Biology subjects

Tobias, P. A.

Publications and source records attributed to Tobias, P. A..

10 recordsLinked to original sources

bioRxiv2026

Lineage-specific expansion of a potential novel class of resistance genes in Myrtaceae

Genes encoding intracellular nucleotide-binding site leucine-rich repeat (NBS-LRR) receptors represent the largest class of resistance (R) genes in plants, yet their evolutionary trajectory in trees remains poorly understood. Using high-quality long-read genome assemblies from eight Myrtaceae species, we identified 15,792 NBS-encoding genes with threefold variation in gene content across species. To investigate potential decoy domains for effector proteins of pathogens, we parsed the annotated NBS-encoding genes and determined 181 unique non-canonical domains. Notably, we observed frequent integration of Jacalin domains into TIR-NBS proteins. This novel gene family, named TNJ, is hypothesized to represent a new R gene class. Further exploration of TNJ sequence analysis shows up to seven Jacalin domains per protein and forming a monophyletic clade; however, AF3 modelling confirmed only six domains. Conserved residues in the TIR domain and functional motifs within the NB-ARC domain supports TNJs potential role in immune signalling. Most hypervariable sites and positively selected sites detected to be surface-exposed were clustered in the Jacalin region of TNJ, suggesting that surfaces of Jacalin domain may harbour residues determining pathogen recognition specificity. These findings support TNJ as a potentially new class of R genes in Myrtaceae with Jacalin as a replacement for LRR.

evolutionary biology↗

bioRxiv2026

Rhizoctonia theobromae isolates causing Vascular-Streak Dieback of Cocoa and Cassava Witches' Broom Disease are likely host-specific, regionally divergent and homothallic

The fastidious basidiomycete Rhizoctonia (Ceratobasidium) theobromae is a biotrophic pathogen that causes Vascular-Streak Dieback (VSD) of Theobroma cacao (cocoa). The fungus has also been identified as the cause of an emergent disease known as Cassava Witches Broom Disease (CWBD) raising concerns that the pathogen is spreading to alternative hosts and to new regions. Interestingly, while VSD of cocoa and CWBD are reported as co-present in several countries, there is currently no evidence for cross-infection between species. The fungus is difficult to culture in vitro due its slow growth and Kochs postulates have not been definitive on either host. The complete fungus life cycle therefore remains enigmatic, though studies have progressed knowledge on pathology within the both the cocoa and cassava hosts. We have conducted limited field trials and sequenced mating (MAT) and ITS loci of isolates from various infected hosts and regions. We hypothesize that (i) genetic variation at MAT loci correlates with region or host (ii) long amplicon ITS sequences between isolates are more definitive for polymorphisms (iii) life-cycle traits of R. theobromae may be inferred from MAT loci (iv) cassava grown under VSD infected cocoa will be infected and develop symptoms of CWBD. We did not find any cross-infection in field trials, and we show that the pathogen is highly homozygous, despite undergoing meiosis, indicating a predominantly homothallic life cycle. Our data indicate that the pathogen is likely host specific and regionally divergent and suggests that host specificity on cocoa and cassava evolved by selection from a common ancestor rather than a host jump.

microbiology↗

bioRxiv2024

Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying responses to Ceratobasidium theobromae

Diseases of Theobroma cacao disrupt cocoa bean supply and economically impact growers. Vascular streak dieback (VSD), caused by Ceratobasidium theobromae, is a new encounter disease of cacao currently contained to southeast Asia and Melanesia. Resistance to VSD has been tested with large progeny trials in Sulawesi, Indonesia, and in Papua New Guinea with the identification of informative quantitative trait loci (QTL). Using a VSD susceptible progeny tree (clone 26), derived from a resistant and susceptible parental cross, we assembled the genome to chromosome-level and discriminated alleles inherited from either resistant or susceptible parents. The parentally phased genomes were annotated for all predicted genes and then specifically for resistance genes of the nucleotide-binding site leucine-rich repeat class (NLR). On investigation, we determined the presence of NLR clusters at informative QTLs, as well as other potential disease response gene candidates. Understanding the genetics underlying resistance and susceptibility to VSD will accelerate the breeding cycle by providing clear targets for molecular screening. Additionally, we provide the first diploid, fully scaffolded and parentally phased genome resource for Theobroma cacao L.

