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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 3' 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")., (© 2024. The Author(s).)

The Caulimoviridae is a family of double-stranded DNA viruses that infect plants. The genomes of most vascular plants contain endogenous caulimovirids (ECVs), a class of repetitive DNA elements that is abundant in some plant genomes, resulting from the integration of viral DNA in the chromosomes of germline cells during episodes of infection that have sometimes occurred millions of years ago. In this review, we reflect on 25 years of research on ECVs that has shown that members of the Caulimoviridae have occupied an unprecedented range of ecological niches over time and shed light on their diversity and macroevolution. We highlight gaps in knowledge and prospects of future research fueled by increased access to plant genome sequence data and new tools for genome annotation for addressing the extent, impact, and role of ECVs on plant biology and the origin and evolutionary trajectories of the Caulimoviridae .

Avocado sunblotch viroid (ASBVd) is a subcellular pathogen of avocado that reduces yield from a tree, diminishes the appearance of the fruit by causing unsightly scarring and impedes trade because of quarantine conditions that are imposed to prevent spread of the pathogen via seed-borne inoculum. For countries where ASBVd is officially reported, permission to export fruit to another country may only be granted if an orchard can be demonstrated to be a pest free production site. The survey requirements to demonstrate pest freedom are usually defined in export protocols that have been mutually agreed upon by the trading partners. In this paper, we introduce a flexible statistical protocol for use in optimizing sampling strategies to establish pest free status from ASBVd in avocado orchards. The protocol, which is supported by an interactive app, integrates statistical considerations of multistage sampling of trees in orchards with a RT-qPCR assay allowing for detection of infection in pooled samples of leaves taken from multiple trees. While this study was motivated by a need to design a survey protocol for ASBVd, the theoretical framework and the accompanying app have broader applicability to a range of plant pathogens in which hierarchical sampling of a target population is coupled with pooling of material prior to diagnosis., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Bonnéry et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

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.

Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that have been captured in the genome of their host organism through a variety of integration mechanisms. While the number of sequenced eukaryotic genomes is rapidly increasing, the annotation and characterization of EVEs remains largely overlooked. EVEs that derive from members of the family Caulimoviridae are widespread across tracheophyte plants, and sometimes they occur in very high copy numbers. However, existing programs for annotating repetitive DNA elements in plant genomes are poor at identifying and then classifying these EVEs. Other than accurately annotating plant genomes, there is intrinsic value in a tool that could identify caulimovirid EVEs as they testify to recent or ancient host-virus interactions and provide valuable insights into virus evolution. In response to this research need, we have developed CAULIFINDER, an automated and sensitive annotation software package. CAULIFINDER consists of two complementary workflows, one to reconstruct, annotate and group caulimovirid EVEs in a given plant genome and the second to classify these genetic elements into officially recognized or tentative genera in the Caulimoviridae. We have benchmarked the CAULIFINDER package using the Vitis vinifera reference genome, which contains a rich assortment of caulimovirid EVEs that have previously been characterized using manual methods. The CAULIFINDER package is distributed in the form of a Docker image., (© 2022. The Author(s).)

The complete genome sequence of pineapple secovirus B (PSV-B), a new virus infecting pineapple (Ananas comosus) on the island of Oahu, Hawaii, was determined by high-throughput sequencing (HTS). The genome comprises two RNAs that are 5,956 and 3,808 nt long, excluding the 3'-end poly-A tails, both coding for a single large polyprotein. The RNA1 polyprotein contains five conserved domains associated with replication, while the RNA2 polyprotein is cleaved into the movement protein and coat protein. PSV-B is representative of a new species in the subgenus Cholivirus (genus Sadwavirus; family Secoviridae), as the level of amino acid sequence identity to recognized members of this subgenus in the Pro-Pol and coat protein regions is below currently valid species demarcation thresholds., (© 2022. The Author(s).)

