Elsinoe perseae, the causal agent of avocado scab disease, is a high-priority biosecurity threat to the Australian avocado industry. Symptom-based diagnosis is unreliable, and morphological identification is hindered by the slow growth of Elsinoe species on artificial media and the absence of a sexual reproductive stage in the field and in axenic culture. Consequently, a rapid and reliable molecular diagnostic tool capable of detecting the pathogen directly from infected fruit or leaf tissue is essential. In this study, we developed a quantitative PCR (qPCR) assay targeting two genomic regions: the internal transcribed spacer 1 (ITS1) region of the rDNA and the RNA polymerase II subunit B (rpb2) gene. The assay can be applied in either singleplex or duplex formats. Both the ITS- and rpb2-targeted assays consistently detected E. perseae DNA from pure cultures. However, detection in infected avocado leaf and fruit tissues was primarily driven by the ITS assay, whereas the rpb2 assay exhibited reduced sensitivity, likely reflecting differences in copy number between multicopy rDNA regions and the single-copy rpb2 gene. No cross-reactivity was observed against other Elsinoe species or common fungal pathogens of avocado. High analytical sensitivity was achieved, with reliable detection of both targets at concentrations of 10³ copies/µL of synthetic gBlocks dsDNA and 0.1 ng/µL of genomic DNA, using a conservative threshold of Ct ≤ 30. Assay performance was unaffected by minor variations in qPCR reagents and instrument platforms. This assay provides a rapid, sensitive, and highly specific diagnostic tool for biosecurity applications, supporting accurate detection, surveillance, and early response to potential incursions of E. perseae.

Myrtle rust, caused by the fungus Austropuccinia psidii, is an invasive disease that has a centre of origin in South America and currently threatens native environments and forestry on nearly all continents. A better understanding of the pathogen and disease process is required to develop new strategies to address the threat posed by A. psidii to a broad range of Myrtaceous plants. To gain a better understanding of this multi-host obligate pathogen we investigated if the pandemic strain of the fungus hosted mycoviruses. We identified at least eight different mycoviruses that included double stranded RNA (dsRNA) and positive sense single stranded RNA (ssRNA) viruses. We demonstrated that the RNA interference pathways of A. psidii are active, but ineffective in suppressing the presence of these viruses.

Endogenous viral elements (EVEs) are viral sequences integrated into host genomes, functioning as molecular fossils of past infections. Most characterised EVEs in plants are derived from the Caulimoviridae , the only family of dsDNA viruses infecting this kingdom. Endogenous caulimovirids (ECVs) occur across taxonomically diverse vascular plant species and represent a significant resource for studying host-virus coevolution, host range dynamics, and the evolution of viral genomes over deep timescales. Previous evolutionary studies utilising ECVs have proposed cospeciation or host switching as the primary drivers of Caulimoviridae diversification; however, these studies were limited by poor representation of genomic data from basal plant lineages. Here, we analysed 93 plant genomes spanning all major embryophyte groups, including ferns and lycophytes, and identified 47,135 ECVs across 75 genomes. These sequences were classified into 71 operational taxonomic units (OTUs), including 35 previously undescribed groups, revealing substantial and previously unrecognised diversity within the Caulimoviridae . Notably, we identified a basal clade restricted to the Araucariaceae , an ancient lineage of Gondwanan conifers. Phylogenetic comparisons between ECVs and host plant lineages support a macroevolutionary model in which cospeciation with tracheophytes played a dominant role in shaping Caulimoviridae diversification. Together, these findings establish Caulimoviridae and their endogenous counterparts as a powerful model system for paleovirology, offering unprecedented insights into the coevolution, diversification, and extinction of plant viruses over deep evolutionary timescales.

Ceratobium mosaic virus (CerMV; species Potyvirus ceratobii) has only been recorded from the east coast of Australia, where it infects native Dendrobium and allied orchid genera. Very little is known about this virus, although based on its classification as a potyvirus, it likely is transmitted in a non-persistent manner by aphids. When first discovered, only a RT-PCR amplicon covering the NIb and coat protein coding regions and 3’ untranslated region of the viral genome was sequenced, which at the time was sufficient for official recognition of this virus as a novel species. However, the standard of evidence now required for taxonomic proposals is a complete or near complete genome sequence. In this report, we present the complete genome sequence of an isolate of CerMV from New South Wales, allowing a more comprehensive analysis of its classification and phylogeny.