plant biology↗

bioRxiv2024

Mating-compatibility genes employed as diagnostic markers to identify novel incursions of the myrtle rust pathogen Austropuccinia psidii

Austropuccinia psidii is the causal agent of myrtle rust in over 480 species within the family Myrtaceae. Lineages of A. psidii are structured by host in its native range, and some have success on new-encounter hosts. For example, the pandemic biotype has spread beyond South America, and proliferation of other lineages is an additional risk to biodiversity and industries. Efforts to manage A. psidii incursions, including lineage differentiation, relies on variable microsatellite markers. Testing these markers is time-consuming and complex, particularly on a large scale. We designed a novel diagnostic approach targeting the fungal mating-type HD (homeodomain) transcription factor locus to address these limitations. The HD locus (bW1/2-HD1 and bE1/2-HD2) is highly polymorphic, facilitating clear biological predictions about its inheritance from founding populations. To be considered the same lineage, all four HD alleles must be identical. Our lineage diagnostics relies on PCR amplification of the HD locus in different genotypes of A. psidii followed by amplicon sequencing using Oxford Nanopore Technologies (ONT) and comparative analysis. The lineage-specific assay was validated on four isolates with existing genomes, uncharacterized isolates, and directly from infected leaf material. We reconstructed HD alleles from amplicons and confirmed their sequence identity relative to their reference. Genealogies using HD alleles confirmed the variations at the HD loci among lineages/isolates. Our study establishes a robust diagnostic tool, for differentiating known lineages of A. psidii based biological predictions. This tool holds promise for detecting new pathogen incursions and can be refined for broader applications, including air-sample detection and mixed-isolate infections.

plant biology↗

bioRxiv2023

Screening of Threatened and Priority listed Melaleuca species from Western Australia reveals high susceptibility to Austropuccinia psidii in controlled inoculations

Austropuccinia psidii causes rust disease on species within the family Myrtaceae and 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 Australia. This study established that 13 previously unscreened species of Melaleuca, including Threatened and Priority species that were grown from seeds sourced from Western Australian populations, were susceptible to the pandemic strain of the pathogen. The proportion of highly susceptible plants within a single species ranged from 2% - 94%, with several species displaying highly variable levels of resistance to A. psidii. These results highlight the importance of disease screening and may direct conservation efforts.

plant biology↗

bioRxiv2023

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

BackgroundThe coastal wetland tree species Melaleuca quinquenervia (Cav.) S.T.Blake (Myrtaceae), commonly named the broad-leaved paperbark, is a foundation species in eastern Australia, Indonesia, Papua New Guinea, and New Caledonia. The species has been widely grown as an ornamental, becoming invasive in areas such as Florida in the United States. Long-lived trees must respond to a wide range pests and pathogens throughout their lifespan, and immune receptors encoded by the nucleotide- binding domain and leucine-rich repeat containing (NLR) gene family play a key role in plant stress responses. Expansion of this gene family is driven largely by tandem duplication, resulting in a clustering arrangement on chromosomes. Due to this clustering and their highly repetitive domain structure, comprehensive annotation of NLR encoding genes within genomes has been difficult. Additionally, as many genomes are still presented in their haploid, collapsed state, the full allelic diversity of the NLR gene family has not been widely published for outcrossing tree species. ResultsWe assembled a chromosome-level pseudo-phased genome for M. quinquenervia and describe the full allelic diversity of plant NLRs using the novel FindPlantNLRs pipeline. Analysis reveals variation in the number of NLR genes on each haplotype, differences in clusters and in the types and numbers of novel integrated domains. ConclusionsWe anticipate that the high quality of the genome for M. quinquenervia will provide a new framework for functional and evolutionary studies into this important tree species. Our results indicate a likely role for maintenance of NLR allelic diversity to enable response to environmental stress, and we suggest that this allelic diversity may be even more important for long-lived plants.

genomics↗

bioRxiv2022

A chromosome-level genome resource for studying virulence mechanisms and evolution of the coffee rust pathogen Hemileia vastatrix