In this brief note, we review the taxonomic history of dahlia mosaic virus (DMV) and related viruses. DMV is the only officially recognized caulimovirus known to infect dahlia (Dahlia variabilis) plants, although this virus appears to be relatively rare as a pathogen compared to a more recently described but unclassified caulimovirus called dahlia common mosaic virus (DCMV). We have undertaken a new set of analyses to test the hypothesis that DCMV represents a new caulimovirus species whose members infect dahlia, but we ultimately reject this hypothesis. A probable sequencing error was identified in the reference genome sequence of DMV, and consequently, we recommend that an alternative virus isolate be nominated as the exemplar for this species. In accordance with the new binomial nomenclatural system, it is proposed that the virus species be called "Caulimovirus dahliae"., (© 2022. The Author(s).)

Bermuda grass latent virus (BGLV; genus Panicovirus) is identified for the first time in Australia and in only the second country after the USA. A full-length genome sequence was obtained, which has 97% nucleotide sequence identity to that of the species exemplar isolate. Surveys for BGLV, utilising a newly designed universal panicovirus RT-PCR assay for diagnosis, demonstrated widespread infection by this virus in a broad variety of Bermuda grass cultivars (Cynodon dactylon and C. dactylon × C. transvaalensis) grown in both New South Wales and Queensland. The virus was also detected in Rhodes grass (Chloris gayana) and Kikuyu grass (Cenchrus clandestinus), which are both important pasture grasses in subtropical Australia, and the latter is also grown as turf. Furthermore, the Rhodes grass plant, which had strong mosaic symptoms, was also infected with sugarcane mosaic virus, warranting further investigations as to whether synergistic interactions occur between these two viruses., (© 2022. The Author(s).)

An easy, rapid and inexpensive method of preparing RNA template for a reverse transcription qPCR assay for avocado sunblotch viroid (ASBVd) is described. This method depends on the principle of reversible binding of viroid RNA to filter paper under different concentrations of monovalent cation. Lysis buffers containing either sodium chloride or lithium chloride were compared, and 1.5 M lithium chloride was shown to be optimal for the adsorption of the viroid RNA to the filter paper. The extraction method was validated using field samples and equivalent yields of viroid RNA were obtained using this method and either a commercial RNA extraction kit or a dsRNA chromatography method. The filter paper method of RNA extraction is ideally suited for the large-scale surveillance for ASBVd., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The Australasian biogeographic realm is a major centre of diversity for orchids, with every subfamily of the Orchidaceae represented and high levels of endemism at the species rank. It is hypothesised that there is a commensurate diversity of viruses infecting this group of plants. In this study, we have utilised high-throughput sequencing to survey for viruses infecting greenhood orchids (Pterostylidinae) in New South Wales and the Australian Capital Territory. The main aim of this study was to characterise Pterostylis blotch virus (PtBV), a previously reported but uncharacterised virus that had been tentatively classified in the genus Orthotospovirus . This classification was confirmed by genome sequencing, and phylogenetic analyses suggested that PtBV is representative of a new species that is possibly indigenous to Australia as it does not belong to either the American or Eurasian clades of orthotospoviruses. Apart from PtBV, putative new viruses in the genera Alphaendornavirus , Amalgavirus , Polerovirus and Totivirus were discovered, and complete genome sequences were obtained for each virus. It is concluded that the polerovirus is likely an example of an introduced virus infecting a native plant species in its natural habitat, as this virus is probably vectored by an aphid, and Australia has a depauperate native aphid fauna that does not include any species that are host-adapted to orchids.