Spider lilies (genus Hymenocallis) are perennial herbaceous plants native to tropical and subtropical America and are popular landscaping plants in similar climes throughout the world. They are susceptible to infection by at least five different orthotospoviruses, and display prominent symptoms of infection, suggesting that they may be useful as sentinel plants for monitoring the presence of orthotospoviruses in the environment. In this study, surveys of spider lilies for orthotospoviral infections were done in three distinct Queensland regions. In southeast Queensland, spider lilies infected by tomato spotted wilt virus (TSWV) were found at 65 locations, whereas spider lilies infected by capsicum chlorosis virus (CaCV) were only found at two locations. Conversely, in central and far north Queensland, CaCV-infected spider lilies were found at 41 locations, while TSWV-infected spider lilies were only found at two locations. Phylogenetic analyses based on the complete nucleocapsid protein sequences indicated a population structure of the virus isolates that correlated with the geographical origins of the samples. Both non-systemic and systemic TSWV infections were identified in spider lilies, and some initially non-systemically infected spider lily plants ended up with systemic infection. We demonstrated that Taeniothrips eucharii (Whetzel), a common thrips species on spider lilies in southeast Queensland, can transmit TSWV and has likely amplified TSWV infections in spider lilies in this region. Overall, the results of this study suggest that spider lilies could be useful sentinel plants for indicating the presence of orthotospoviruses in the environment.

Collectively, orthotospoviruses and their thrips vectors are some of the most economically important pathogens and pests of crops worldwide. Rapid identification tools are needed, and variants of polymerase chain reaction (PCR) or reverse transcription-PCR (RT-PCR) still have an important role to play, but there are deficiencies in existing assays for both groups of organisms. The number of known orthotospoviruses has rapidly expanded in recent years, and existing universal RT-PCR assays no longer account for all possible sequence variation. The cytochrome c oxidase subunit I gene (COX1) is the international standard for DNA barcoding of insects, but the PCR primers used to amplify this gene were designed many years ago using limited sequence datasets, and these primers have many primer-template mismatches when used with thrips. In this study, a universal RT-PCR assay for orthotospoviruses has been developed targeting the RNA-dependent RNA polymerase gene (RdRp) on the L RNA segment by identifying the most conserved protein motifs and taking advantage of the presence of codon usage biases in the virus genus. There is potential for a vector-enabled metabarcoding strategy to monitor the presence of orthotospoviruses using this universal RT-PCR assay. For robust virus testing in thrips, an internal control assay targeting the translation elongation factor 1-alpha RNA transcripts has been developed, which is predicted to be applicable to not only thrips but all hemipteran plant virus vectors. New COX1 DNA barcoding primers for thrips have also been designed that theoretically cover all species in the suborder Terebrantia, which includes all orthotospoviral vectors. All assays were validated using both synthetic nucleic acid templates and biological samples.

Stenotaphrum secundatum is a premium turf grass in warm temperate and subtropical regions of the world and is the most important turf species in Australia based on the value of its production. A new disease called buffalo grass yellows (BGY) has become a problem on turf farms in Australia. We surveyed turf farms in New South Wales, Queensland, and Western Australia to determine whether panicum mosaic virus (PMV) and sugarcane mosaic virus (SCMV) were associated with BGY. PMV was only found on three farms, two located in the Hawkesbury Valley near Sydney and a third at Echuca, about 800 km to the southwest of the former location. SCMV was more prevalent, present in all major cultivars and states surveyed. We analyzed phylogenetic relationships for SCMV and found that isolates infecting S. secundatum in Australia belonged to three clades. The first included Australian isolates typical of the population of viruses circulating in Digitaria didactyla. The second included a single New South Wales isolate from S. secundatum 'SS100' that grouped with otherwise American isolates of SCMV recorded in S. secundatum and Saccharum officinale from Florida and Zea mays from Ohio. Finally, an isolate of SCMV from S. secundatum originating from a turf farm in South East Queensland grouped with viruses mostly infecting maize; this record is potentially the first maize-adapted strain of SCMV in Australia. Our study sheds light on the etiology of the BGY disease syndrome and invasion history of PMV and SCMV in Australia.

Progress to resolve the aetiology of abnormal vertical growth (AVG) in macadamia has been slow, hindering development of disease control strategies. In this study, evidence is provided that AVG is caused by a bacterial pathogen that infects the roots of macadamia trees. Analysis of samples from symptomatic and asymptomatic macadamia trees using conventional culturing and DNA metabarcoding techniques revealed that multiple species in the genera Bacillus, Serratia and Paenibacillus were predominant in leaf, stem and root samples from macadamia. Of the 15 bacterial taxa isolated, Serratia fonticola was exclusively isolated from the roots of all AVG symptomatic trees, making it a prime suspect as the cause of AVG. Elsewhere in the literature, this bacterium is documented as modulating hormone levels in the plant. In AVG trees, elevated levels of gibberellic acid are detected in apical buds, while higher levels of abscisic acid are found in lateral buds, which may support the characteristics of the reduced lateral branching and dominance of apical buds in symptomatic trees. We discuss how this bacterium fits the known epidemiology of AVG, and suggest further research to confirm that it is in fact the pathogen responsible for AVG.

