Andrew D W Geering

University of Queensland | UQ · Queensland Alliance for Agriculture and Food Innovation (QAAFI)

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 tw...

Text Abnormal vertical growth is a disease syndrome that affects macadamia, an evergreen tree nut crop. The syndrome is expressed as physiological and morphological aberrations causing significant yield losses to farmers. Based on the symptoms including abnormal elongation and reduced lateral branching and flowering, this study hypothesised that a...

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 h...

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, pe...

The main purpose of the Avocado Nursery Voluntary Accreditation Scheme (ANVAS) in Australia is to prevent the spread of pathogens such as avocado sunblotch viroid (ASBVd) in planting material by implementing rigorous testing regimes for these pathogens during the propagation stages. There can sometimes be significant delays in delivery of a plant s...

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 characte...

Abnormal vertical growth (AVG) is a syndrome that reduces flowering and alters tree architecture, resulting in significant yield losses in macadamia. The epidemiological parameters suggest the cause is likely a biotic agent with the ability to modulate plant hormone production or signalling. To determine if a fungal pathogen is the cause of AVG, we...

Banana bunchy top virus is reported for the first time in Laos. Infected plants showed typical disease symptoms and the two complete genome sequences reported place the isolates in the Southeast Asian subgroup.

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 orcha...

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 p...

Two near complete polerovirus genomes were assembled using high throughput sequencing (HTS) data from two separate samples of garlic cultivar ‘Glenlarge’ grown in Gatton, Queensland, Australia. Whole genome sequence comparisons showed that one contig shared 96.7% nucleotide identity with phasey bean mild yellows virus (MT966032.1) and the other, 99...

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 as...

The complete genome sequence of a member of a novel species of Sadwavirus (family Secoviridae ) infecting pineapple on the island of Oahu, Hawaii was determined by high throughput sequencing. The genome comprised two RNA molecules of 5,956 nt and 3,808 nt in length, excluding the poly-A tails at the 3’ end and each encoding a single large polyprote...

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 surve...

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 or lithium chlo...

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 use...

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...

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 par...

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 2,000 plasmid copies per...

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...

Abnormal vertical growth (AVG) causes significant yield losses to the Australian macadamia industry and the cause is unknown. Studies on the spread of AVG and molecular analysis of trees with AVG symptoms suggest the involvement of a slow spreading pathogen that does not produce copious amount of inoculum nor is spread by flying insects. The possib...

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 a...

Full genome sequences are presented for two isolates of Spartina mottle virus (SpMoV) from two accessions of the hybrid turf grass Cynodon dactylon × Cynodon transvaalensis (Bermuda grass, green couch), originally from the USA but detected during post‐entry quarantine in Australia. Both isolates had a genome of 9346 nucleotides, encoding a single p...

Australian macadamia production is threatened by a disorder known as abnormal vertical growth (AVG), for which the aetiology 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...

Couch smut, caused by Ustilago cynodontis, is an economically important disease of Cynodon dactylon, the most widely planted warm season turfgrass in Australia. The disease is distributed across all states and mainland territories of Australia, and is found worldwide wherever the host plant is present. The most characteristic disease symptoms are e...

Macadamia is a popular tree nut worldwide, and the demand is increasing globally. In Australia, a syndrome known as abnormal vertical growth (AVG) poses a serious threat to macadamia production. AVG is characterized by an upright growth habit, increased vegetative vigour, reduced branching, flowering and nut set, and over 70% reduction in yield. Th...

Changes in the endophytic microbiome of macadamia trees affected by abnormal vertical growth Mohamed C. M. Zakeel, Andrew D. W. Geering and Olufemi A. Akinsanmi Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia Macadamia is a popular tree nut in Aust...

Endogenous viral elements (EVEs) are viral sequences that were captured in the genomes of their hosts through active or passive horizontal gene transfer (HGT). In plants, most characterized EVEs originate from viruses in the family Caulimoviridae. EVEs from a yet unknown genus in the family Caulimoviridae were discovered recently and found to be di...

The United States Department of Agriculture (USDA) Agricultural Research Service (ARS) Subtropical Horticulture Research Station (SHRS) in Miami, FL holds a large germplasm collection of avocado (Persea americana). The recent threat of infection by laurel wilt has encouraged the creation of a backup collection at a disease-free site. Creating the b...