An apscaviroid, tentatively named citrus viroid VII (CVd-VII), was recently discovered in citrus in Australia. A diagnostic assay using real-time reverse transcription polymerase chain reaction was developed and validated to detect the viroid in citrus plants. The assay showed a high level of sensitivity, reliably detecting 2000 plasmid copies per reaction, while down to 20 plasmid copies per reaction were occasionally detected. The assay showed high specificity, producing no false positives or cross-reactivity with a range of other citrus graft-transmissible pathogens, including viroids, viruses and bacteria. The real-time assay was also found to be more sensitive than the available end-point reverse transcription polymerase chain reaction assay by a factor of 100,000 and could be a useful tool for the rapid detection of CVd-VII in diagnostic and research environments., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Abnormal vertical growth (AVG) syndrome is a serious threat to the Australian macadamia industry as it decreases the yield of nuts by as much as 70% per annum. A lack of information on the cause of AVG has hindered the development of an effective disease management strategy. Discovery of genetic markers associated with disease resistance can be used as tool for rapid selection of elite cultivars, hence helps in efficient disease management. Differences in field susceptibility of macadamia cultivars provide an opportunity for discovery of genetic markers that are associated with host resistance. REML mixed model analysis was performed to estimate the AVG rating of 51 cultivars from multiple origins using phenotypic data from 359 trees planted in four sites. Most of the Hawaiian cultivars were found as susceptible, while selections from the Australian macadamia industry breeding program were predominantly resistant. All the cultivars were genotyped for 13,221 DArTseq-based single nucleotide polymorphism (SNP) markers. A bulked sample analysis was performed using 20 genotypes each at the extremes of AVG phenotypic ratings. Ten SNP markers were predicted to be associated with AVG resistance and two arbitrarily selected SNP markers were validated using PCR and Sanger sequencing. Our findings suggest that AVG resistance in the commercial cultivars may be derived from the genomic introgression of Macadamia tetraphylla through interspecific hybridization. The results may support marker-assisted selection for macadamia germplasm with AVG resistance., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Zakeel, Alam, Geering, Topp and Akinsanmi.)