Endogenous viral elements (EVEs) result from the integration of viral sequences into the genome of their hosts. EVEs can be considered molecular fossils of ancient or unknown viruses. Through paleovirological approaches, EVEs can help unravel the evolutionary trajectories of related viruses across extended temporal scales. In plants, most characterized EVEs belong to the family Caulimoviridae , the only family of retrotranscribed plant viruses, and are termed endogenous caulimovirids (ECVs). Previous studies of ECVs have proposed either cospeciation or host-switching as the primary mode of Caulimoviridae transmission through plant divisions, both scenarios assuming an emergence predating the euphyllophytes. However, robust assessments of ECV diversity and hosts were hindered by the underrepresentation of basal plant genome assemblies. Taking advantage of newly available genomic resources, we analyzed a dataset of 93 plant genome sequences representing all subdivisions of embryophytes, including basal groups such as ferns and lycophytes. We identified 47,135 ECVs in 75 genomes from lycophytes, ferns, gymnosperms, and angiosperms. Based on their diversity, these ECVs were classified into 71 operational taxonomic units (OTUs), 35 of which were previously undescribed. Our work revealed an unexpected diversity of Caulimoviridae in tracheophytes and identified a new clade restricted to gymnosperms. By comparing the phylogenetic relationships of Caulimoviridae with host plant taxonomy, we propose a new macroevolutionary scenario in which cospeciation with the tracheophytes is the main driver of Caulimoviridae diversification. ### Competing Interest Statement The authors have declared no competing interest. Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-17-EUR-0007 European Regions Research and Innovation Network, https://ror.org/02wbb9367, REU005756

A novel species in the genus Closterovirus, family Closteroviridae, has been identified by high throughput sequencing in legume samples collected during plant pathogen surveys on Norfolk Island in 2014. The complete genome sequence of 16,815 nucleotides was obtained from a French bean (Phaseolus vulgaris) plant with symptoms of interveinal chlorosis in the older leaves. Complete or near complete coding sequences for the 10 open reading frames were also obtained from a second French bean plant, and batch samples of white clover (Trifolium repens) and pea (Pisum sativum). All isolates shared 99.7–99.9

Viroids occur in plants as swarms of sequence variants clustered around a dominant variant, leading to adoption of the term ‘quasispecies’ to describe the viroid population in an individual host. The composition of the quasispecies can potentially change according to the age of the infection, the position of the leaf or branch in the canopy, and the host species. The primary aim of this study was to investigate the quasispecies concept for citrus viroid VII (CVd-VII), a recently discovered member of the family Pospiviroidae. Three experiments were conducted to determine factors affecting viroid variability (i) within different tissues of a lemon plant, (ii) among different plants of the same species (citron), and (iii) among different species and hybrids of citrus. Using two primer sets to produce amplicons for high-throughput sequencing, viroid population profiles were generated for each sample. The number of variants that were identified with both primer sets ranged from 2 to 13 per sample, and each sample comprised 1 to 4 major (> 10

In this chapter, minor viral pathogens of banana, plantain and abacá are discussed. Some such as banana bract mosaic virus and the abacá strain of sugarcane mosaic virus have the potential to cause much more serious problems if they are allowed to spread unchecked around the world. Other viruses such as banana mild mosaic virus are already ubiquitous but do not appear to have an appreciable impact on yield or quality. Cucumber mosaic virus has a very broad host range and is an economically important pathogen of many crops, but banana is not among those worst affected. Due to the limited amount of research devoted to this miscellaneous group of viruses, there are many unanswered questions surrounding their biology, some of which are highlighted in this chapter.

