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

Histological, chemical and gene expression differences between western redcedar seedlings resistant and susceptible to cedar leaf blight

Introduction

Western redcedar (Thuja plicata) is an important species in the Cupressaceae both at economic and cultural levels in the Pacific Northwest of North America. In adult trees, the species produces one of the most weathering-resistant heartwoods among conifers, making it one of the preferred species for outdoor applications. However, young T. plicata plants are susceptible to infection with cedar leaf blight (Didymascella thujina), an important foliar pathogen that can be devastating in nurseries and small-spaced plantations. Despite that, variability in the resistance against D. thujina in T. plicata has been documented, and such variability can be used to breed T. plicata for resistance against the pathogen.

Objective

This investigation aimed to discern the phenotypic and gene expression differences between resistant and susceptible T. plicata seedlings to shed light on the potential constitutive resistance mechanisms against cedar leaf blight in western redcedar.

Methods

The study consisted of two parts. First, the histological differences between four resistant and four susceptible families that were never infected with the pathogen were investigated. And second, the differences between one resistant and one susceptible family that were infected and not infected with the pathogen were analyzed at the chemical (C, N, mineral nutrients, lignin, fiber, starch, and terpenes) and gene expression (RNA-Seq) levels.

Results

The histological part showed that T. plicata seedlings resistant to D. thujina had constitutively thicker cuticles and lower stomatal densities than susceptible plants. The chemical analyses revealed that, regardless of their infection status, resistant plants had higher foliar concentrations of sabinene and α-thujene, and higher levels of expression of transcripts that code for leucine-rich repeat receptor-like protein kinases and for bark storage proteins.

Conclusion

The data collected in this study shows that constitutive differences at the phenotypic (histological and chemical) and gene expression level exist between T. plicata seedlings susceptible and resistant to D. thujina. Such differences have potential use for marker-assisted selection and breeding for resistance against cedar leaf blight in western redcedar in the future.

The In Planta Gene Expression of Austropuccinia psidii in Resistant and Susceptible Eucalyptus grandis

Austropuccinia psidii, commonly known as myrtle rust, is an obligate, biotrophic rust pathogen that causes rust disease in a broad host range of Myrtaceae species. Eucalyptus grandis, a widely cultivated hardwood Myrtaceae species, is susceptible to A. psidii infection, with this pathogen threatening both their natural range and various forest plantations across the world. This study aimed to investigate the A. psidii transcriptomic responses in resistant and susceptible E. grandis at four time points. RNA-seq reads were mapped to the A. psidii reference genome to quantify expressed genes at 12 h postinoculation and 1, 2, and 5 days postinoculation (dpi). A total of eight hundred and ninety expressed genes were found, of which 43 were candidate effector protein genes. These included rust transferred protein 1 (RTP1), expressed in susceptible hosts at 5 dpi, and a hydrolase protein gene expressed in both resistant and susceptible hosts over time. Functional categorization of expressed genes revealed processes enriched in susceptible hosts, including malate metabolic and malate dehydrogenase activity, implicating oxalic acid in disease susceptibility. These results highlight putative virulence or pathogenicity mechanisms employed by A. psidii to cause disease, and they provide the first insight into the molecular responses of A. psidii in E. grandis over time.

A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes

BACKGROUND

Melaleuca quinquenervia (broad-leaved paperbark) is a coastal wetland tree species that serves as a foundation species in eastern Australia, Indonesia, Papua New Guinea, and New Caledonia. While extensively cultivated for its ornamental value, it has also become invasive in regions like Florida, USA. Long-lived trees face diverse pest and pathogen pressures, and plant stress responses rely on immune receptors encoded by the nucleotide-binding leucine-rich repeat (NLR) gene family. However, the comprehensive annotation of NLR encoding genes has been challenging due to their clustering arrangement on chromosomes and highly repetitive domain structure; expansion of the NLR gene family is driven largely by tandem duplication. Additionally, the allelic diversity of the NLR gene family remains largely unexplored in outcrossing tree species, as many genomes are presented in their haploid, collapsed state.

RESULTS

We assembled a chromosome-level pseudo-phased genome for M. quinquenervia and described the allelic diversity of plant NLRs using the novel FindPlantNLRs pipeline. Analysis reveals variation in the number of NLR genes on each haplotype, distinct clustering patterns, and differences in the types and numbers of novel integrated domains.

CONCLUSIONS

The high-quality M. quinquenervia genome assembly establishes a new framework for functional and evolutionary studies of this significant tree species. Our findings suggest that maintaining allelic diversity within the NLR gene family is crucial for enabling responses to environmental stress, particularly in long-lived plants.

Both Constitutive and Infection-Responsive Secondary Metabolites Linked to Resistance against Austropuccinia psidii (Myrtle Rust) in Melaleuca quinquenervia

Austropuccinia psidii is a fungal plant pathogen that infects species within the Myrtaceae, causing the disease myrtle rust. Myrtle rust is causing declines in populations within natural and managed ecosystems and is expected to result in species extinctions. Despite this, variation in response to A. psidii exist within some species, from complete susceptibility to resistance that prevents or limits infection by the pathogen. Untargeted metabolomics using Ultra Performance Liquid Chromatography with Ion Mobility followed by analysis using MetaboAnalyst 3.0, was used to explore the chemical defence profiles of resistant, hypersensitive and susceptible phenotypes within Melaleuca quinquenervia during the early stages of A. psidii infection. We were able to identify three separate pools of secondary metabolites: (i) metabolites classified structurally as flavonoids that were naturally higher in the leaves of resistant individuals prior to infection, (ii) organoheterocyclic and carbohydrate-related metabolites that varied with the level of host resistance post-infection, and (iii) metabolites from the terpenoid pathways that were responsive to disease progression regardless of resistance phenotype suggesting that these play a minimal role in disease resistance during the early stages of colonization of this species. Based on the classes of these secondary metabolites, our results provide an improved understanding of key pathways that could be linked more generally to rust resistance with particular application within Melaleuca.

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.

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.

Identifying genetic markers for a range of phylogenetic utility-From species to family level

Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci. To validate our method we present data from Eucalyptus and Melaleuca, two large and phylogenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the data. The methods developed here should be applicable across a large range of taxa across all kingdoms. The core methods are very flexible, providing a platform for various genomic resource availabilities and are useful from shallow to deep phylogenies.

Comparison of host susceptibilities to native and exotic pathogens provides evidence for pathogen-imposed selection in forest trees

The extent to which spatial structuring of host resistance in wild plant populations reflects direct pathogen-imposed selection is a subject of debate. To examine this issue, genetic susceptibilities to an exotic and a coevolved native fungal pathogen were compared using two Australian host tree species. Damage to common host germplasm of Corymbia citriodora ssp. variegata (CCV) and Eucalyptus globulus, caused by recently introduced (Austropuccinia psidii) and native (Quambalaria pitereka and Teratosphaeria sp.) pathogens was evaluated in common-garden experiments. There was significant additive genetic variation within host species for susceptibility to both the exotic and native pathogens. However, susceptibility to A. psidii was not genetically correlated with susceptibility to either native pathogen, providing support for pathogen-specific rather than general mechanisms of resistance. Population differentiation (Q_ST ) for susceptibility to the native pathogens was greater than neutral expectations (molecular F_ST ), arguing for divergent selection. Coupled with lower native, but not exotic, pathogen susceptibility in host populations from areas climatically more prone to fungal proliferation, these findings suggest that pathogen-imposed selection has contributed directly to a geographic mosaic of host resistance to native pathogens.