Novel species of fungi described in this study include those from various countries as follows: Antartica , Cladosporium austrolitorale from coastal sea sand. Australia , Austroboletus yourkae on soil, Crepidotus innuopurpureus on dead wood, Curvularia stenotaphri from roots and leaves of Stenotaphrum secundatum and Thecaphora stajsicii from capsules of Oxalis radicosa. Belgium , Paraxerochrysium coryli (incl. Paraxerochrysium gen. nov.) from Corylus avellana. Brazil , Calvatia nordestina on soil, Didymella tabebuiicola from leaf spots on Tabebuia aurea, Fusarium subflagellisporum from hypertrophied floral and vegetative branches of Mangifera indica and Microdochium maculosum from living leaves of Digitaria insularis. Canada , Cuphophyllus bondii from a grassland. Croatia , Mollisia inferiseptata from a rotten Laurus nobilis trunk. Cyprus , Amanita exilis on calcareous soil. Czech Republic , Cytospora hippophaicola from wood of symptomatic Vaccinium corymbosum. Denmark , Lasiosphaeria deviata on pieces of wood and herbaceous debris. Dominican Republic , Calocybella goethei among grass on a lawn. France (Corsica) , Inocybe corsica on wet ground. France (French Guiana) , Trechispora patawaensis on decayed branch of unknown angiosperm tree and Trechispora subregularis on decayed log of unknown angiosperm tree. Germany , Paramicrothecium sambuci (incl. Paramicrothecium gen. nov.) on dead stems of Sambucus nigra. India , Aureobasidium microtermitis from the gut of a Microtermes sp. termite, Laccaria diospyricola on soil and Phylloporia tamilnadensis on branches of Catunaregam spinosa . Iran , Pythium serotinoosporum from soil under Prunus dulcis. Italy , Pluteus brunneovenosus on twigs of broadleaved trees on the ground. Japan , Heterophoma rehmanniae on leaves of Rehmannia glutinosa f. hueichingensis. Kazakhstan , Murispora kazachstanica from healthy roots of Triticum aestivum. Namibia , Caespitomonium euphorbiae (incl. Caespitomonium gen. nov.) from stems of an Euphorbia sp. Netherlands , Alfaria junci, Myrmecridium junci, Myrmecridium juncicola, Myrmecridium juncigenum, Ophioceras junci, Paradinemasporium junci (incl. Paradinemasporium gen. nov.), Phialoseptomonium junci, Sporidesmiella juncicola, Xenopyricularia junci and Zaanenomyces quadripartis (incl. Zaanenomyces gen. nov.), from dead culms of Juncus effusus, Cylindromonium everniae and Rhodoveronaea everniae from Evernia prunastri, Cyphellophora sambuci and Myrmecridium sambuci from Sambucus nigra, Kiflimonium junci, Sarocladium junci, Zaanenomyces moderatricis-academiae and Zaanenomyces versatilis from dead culms of Juncus inflexus, Microcera physciae from Physcia tenella, Myrmecridium dactylidis from dead culms of Dactylis glomerata, Neochalara spiraeae and Sporidesmium spiraeae from leaves of Spiraea japonica, Neofabraea salicina from Salix sp., Paradissoconium narthecii (incl. Paradissoconium gen. nov.) from dead leaves of Narthecium ossifragum, Polyscytalum vaccinii from Vaccinium myrtillus, Pseudosoloacrosporiella cryptomeriae (incl. Pseudosoloacrosporiella gen. nov.) from leaves of Cryptomeria japonica, Ramularia pararhabdospora from Plantago lanceolata, Sporidesmiella pini from needles of Pinus sylvestris and Xenoacrodontium juglandis (incl. Xenoacrodontium gen. nov. and Xenoacrodontiaceae fam. nov.) from Juglans regia . New Zealand , Cryptometrion metrosideri from twigs of Metrosideros sp., Coccomyces pycnophyllocladi from dead leaves of Phyllocladus alpinus, Hypoderma aliforme from fallen leaves Fuscopora solandri and Hypoderma subiculatum from dead leaves Phormium tenax. Norway , Neodevriesia kalakoutskii from permafrost and Variabilispora viridis from driftwood of Picea abies. Portugal , Entomortierella hereditatis from a biofilm covering a deteriorated limestone wall. Russia , Colpoma junipericola from needles of Juniperus sabina, Entoloma cinnamomeum on soil in grasslands, Entoloma verae on soil in grasslands, Hyphodermella pallidostraminea on a dry dead branch of Actinidia sp., Lepiota sayanensis on litter in a mixed forest, Papiliotrema horticola from Malus communis , Paramacroventuria ribis (incl. Paramacroventuria gen. nov.) from leaves of Ribes aureum and Paramyrothecium lathyri from leaves of Lathyrus tuberosus. South Africa , Harzia combreti from leaf litter of Combretum collinum ssp. sulvense, Penicillium xyleborini from Xyleborinus saxesenii , Phaeoisaria dalbergiae from bark of Dalbergia armata, Protocreopsis euphorbiae from leaf litter of Euphorbia ingens and Roigiella syzygii from twigs of Syzygium chordatum . Spain , Genea zamorana on sandy soil, Gymnopus nigrescens on Scleropodium touretii, Hesperomyces parexochomi on Parexochomus quadriplagiatus, Paraphoma variabilis from dung, Phaeococcomyces kinklidomatophilus from a blackened metal railing of an industrial warehouse and Tuber suaveolens in soil under Quercus faginea. Svalbard and Jan Mayen , Inocybe nivea associated with Salix polaris. Thailand , Biscogniauxia whalleyi on corticated wood. UK , Parasitella quercicola from Quercus robur. USA , Aspergillus arizonicus from indoor air in a hospital, Caeliomyces tampanus (incl. Caeliomyces gen. nov.) from office dust, Cippumomyces mortalis (incl. Cippumomyces gen. nov.) from a tombstone, Cylindrium desperesense from air in a store, Tetracoccosporium pseudoaerium from air sample in house, Toxicocladosporium glendoranum from air in a brick room, Toxicocladosporium losalamitosense from air in a classroom, Valsonectria portsmouthensis from air in men's locker room and Varicosporellopsis americana from sludge in a water reservoir. Vietnam , Entoloma kovalenkoi on rotten wood, Fusarium chuoi inside seed of Musa itinerans , Micropsalliota albofelina on soil in tropical evergreen mixed forests and Phytophthora docyniae from soil and roots of Docynia indica. Morphological and culture characteristics are supported by DNA barcodes. Citation : Crous PW, Osieck ER, Jurjević Ž, et al. 2021. Fungal Planet description sheets: 1284-1382. Persoonia 47: 178-374. https://doi.org/10.3767/persoonia.2021.47.06., (© 2021 Naturalis Biodiversity Center & Westerdijk Fungal Biodiversity Institute.)

