis against C. austroafricana.

RESULTS

Hormone profiling of susceptible and moderately resistant clonal E. grandis genotypes indicated a reduction in salicylic acid and gibberellic acid levels at 3 days post inoculation. We hypothesized that these signaling pathways may facilitate resistance. To further investigate other defence mechanisms at this time point, transcriptome profiling was performed. This revealed that cell wall modifications and response to oxidative stress form part of the defence responses common to both genotypes, whilst changes in the hormone signaling pathways may contribute to resistance. Additionally the expression of selected candidate defence response genes was induced earlier in moderately resistant trees than in susceptible trees, supporting the hypothesis that a delayed defence response may occur in the susceptible interaction.

CONCLUSION

The ability of a host to fine-tune its defence responses is crucial and the responses identified in this study extends our understanding of plant defence, gained from model systems, to woody perennials.