In June 2103, “Candidatus Liberibacter solanacearum” (CLso) (haplotype A) was detected in tomato plants (Solanum lycopersicon) with yellowing symptoms growing on Norfolk Island, non-self-governing external Australian Territory in the western Pacific Ocean. This appears to be only the second record, after New Zealand, of CLso haplotype A outside Nor...

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 d...

A new insight to abnormal vertical growth in macadamia Abnormal vertical growth (AVG) is a severe and wide-spread problem in the Australian macadamia industry. Over ¼ million trees are currently affected in Australia, causing annual yield reduction of 30-88%, depending on the variety affected. Lack of knowledge of the cause has hindered control in...

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,...

We report the first fully sequenced genome of an Australian isolate of Cauliflower mosaic virus. The circular genome is 8022 base pairs in length. A phylogenetic analysis suggests recent common ancestry of this virus isolate with those from Japan and the USA, and origins of the clade in western Europe.

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,...

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 tha...

Evidence for the presence of Chilli ringspot virus and Shallot yellow stripe virus in Laos is provided for the first time. RT-PCR assays to amplify the coat protein genes of these viruses are described.

Papaya ringspot virus is recorded for the first time in Cambodia and confirmed to be present in Laos. An RT-PCR assay to amplify the coat protein gene of this virus is described.

The classification of two root-infecting fungi, Magnaporthe garrettii and M. griffinii, was examined by phylogenetic analysis of multiple gene sequences. This analysis demonstrated that M. garrettii and M. griffinii were sister species that formed a well-supported separate clade in Papulosaceae (Diaporthomycetidae, Sordariomycetes), which clusters...

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 CP isoforms of about 44 and 40 kDa (CP1 and CP2) and the virion-associated protein (VAP) were consistently associated with purified virio...

Collections of rust fungi (Pucciniales) on species of Allium in Australia have previously been identified as Puccinia allii. These identifications are unsatisfactory as P. allii is a species complex that has yet to be taxonomically resolved. Some of the cryptic species in this complex may represent new introductions and have potential biosecurity c...

During surveys of wild and cultivated rice in northern Queensland in 2014 and 2015, 92 fungal isolates were obtained from plants that were afflicted by foliar diseases, including the rice blast pathogen, Pyricularia oryzae, and the brown spot pathogen, Bipolaris oryzae. Seven species of Curvularia were found, viz. Curvularia aeria, C. alcornii, C....

This work reports the complete genome sequence, production of a polyclonal antiserum, and host range of a Brazilian strain of johnsongrass mosaic virus (JGMV) found infecting Panicum maximum in the state of São Paulo, Brazil. The complete genome sequence of this potyvirus, comprising 9874 nucleotides, showed 82 % amino acid sequence identity in the...

Novel species of fungi described in the present study include the following from Australia: Neoseptorioides eucalypti gen. & sp. nov. from Eucalyptus radiata leaves, Phytophthora gondwanensis from soil, Diaporthe tulliensis from rotted stem ends of Theobroma cacao fruit, Diaporthe vawdreyi from fruit rot of Psidium guajava, Magnaporthiopsis agrosti...

Novel species of fungi described in the present study include the following from Australia: Neoseptorioides eucalypti gen. & sp. nov. from Eucalyptus radiata leaves, Phytophthora gondwanensis from soil, Diaporthe tulliensis from rotted stem ends of Theobroma cacao fruit, Diaporthe vawdreyi from fruit rot of Psidium guajava, Magnaporthiopsis agrosti...

The purification of viruses from bananas is a complex and laborious process due to the large quantities of polysaccharides and secondary metabolites in the plant tissue. The banana streak viruses (BSVs) are generally difficult to purify to a level that allows generation of high quality antisera. This study presents an improved method of purificatio...

Novel species of fungi described in the present study include the following from Malaysia: Castanediella eucalypti from Eucalyptus pellita, Codinaea acacia from Acacia mangium, Emarcea eucalyptigena from Eucalyptus brassiana, Myrtapenidiella eucalyptorum from Eucalyptus pellita, Pilidiella eucalyptigena from Eucalyptus brassiana and Strelitziana ma...

Novel species of fungi described in the present study include the following from Malaysia: Castanediella eucalypti from Eucalyptus pellita, Codinaea acacia from Acacia mangium, Emarcea eucalyptigena from Eucalyptus brassiana, Myrtapenidiella eucalyptorum from Eucalyptus pellita, Pilidiella eucalyptigena from Eucalyptus brassiana and Strelitziana ma...