Background: The presence of geminivirus sequences in a preliminary analysis of sRNA sequences from the leaves of macadamia trees with abnormal vertical growth (AVG) syndrome was investigated., Results: A locus of endogenous geminiviral elements (EGE) in the macadamia genome was analysed, and the sequences revealed a high level of deletions and/or partial integrations, thus rendering the EGE transcriptionally inactive. The replication defective EGE in the macadamia genome indicates its inability to be the source of new viral infections and thus cause AVG or any other disease in macadamia. The EGE sequences were detected in two edible Macadamia species that constitute commercial cultivars and the wild germplasm of edible and inedible species of Macadamia. This strongly suggests that the integration preceded speciation of the genus Macadamia. A draft genome of a locus of EGE in Macadamia was developed. The findings of this study provide evidence to suggest the endogenization of the geminiviral sequences in the macadamia genome and the ancestral relationship of EGE with Macadamia in the Proteaceae family. Random mutations accumulating in the EGE inform that the sequence is evolving., Conclusions: The EGE in Macadamia is inactive and thus not a direct cause of any diseases or syndromes including AVG in macadamia. The insertion of the EGE in the macadamia genome preceded speciation of the genus Macadamia., (© 2021. The Author(s).)

The genome sequence of a new subgroup C nepovirus from Stenotaphrum secundatum in Australia is described. This virus, tentatively named Stenotaphrum nepovirus (SteNV), was present in separate plants as a mixed infection with either sugarcane mosaic virus or Panicum mosaic virus. The virus genome was divided between two RNA segments, 7,824 and 7,104 nucleotides (nt) in length, which each encode a single long polyprotein with putative 3C-like cysteine protease sites of the type H/G, H/S or L/S. The 3' untranslated region of RNA2, at 2,155 nt, is the longest observed for any subgroup C nepovirus. Phylogenetic analyses using protease-polymerase and coat protein amino acid alignments suggest that SteNV is most closely related to cherry leaf roll virus. Using a newly developed RT-PCR assay, this virus was detected at multiple localities in New South Wales, Queensland and Western Australia, and in a second host species, Digitaria didactyla. No consistent association between virus infection and symptoms could be established. The economic importance, pathogenicity and transmission of this novel virus species warrant further investigation., (Copyright © 2021. Published by Elsevier B.V.)

Endogenous viral elements (EVEs) are widespread in plant genomes. They result from the random integration of viral sequences into host plant genomes by horizontal DNA transfer and have the potential to alter host gene expression. We performed a large-scale search for co-transcripts including caulimovirid and plant sequences in 1,678 plant and 230 algal species and characterized 50 co-transcripts in 45 distinct plant species belonging to lycophytes, ferns, gymnosperms and angiosperms. We found that insertion of badnavirus EVEs along with Ty-1 copia mobile elements occurred into a late blight resistance gene ( R1 ) of brinjal eggplant ( Solanum melongena ) and wild relatives in genus Solanum and disrupted R1 orthologs. EVEs of two previously unreported badnaviruses were identified in the genome of S. melongena , whereas EVEs from an additional novel badnavirus were identified in the genome of S. aethiopicum , the cultivated scarlet eggplant. Insertion of these viruses in the ancestral lineages of the direct wild relatives of the eggplant would have occurred during the last 3 Myr, further supporting the distinctiveness of the group of the eggplant within the giant genus Solanum ., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Serfraz, Sharma, Maumus, Aubriot, Geering and Teycheney.)

A new badnavirus, aucuba ringspot virus (AuRV), was identified in plants of Aucuba japonica showing mild mosaic, vein banding, and yellow ringspot symptoms on the leaves. The complete nucleotide sequence of the AuRV genome was determined and found to be 9,092 nt in length, and the virus was found to have a genome organization typical of members of the genus Badnavirus. ORF3 was predicted to encode a polyprotein containing conserved movement protein, coat protein, aspartic protease, reverse transcriptase (RT), and RNase H domains. Phylogenetic analysis suggested that this virus is most closely related to codonopsis vein clearing virus but belongs to a distinct species, based on only 69.6% nucleotide sequence identity within the part of ORF 3 encoding the RT and RNase H domains. The vector of AuRV is unknown, but based on phylogenetic relationships, it is predicted to be a type of aphid.