Plant pathology researchers play a pivotal role in thought leadership and its translation to action regarding the recognition and demonstration of the value of Indigenous knowledge and science. For many scientists, navigating the space of Indigenous rights and perspectives is challenging. In pursuit of a cultural shift in research and development within the field of plant pathology, the 2019–2021 Management Committee of the Australasian Plant Pathology Society (APPS) undertook a review and modernization of the Society’s Constitution. The aim was to ensure its alignment with principles that foster inclusivity of Indigenous peoples in the development and implementation of relevant research projects impacting their communities. Additionally, a dynamic repository of guidelines and resources was compiled. These resources are designed to assist plant pathologists, while respecting and not superseding the guidance provided by local Indigenous researchers, practitioners, and advisors. The collective efforts of plant pathologists hold immense potential in championing Indigenous Peoples and their rights, steering the field toward a more inclusive and equitable future. This paper builds upon the thesis presented in the APPS Presidential Address at the Biennial APPS Conference in 2021, held virtually in lutruwita (Tasmania) on the unceded lands of the Palawa people. It underscores the potential impact when plant pathologists unite in advocating for Indigenous Peoples and their rightful place within the field.

The chapter gives an overview of the biology, epidemiology, diagnostics, and control of the banana streak complex of viruses in bananas.

Historical Records of Australian Science publishes peer-reviewed articles and book reviews on the history of science and scientists in Australia and the southwest Pacific, biographical memoirs of deceased Fellows of the Academy, and an annual bibliography of the history of Australian science

In 2019, symptoms typical of infection by iris yellow spot virus (IYSV; family Tospoviridae, genus Orthotospovirus) were observed on shallot (A. cepa var. aggregatum) grown at the Gatton Research Facility, Department of Agriculture and Fisheries, Queensland. Initial testing by DAS-ELISA was positive for IYSV, and subsequent specific RT-PCR amplifying part of the RdRp (L-segment) and sequencing of amplicons confirmed the IYSV infection. This is the first record of IYSV infection of shallot in Australia.

The complete genome sequence of a novel sadwavirus infecting cattleya orchids in South East Queensland is described. Isometric virions of c . 27 nm diameter were observed in sap extracts viewed under a transmission electron microscope, and the genome sequence of this virus was determined by high-throughput sequencing. The viral genome consists of two RNA components, 5,910 and 4,435 nucleotides (nt) in length, each encoding a long polyprotein, with predicted cleavage sites at H/Y, E/G, Q/S, and Q/G for the RNA1 and T/G for the RNA2 translation products, respectively. RNA2 has an additional small ORF of 684 nt near the 3ʹ untranslated region. Phylogenetic analysis based on an amino acid sequence alignment of the Pro-Pol region suggested that this virus is most closely related to pineapple secovirus A, a member of the subgenus Cholivirus , but warrants classification as a member of a new species because it exhibited no more than 64% amino acid identity in pairwise sequence comparisons. Because of the prominent purple ringspots that were observed on the leaves of some of the plants, we propose the name “cattleya purple ringspot virus” for this virus (suggested species name: “ Sadwavirus cattleyacola ”).

Members of the genus Cilevirus are causative agents of citrus leprosis, an economically important disease of citrus in the Americas. Using high-throughput sequencing, we detected the hibiscus strain of citrus leprosis virus C2 (CiLV-C2H) infecting a cultivated Hoya macgillivrayi plant in Brisbane, Australia. The infection was not systemic, and presumably resulted from the feeding action of false spider mites (Brevipalpus spp.) that acquired the virus from an unidentified source of inoculum. Capsicum chlorosis virus, an orthotospovirus, was also present as a mixed infection, preventing the attribution of symptoms to CiLV-C2H.

Avocado is one of the world's fastest growing tropical fruit industries, and the pathogen avocado sunblotch viroid (ASBVd) is a major threat to both production and access to international export markets. ASBVd is seed transmissible, with infection possible via either the male (pollen) or female gametes. Surveillance for ASBVd across commercial orchards is a major logistical task, particularly when aiming to meet the stringent standards of evidence required for a declaration of pest freedom. As with many fruit crops, insect pollination is important for high avocado yields, and honey bee (Apis mellifera) hives are typically moved into orchards for paid pollination services. Exploiting the foraging behavior of honey bees can provide a complementary strategy to traditional surveillance methods. High-throughput sequencing (HTS) of bee samples for plant viruses shows promise, but this surveillance method has not yet been tested for viroids or in a targeted plant biosecurity context. Here, we tested samples of bees and pollen collected from pollination hives in two ASBVd orchard locations, one in Australia, where only four trees in a block were known to be infected, and a second in South Africa, where the estimated incidence of infection was 10%. Using real-time RT-PCR and HTS (total RNA-seq and small RNA-seq), we demonstrated that ASBVd can be confidently detected in bees and pollen samples from hives within 100 m of infected trees. The potential for using this approach in ASBVd surveillance for improved orchard management and supporting market access is discussed.