Recurrent epidemics of coffee leaf rust, caused by the fungal pathogen Hemileia vastatrix, have constrained the sustainable production of Arabica coffee for over 150 years. The ability of H. vastatrix to overcome resistance in coffee cultivars and evolve new races is inexplicable for a -pathogen that supposedly only utilizes clonal reproduction. Understanding the evolutionary complexity between H. vastatrix and its only known host, including determining how the pathogen evolves virulence so rapidly is crucial for disease management. Achieving such goals relies on the availability of a comprehensive and high-quality genome reference assembly. To date, two reference genomes have been assembled and published for H. vastatrix that, while useful, remain fragmented and do not represent chromosomal scaffolds. Here, we present a complete scaffolded pseudochromosome-level genome resource for H. vastatrix strain 178a (Hv178a). Our initial assembly revealed an unusually high degree of gene duplication (over 50% BUSCO basidiomycota_odb10 genes). Upon inspection, this was predominantly due to a single scaffold that itself showed 91.9% BUSCO Completeness. Taxonomic analysis of predicted BUSCO genes placed this scaffold in Exobasidiomycetes and suggests it is a distinct genome, which we have named Hv178a associated fungal genome (Hv178a AFG). The high depth of coverage and close association with Hv178a raises the prospect of symbiosis, although we cannot completely rule out contamination at this time. The main Ca. 546 Mbp Hv178a genome was primarily (97.7%) localised to 11 pseudochromosomes (51.5 Mb N50), building the foundation for future advanced studies of genome structure and organization.

genomics↗

bioRxiv2022

Three species of Melaleuca from Western Australia are highly susceptible to Austropuccinia psidii in controlled inoculations

Austropuccinia psidii, the fungus causing myrtle rust, was detected in Western Australia for the first time in June 2022. Few Western Australian plant species have been screened for response to the pathogen. Melaleuca thyoides, Melaleuca marginata and Melaleuca leucadendra grown from seeds sourced from Western Australian populations were all highly susceptible to an isolate of the pathogen from eastern Australia.

plant biology↗

bioRxiv2022

A phased chromosome-level genome and full mitochondrial sequence for the dikaryotic myrtle rust pathogen, Austropuccinia psidii

The fungal plant pathogen Austropuccinia psidii is spreading globally and causing myrtle rust disease symptoms on plants in the family Myrtaceae. A. psidii is dikaryotic, with two nuclei that do not exchange genetic material during the dominant phase of its life-cycle. Phased and scaffolded genome resources for rust fungi are important for understanding heterozygosity, mechanisms of pathogenicity, pathogen population structure and for determining the likelihood of disease spread. We have assembled a chromosome-level phased genome for the pandemic biotype of A. psidii and, for the first time, show that each nucleus contains 18 chromosomes, in line with other distantly related rust fungi. We show synteny between the two haplo-phased genomes and provide a new tool, ChromSyn, that enables efficient comparisons between chromosomes based on conserved genes. Our genome resource includes a fully assembled and circularised mitochondrial sequence for the pandemic biotype.

genomics↗

bioRxiv2020

Long read assembly of the pandemic strain of Austropuccinia psidii (myrtle rust) reveals an unusually large (gigabase sized) and repetitive fungal genome.

Austropuccinia psidii, originating in South America, is a globally invasive fungal plant pathogen that causes rust disease on Myrtaceae. Several biotypes are recognized, with the most widely distributed pandemic biotype spreading throughout the Asia-Pacific and Oceania regions over the last decade. Austropuccinia psidii has a broad host range with more than 480 myrtaceous species. Since first detected in Australia in 2010, the pathogen has caused the near extinction of at least three species and negatively affected commercial production of several Myrtaceae. To enable molecular and evolutionary studies into A. psidii pathogenicity, we assembled a highly contiguous genome for the pandemic biotype. With an estimated haploid genome size of just over 1 Gb (gigabases), it is the largest assembled fungal genome to date. The genome has undergone massive expansion via distinct transposable element (TE) bursts. Over 90% of the genome is covered by TEs predominantly belonging to the Gypsy superfamily. These TE bursts have likely been followed by deamination events of methylated cytosines to silence the repetitive elements. This in turn led to the depletion of CpG sites in transposable elements and a very low overall GC content of 33.8%. The overall gene content is highly conserved, when compared to other closely related Pucciniales, yet the intergenic distances are increased by an order of magnitude indicating a general insertion of TEs between genes. Overall, we show how transposable elements shaped the genome evolution of A. psidii and provide a greatly needed resource for strategic approaches to combat disease spread.

genomics↗