The badnavirus replication cycle is poorly understood and most knowledge is based on extrapolations from model viruses such as Cauliflower mosaic virus (CaMV). However, in contrast to CaMV, badnaviruses are thought not to produce viroplasms and therefore it has been a mystery as to where virion assembly occurs. In this study, ultrathin sections of a banana leaf infected with a badnavirus, banana streak MY virus (BSMYV), were examined by transmission electron microscopy. Electron-dense inclusion bodies (EDIBs) were sporadically distributed in parenchymatous tissues of the leaf, most commonly in the palisade and spongy mesophyll cells. These EDIBs had a characteristic structure, comprising an electron-dense core, a single, encircling lacuna and an outer ring of electron-dense material. However, much less frequently, EDIBs with two or three lacunae were observed. In the outer ring, densely packed virions were visible with a shape and size consistent with that expected for badnaviruses. Immunogold labelling was done with primary antibodies that detected the N-terminus of the capsid protein and strong labelling of the outer ring but not the central core or lacuna was observed. It is concluded that the EDIBs that were observed are equivalent in function to the viroplasms of CaMV, although obviously different in composition as there is not a paralogue of the transactivation/viroplasm protein in the badnavirus genome. It is postulated that production of a viroplasm could be a conserved characteristic of all members of the Caulimoviridae .

Caulimoviridae is a family of non-enveloped reverse-transcribing plant viruses with non-covalently closed circular dsDNA genomes of 7.1-9.8 kbp in the order Ortervirales . They infect a wide range of monocots and dicots. Some viruses cause economically important diseases of tropical and subtropical crops. Transmission occurs through insect vectors (aphids, mealybugs, leafhoppers, lace bugs) and grafting. Activation of infectious endogenous viral elements occurs in Musa balbisiana , Petunia hybrida and Nicotiana edwardsonii . However, most endogenous caulimovirids are not infectious. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Caulimoviridae, which is available at ictv.global/report/caulimoviridae.

Australian macadamia production is threatened by a disorder known as abnormal vertical growth (AVG), for which the etiology is unknown. AVG is characterized by vigorous upright growth and reduced lateral branching, flowering, and nut set that results in over 70% yield loss annually. Six commercial macadamia orchards were surveyed in 2012 and again in 2018 to examine spatiotemporal dynamics of the epidemic. Data were subjected to point-pattern and geostatistical analyses. AVG incidence in all orchards showed a better fit to the beta-binomial distribution than the binomial distribution. AVG incidence in the different orchards varied between 5 and 47% in 2012, and 13 and 55% in 2018 and the rate of spread was slow, averaging at about 2% increase in disease incidence per annum. Spatial patterns of AVG were highly aggregated on both survey years and spread was mainly between neighboring trees in a row or trees that were opposite to each other in different rows. Semivariograms showed large range values (approximately 15 to 120), indicating aggregation of AVG-affected trees beyond quadrat levels. Furthermore, clusters of disease were mainly at the edge of the orchard on the first survey date and the disease progressed toward the center of the orchard over time. It is concluded that AVG is caused by an infectious agent, and based on patterns of spread, we hypothesize that spread is facilitated by root grafting or root-to-root contact. Furthermore, a vascular-limited pathogen could be involved that modulates plant hormone production.

The Ambrosia Fusarium Clade (AFC) comprises at least 16 genealogically exclusive species-level lineages within clade 3 of the Fusarium solani species complex (FSSC). These fungi are either known or predicted to be farmed by Asian Euwallacea ambrosia beetles (Coleoptera: Curculionidae: Scolytinae) in the tribe Xyleborini as a source of nutrition. To date, only 4 of the 16 AFC lineages have been described formally. In the absence of Latin binomials, an ad hoc nomenclature was developed to distinguish the 16 species lineages as AF-1 to AF-16. Herein, Fusarium species AF-3, AF-5, and AF-7 were formally described as F. floridanum, F. tuaranense , and F. obliquiseptatum , respectively. Fusarium floridanum farmed by E. interjectus on box elder ( Acer negundo ) in Gainesville, Florida, was distinguished morphologically by the production of sporodochial conidia that were highly variable in size and shape together with greenish-pigmented chlamydospores. Fusarium tuaranense was isolated from a beetle-damaged Paŕa rubber tree ( Hevea brasiliense ) in North Borneo, Malaysia, and was diagnosed by production of the smallest sporodochial conidia of any species within the AFC. Lastly, F. obliquiseptatum was farmed by an unnamed ambrosia beetle designated Euwallacea sp. 3 ( E. fornicatus species complex) on avocado ( Persea americana ) in Queensland, Australia. It uniquely produces some clavate sporodochial conidia with oblique septa. Maximum likelihood analysis of a multilocus data set resolved these three novel AFC taxa as phylogenetically distinct species based on genealogical concordance. Particularly where introduced into exotic environments, these exotic mutualists pose a serious threat to the avocado industry, native forests, and urban landscapes in diverse regions throughout the world.