Novel species of fungi described in the present study include the following from Malaysia: Castanediella eucalypti from Eucalyptus pellita, Codinaea acacia from Acacia mangium, Emarcea eucalyptigena from Eucalyptus brassiana, Myrtapenidiella eucalyptorum from Eucalyptus pellita, Pilidiella eucalyptigena from Eucalyptus brassiana and Strelitziana ma...

Endoraecium is a genus of rust fungi that infects several species of Acacia in Australia, South-East Asia and Hawaii. This study investigated the systematics of Endoraecium from 55 specimens in Australia based on a combined morphological and molecular approach. Phylogenetic analyses were conducted on partitioned datasets of loci from ribosomal and...

The extent and importance of endogenous viral elements have been extensively described in animals but are much less well understood in plants. Here we describe a new genus of Caulimoviridae called 'Florendovirus', members of which have colonized the genomes of a large diversity of flowering plants, sometimes at very high copy numbers (>0.5% total g...

Systematic relationships between the rusts on Goodeniaceae and Stylidiaceae were examined using phylogenetic analyses with two loci (internal transcribed spacer, large subunit region) from ribosomal DNA. Fresh specimens and herbarium material of four rust species (Puccinia dampierae, P. gilgiana, P. saccardoi and Uromyces scaevolae) from the Gooden...

Two species of rust fungi, Uredinopsis pteridis on Pteridium esculentum and Desmella aneimiae on Nephrolepis hirsutula, are reported from Australia. These are the first records of rust fungi on species of fern in Australia and the first reports of the genera Uredinopsis and Desmella in Australia.

Family Caulimoviridae comprises seven genera of plant viruses whose members replicate by reverse transcription and whose virions contain double‐stranded deoxyribonucleic acid . In a recent survey of the international scientific community, Cauliflower mosaic virus (CaMV), the type species of the family, was ranked sixth in the world in a list of the...

In 2011, an outbreak of the quarantine-regulated pathogen Potato spindle tuber viroid (PSTVd) occurred in a commercial glasshouse-grown tomato crop in Queensland, Australia. Phylogenetic studies showed that the genotype of this isolate grouped in a cluster of PSTVd genotypes from tomato and Physalis peruviana, and exhibited an interesting mutation...

Efficient and reliable diagnostic tools for the routine indexing and certification of clean propagating material are essential for the management of pospiviroid diseases in horticultural crops. This study describes the development of a true multiplexed diagnostic method for the detection and identification of all nine currently recognized pospiviro...

The gall rusts on Acacia spp. and Paraserianthes falcataria are caused by species of Uromycladium. Morphology and a phylogenetic analysis of four loci from ribosomal (SSU, ITS, LSU) and mitochondrial (CO3) DNA, showed that the rust on P. falcataria differed from U. tepperianum. Uromycladium falcatarium sp. nov. is described to accommodate this taxo...

The cause of blueberry rust in eastern Australia was determined by molecular and morphological analysis as Thekopsora minima.

Background / Purpose: Endoraecium is a rust fungus pathogenic to Acacia. Endoraecium digitatum is a known species complex in Australia. We investigated the systematic relationships between approximately 50 specimens to determine if new species could be defined based on morphology and host. Main conclusion: Endoraecium diversified with Acacia i...

A new approach for the simultaneous identification of the viruses and vectors responsible for tomato yellow leaf curl dis-ease (TYLCD) epidemics is presented. A panel of quantitative multiplexed real-time PCR assays was developed for the sensitive and reliable detection of Tomato yellow leaf curl virus-Israel (TYLCV-IL), Tomato leaf curl virus (ToL...

The genus Musa is not native to Africa. It evolved in tropical Asia, from southwest India eastward to the island of New Guinea. There is a growing circumstantial evidence which suggests that the East African Highland banana and the tropical lowland plantain were cultivated on the African continent since before 1 AD. It is also probable that ABB coo...

The fungal genera Ustilago, Sporisorium and Macalpinomyces represent an unresolved complex. Taxa within the complex often possess characters that occur in more than one genus, creating uncertainty for species placement. Previous studies have indicated that the genera cannot be separated based on morphology alone. Here we chronologically review the...