Taxonomy of mayapple rust: the genus Allodus resurrected

Mayapple rust is a common, disfiguring disease that is widespread in temperate eastern North America wherever the host, Podophyllum peltatum, occurs. Puccinia podophylli, the etiological agent of this rust, has been shown to be distantly related to both Puccinia and Uromyces as exemplified by their types. A systematic study was made to determine the generic classification of P. podophylli. Phylogenetic analyses of two rDNA loci from multiple specimens support the recognition of this taxon as a separate genus of Pucciniaceae. Based on historical literature and type material, P. podophylli was found to represent the type of the forgotten genus Allodus and it is correctly named Allodus podophylli. A neotype is designated for Puccinia podophylli Schwein. (; Allodus podophylli) and a lectotype is designated for Aecidium podophylli

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

Alfalfa plants in the field can display a range of virus-like symptoms, especially when grown over many years for seed production. Most known alfalfa viruses have RNA genomes, some of which can be detected using diagnostic assays, but many viruses of alfalfa are not well characterized. This study aims to identify the RNA and DNA virus complexes associated with alfalfa plants in Australia. To maximize the detection of RNA viruses, we purified double-stranded RNA (dsRNA) for high throughput sequencing and characterized the viromes of ten alfalfa samples that showed diverse virus-like symptoms. Using Illumina sequencing of tagged cDNA libraries from immune-captured dsRNA, we identified sequences of the single-stranded RNA viruses, alfalfa mosaic virus (AMV), bean leafroll virus, a new emaravirus tentatively named alfalfa ringspot-associated virus, and persistent dsRNA viruses belonging to the families Amalgaviridae and Partitiviridae. Furthermore, rolling circle amplification and restriction enzyme digestion revealed the complete genome of chickpea chlorosis Australia virus, a mastrevirus (family Geminiviridae) previously reported only from chickpea and French bean that was 97% identical to the chickpea isolate. The sequence data also enabled the assembly of the first complete genome (RNAs 1–3) of an Australian AMV isolate from alfalfa

The PhyloCode applied to Cintractiellales, a new order of smut fungi with unresolved phylogenetic relationships in the Ustilaginomycotina

The PhyloCode is used to classify taxa based on their relation to a most recent common ancestor as recovered from a phylogenetic analysis. We examined the first specimen of Cintractiella (Ustilaginomycotina) collected from Australia and determined its systematic relationship to other Fungi. Three ribosomal DNA loci were analysed both with and without constraint to a phylogenomic hypothesis of the Ustilaginomycotina. Cintractiella did not share a most recent common ancestor with other orders of smut fungi. We used the PhyloCode to define the Cintractiellales, a monogeneric order with four species of Cintractiella, including C. scirpodendri sp. nov. on Scirpodendron ghaeri. The Cintractiellales may have shared a most recent common ancestor with the Malasseziomycetes, but are otherwise unresolved at the rank of class.https://fuse-journal.orghj2021Forestry and Agricultural Biotechnology Institute (FABI)Plant Production and Soil Scienc

Epidemic spread of smut fungi (Quambalaria) by sexual reproduction in a native pathosystem

Quambalaria are fungal pathogens of Corymbia, Eucalyptus and related genera of Myrtaceae. They are smut fungi (Ustilaginomycota) described from structures that resemble conidia and conidiophores. Whether these spore forms have asexual or sexual roles in life cycles of Quambalaria is unknown. An epidemic of Q. pitereka destroyed plantations of Corymbia in New South Wales and Queensland (Australia) in 2008. We sampled 177 individuals from three plantations of C. variegata and used AFLPs to test hypotheses that the epidemic was spread by asexual reproduction and dominated by a single genotype. There was high genotypic diversity across ≥600 AFLP loci in the pathogen populations at each plantation, and evidence of sexual reproduction based on neighbour-net analyses and rejection of linkage disequilibrium. The populations were not structured by host or location. Our data did not support a hypothesis of asexual reproduction but instead that Q. pitereka spreads exclusively by sexual reproduction, similar to life cycles of other smut fungi. Epidemics were exacerbated by monocultures of Corymbia established from seed collected from a single provenance. This study showcases an example of an endemic pathogen, Q. pitereka, with a strictly outbreeding life cycle that has caused epidemics when susceptible hosts were planted in large monoculture plantations

Uromycladium acaciae, the cause of a sudden, severe disease epidemic on Acacia mearnsii in South Africa

A severe rust disease has caused extensive damage to plantation grown Acacia mearnsii trees in the KwaZulu- Natal Province of South Africa since 2013. The symptoms are characterized by leaf spots, petiole and rachis deformation, defoliation, gummosis, stunting of affected trees and dieback of seedlings. The cause of this new disease was identified using a combined morphological and DNA sequence approach. Based on morphology, the rust fungus was identified as a species of Uromycladium. It formed powdery, brown telia on petioles, stems, leaves, seedpods and trunks of affected trees. The teliospores were two per pedicel and either lacked or had a collapsed sterile vesicle. Sequence data and morphology showed that the collections from South Africa were conspecific, however telia were not produced in all provinces. Uromycladium acaciae is the most suitable name for this rust fungus, based on morphology and phylogenetic analyses of the internal transcribed spacer and large subunit regions of ribosomal DNA. The rust was first identified as U. alpinum in 1988, from minor symptoms on the leaflets caused by its uredinial stage on A. mearnsii in South Africa. It has now become a threat to plantations of A. mearnsii, with an altered life cycle and increased disease severity.Tree Protection Cooperative Programme (TPCP), the THRIP initiative of the Department of Trade and Industry, and the Department of Science and Technology (DST) / National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology (CTHB).http://link.springer.com/journal/133132016-11-30hb201