Garlic mite-borne filamentous virus is one of the oldest recognized allexivirus species but, paradoxically, one with the least well studied member viruses. In this paper, we review the history of this taxon and highlight problems in designating a holotype (exemplar isolate). Analyses are presented that suggest that GarMbFV is conspecific with Garlic virus A, and therefore the former taxon should be abolished.

Uromycladium tepperianum has been reported on over 100 species of Acacia , as well as on the closely related plant genera, Falcataria , Racosperma and Paraserianthes . Previous studies have indicated that U. tepperianum may represent a complex of host-specific, cryptic species. The phylogenetic relationships between 79 specimens of Uromycladium were determined based on a concatenated dataset of the Small Subunit, the Internal Transcribed Spacer and the Large Subunit regions of nuclear ribosomal DNA, and the mitochondrial cytochrome c oxidase subunit 3. This study showed that the host range of U. tepperianum s.str. was restricted to species of Acacia in the ' A. bivenosa group' sensu Chapman & Maslin (1992). An epitype of U. tepperianum on A. ligulata is designated to create a stable taxonomy for the application of this name. Sixteen novel species of Uromycladium are described, based on host preference, morphology and a phylogenetic species concept.

Endogenous viral elements (EVEs) are viral sequences that are integrated in the nuclear genomes of their hosts and are signatures of viral infections that may have occurred millions of years ago. The study of EVEs, coined paleovirology, provides important insights into virus evolution. The Caulimoviridae is the most common group of EVEs in plants, although their presence has often been overlooked in plant genome studies. We have refined methods for the identification of caulimovirid EVEs and interrogated the genomes of a broad diversity of plant taxa, from algae to advanced flowering plants. Evidence is provided that almost every vascular plant (tracheophyte), including the most primitive taxa (clubmosses, ferns and gymnosperms) contains caulimovirid EVEs, many of which represent previously unrecognized evolutionary branches. In angiosperms, EVEs from at least one and as many as five different caulimovirid genera were frequently detected, and florendoviruses were the most widely distributed, followed by petuviruses. From the analysis of the distribution of different caulimovirid genera within different plant species, we propose a working evolutionary scenario in which this family of viruses emerged at latest during Devonian era (approx. 320 million years ago) followed by vertical transmission and by several cross-division host swaps.

Most known mastreviruses (family Geminiviridae) infect members of the grass family, Poaceae. Although the greatest number of grass-infecting mastrevirus species have been discovered in Africa, it is apparent that the ten grass-infecting mastrevirus species that have so far only been discovered in south-east Queensland have a degree of diversity that rivals that observed in Africa. In this study, we have used a deep sequencing approach to identify two new mastrevirus species, tentatively named rice latent virus 1 and 2 (RLV 1 and 2), from two, undescribed wild rice species (Oryza AA genome group) in Cape York Peninsula, Queensland. The sequences of these new viruses had less than 70% identity with any previously identified mastrevirus, and therefore their discovery vastly expands the known diversity of monocot-infecting mastreviruses in Australia. This study also highlights the potential risks of novel crop pathogens emerging from uncultivated grass species, as the wild rice hosts are very closely related to domesticated rice., (Copyright © 2017 Elsevier B.V. All rights reserved.)

