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Workflow for identifying, filtering and trimming of NBS-LRR sequences in M. alternifolia and M. quinquenervia to analyse phylogenetic relationships with TIR- and CC-clade NBS-LRR genes of E. grandis (Christie et al. 2016)
Source publication
Myrtaceous plants such as Eucalyptus and Melaleuca are economically and ecologically important. Many species, including M. alternifolia and M. quinquenervia, are known to be susceptible to the exotic rust fungus Austropuccinia psidii. Identifying the molecular basis of resistance against A. psidii would assist in incorporating resistance to this pa...
Similar publications
Austropuccinia psidii causes rust disease on species within the family Myrtaceae. It was first detected in Australia in 2010, with the first detection in Western Australia in 2022. While species within the genus Melaleuca from eastern Australia show variable responses to the pathogen, little is known of the response of species from Western Australi...
Citations
... Consistent with the E. grandis NLR annotation is the higher proportion of TNL-to CNL-type genes supporting an expansion of the TNL clade within the Myrtaceae [ 61 ]. This is further validated by r ecent phylogenetic anal yses using tr anscripts fr om M. quinquenervia and M. alternifolia that r e v ealed a ppr oximatel y tw o-thir ds of NLR transcripts clustering with TNLs from E. grandis [ 71 ]. We found TNL to CNL ratios of ∼3:1 in haplotype A and ∼3:2 in haplotype B of M. quinquenervia . ...
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.
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.