Sexual reproduction is the null hypothesis for life cycles of rust fungi

Sexual reproduction, mutation, and reassortment of nuclei increase genotypic diversity in rust fungi. Sexual reproduction is inherent to rust fungi, coupled with their coevolved plant hosts in native pathosystems. Rust fungi are hypothesised to exchange nuclei by somatic hybridisation with an outcome of increased genotypic diversity, independent of sexual reproduction. We provide criteria to demonstrate whether somatic exchange has occurred, including knowledge of parental haplotypes and rejection of fertilisation in normal rust life cycles

Genetic diversity and recombination between turnip yellows virus strains in Australia

Disease outbreaks caused by turnip yellows virus (TuYV), a member of the genus Polerovirus, family Luteoviridae, regularly occur in canola and pulse crops throughout Australia. To understand the genetic diversity of TuYV for resistance breeding and management, genome sequences of 28 TuYV isolates from different hosts and locations were determined using high-throughput sequencing (HTS). We aimed to identify the parts of the genome that were most variable and clarify the taxonomy of viruses related to TuYV. Poleroviruses contain seven open reading frames (ORFs): ORF 0–2, 3a, and 3–5. Phylogenetic analysis based on the genome sequences, including isolates of TuYV and brassica yellows virus (BrYV) from the GenBank database, showed that most genetic variation among isolates occurred in ORF 5, followed by ORF 0 and ORF 3a. Phylogenetic analysis of ORF 5 revealed three TuYV groups; P5 group 1 and group 3 shared 45–49% amino acid sequence identity, and group 2 is a recombinant between the other two. Phylogenomic analysis of the concatenated ORFs showed that TuYV is paraphyletic with respect to BrYV, and together these taxa form a well-supported monophyletic group. Our results support the hypothesis that TuYV and BrYV belong to the same species and that the phylogenetic topologies of ORF 0, 3a and 5 are incongruent and may not be informative for species demarcation. A number of beet western yellow virus (BWYV)- and TuYV-associated RNAs (aRNA) were also identified by HTS for the first time in Australia

Population genomics reveals historical and ongoing recombination in the Fusarium oxysporum species complex

The Fusarium oxysporum species complex (FOSC) is a group of closely related plant pathogens long-considered strictly clonal, as sexual stages have never been recorded. Several studies have questioned whether recombination occurs in FOSC, and if it occurs its nature and frequency are unknown. We analysed 410 assembled genomes to answer whether FOSC diversified by occasional sexual reproduction interspersed with numerous cycles of asexual reproduction akin to a model of predominant clonal evolution (PCE). We tested the hypothesis that sexual reproduction occurred in the evolutionary history of FOSC by examining the distribution of idiomorphs at the mating locus, phylogenetic conflict and independent measures of recombination from genome-wide SNPs and genes. A phylogenomic dataset of 40 single copy orthologs was used to define structure a priori within FOSC based on genealogical concordance. Recombination within FOSC was tested using the pairwise homoplasy index and divergence ages were estimated by molecular dating. We called SNPs from assembled genomes using a k-mer approach and tested for significant linkage disequilibrium as an indication of PCE. We clone-corrected and tested whether SNPs were randomly associated as an indication of recombination. Our analyses provide evidence for sexual or parasexual reproduction within, but not between, clades of FOSC that diversified from a most recent common ancestor about 500 000 years ago. There was no evidence of substructure based on geography or host that might indicate how clades diversified. Competing evolutionary hypotheses for FOSC are discussed in the context of our results.The University of Queensland Development Fellowships, the Department of the Environment and Energy under the Australian Biological Resources Study; the Tree Protection Co-operative Programme (TPCP), the National Research Foundation of South Africa and the DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB).http://www.studiesinmycology.orgam2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Host jumps shaped the diversity of extant rust fungi (Pucciniales)

* The aim of this study was to determine the evolutionary time line for rust fungi and date key speciation events using a molecular clock. Evidence is provided that supports a contemporary view for a recent origin of rust fungi, with a common ancestor on a flowering plant. * Divergence times for > 20 genera of rust fungi were studied with Bayesian evolutionary analyses. A relaxed molecular clock was applied to ribosomal and mitochondrial genes, calibrated against estimated divergence times for the hosts of rust fungi, such as Acacia (Fabaceae), angiosperms and the cupressophytes. * Results showed that rust fungi shared a most recent common ancestor with a mean age between 113 and 115 million yr. This dates rust fungi to the Cretaceous period, which is much younger than previous estimations. Host jumps, whether taxonomically large or between host genera in the same family, most probably shaped the diversity of rust genera. Likewise, species diversified by host shifts (through coevolution) or via subsequent host jumps. This is in contrast to strict coevolution with their hosts. * Puccinia psidii was recovered in Sphaerophragmiaceae, a family distinct from Raveneliaceae, which were regarded as confamilial in previous studies

The pandemic strain of Austropuccinia psidii causes myrtle rust in New Zealand and Singapore

The myrtle rust pathogen, Austropuccinia psidii, was recently detected in New Zealand and Singapore. We used microsatellite markers to identify the strain of A. psidii that caused these incursions. Our results show that the pandemic strain of the pathogen caused outbreaks in both New Zealand and Singapore.The Tree Protection Co-operative Programme (TPCP) and the National Research Foundation of South Africa (Grant specific unique reference numbers UID 78566 and UID 83924) and the DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB). ARM acknowledges the University of Queensland Development Fellowships (UQFEL1718905) and support from the Department of the Environment and Energy under the Australian Biological Resources Study (grant number RG18-43). WHH and BJRA acknowledge the support from the Ministry for Primary Industries (MPI) Plant Health and Environment Laboratory and the MPI Myrtle Rust Response Team.http://link.springer.com/journal/133132020-05-01hj2020BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyPlant Production and Soil Scienc