This study identified the structural proteins of two badnavirus species, Banana streak MY virus (BSMYV) and Banana streak OL virus (BSOLV), and mapped the distribution of continuous B-cell epitopes. Two different capsid protein (CP) isoforms of about 44 and 40 kDa (CP1 and CP2) and the virion-associated protein (VAP) were consistently associated with purified virions. For both viral species, the N terminus of CP2 was successfully sequenced by Edman degradation but that of CP1 was chemically blocked. De novo peptide sequencing of tryptic digests suggested that CP1 and CP2 derive from the same region of the P3 polyprotein but differ in the length of either the N or the C terminus. A three-dimensional model of the BSMYV-CP was constructed, which showed that the CP is a multi-domain structure, containing homologues of the retroviral capsid and nucleocapsid proteins, as well as a third, intrinsically disordered protein region at the N terminus, henceforth called the NID domain. Using the Pepscan approach, the immunodominant continuous epitopes were mapped to the NID domain for five different species of banana streak virus. Anti-peptide antibodies raised against these epitopes in BSMYV were successfully used for detection of native virions and denatured CPs in serological assays. Immunoelectron microscopy analysis of the virion surface using the anti-peptide antibodies confirmed that the NID domain is exposed on the surface of virions, and that the difference in mass of the two CP isoforms is due to variation in length of the NID domain.

Tomato yellow leaf curl virus (TYLCV) seriously impacts tomato production throughout tropical and sub-tropical regions of the world. It has a broad geographical distribution and continues to spread to new regions in the Indian and Pacific Oceans including Australia, New Caledonia and Mauritius. We undertook a temporally-scaled, phylogeographic analysis of all publicly available, full genome sequences of TYLCV, together with 70 new genome sequences from Australia, Iran and Mauritius. This revealed that whereas epidemics in Australia and China likely originated through multiple independent viral introductions from the East-Asian region around Japan and Korea, the New Caledonian epidemic was seeded by a variant from the Western Mediterranean region and the Mauritian epidemic by a variant from the neighbouring island of Reunion. Finally, we show that inter-continental scale movements of TYLCV to East Asia have, at least temporarily, ceased, whereas long-distance movements to the Americas and Australia are probably still ongoing., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Banana streak disease is caused by several distinct badnavirus species, one of which is Banana streak Obino l'Ewai virus. Banana streak Obino l'Ewai virus has severely hindered international banana (Musa spp.) breeding programmes, as new hybrids are frequently infected with this virus, curtailing any further exploitation. This infection is thought to arise from viral DNA integrated in the nuclear genome of Musa balbisiana (B genome), one of the wild species contributing to many of the banana cultivars currently grown. In order to determine whether the DNA of other badnavirus species is integrated in the Musa genome, PCR-amplified DNA fragments from Musa acuminata, M. balbisiana and Musa schizocarpa, as well as cultivars 'Obino l'Ewai' and 'Klue Tiparot', were cloned. In total, 103 clones were sequenced and all had similarity to open reading frame III in the badnavirus genome, although there was remarkable variation, with 36 distinct sequences being recognized with less than 85 % nucleotide identity to each other. There was no commonality in the sequences amplified from M. acuminata and M. balbisiana, suggesting that integration occurred following the separation of these species. Analysis of rates of non-synonymous and synonymous substitution suggested that the integrated sequences evolved under a high degree of selective constraint as might be expected for a living badnavirus, and that each distinct sequence resulted from an independent integration event.

Gooseberry vein banding disease (GVBD) affects Ribes species and cultivars worldwide. It is the second most important virus-like disease in these crops after black currant reversion disease. In this paper, we describe a bacilliform virus, Gooseberry vein banding associated virus (GVBAV), which is associated closely with GVBD, and provide evidence that GVBAV is a distinct species within the genus Badnavirus. Purified GVBAV particles were ca. 120 × 30 nm in size and contained dsDNA. The sequence of a 1.5-kb DNA fragment amplified from viral genomic DNA was similar to those of a wide range of badnaviruses and contained motifs characteristic of the RNase H domain of the badnavirus open reading frame (ORF) III polyprotein. Phylogenetic analyses suggest that GVBAV is most closely related to Spiraea yellow leaf spot virus. Using sequence derived from the polymerase chain reaction (PCR)-amplified DNA fragment, virus-specific primers were designed. These primers were used in PCR to assay for GVBAV in a range of Ribes germplasm affected with GVBD, with other unrelated virus-like diseases and viruses found in Ribes, and in healthy plants. GVBAV was detected in all of 58 GVBD-affected plants from diverse sources, but not from healthy Ribes plants nor from plants infected with other viruses.