Discordance Down Under: Combining phylogenomics & fungal symbioses to detangle difficult nodes in a diverse tribe of Australian terrestrial orchids.

Orchid mycorrhizal fungi (OMF) associations in the Orchidaceae are thought to have been a major driver of diversification in the family. In the terrestrial orchid tribe Diurideae, it has long been hypothesised that OMF symbiont associations may reflect evolutionary relationships among orchid hosts. Given that recent phylogenomic efforts have been unable to fully resolve relationships among subtribes in the Diurideae, we sought to ascertain whether orchid OMF preferences may lend support to certain phylogenetic hypotheses.

Temporal turnover of Ceratobasidiaceae orchid mycorrhizal fungal communities with ontogenetic and phenological development in Prasophyllum (Orchidaceae).

Background And Aims: Plant-fungus symbioses may experience temporal turnover during the host's ontogenetic or phenological development, which can influence the host plant's ecological requirements. This study investigates temporal turnover of Ceratobasidiaceae orchid mycorrhizal fungal (OMF) communities in Prasophyllum (Orchidaceae), asking if OMF communities are subject to temporal change due to orchid phenology or ontogeny.

Methods: Roots of adult Prasophyllum frenchii, P.

Predominant Clonal Reproduction with Infrequent Genetic Recombination of Phaeoacremonium minimum in Western Cape Vineyards.

Phaeoacremonium minimum is an important esca and Petri disease pathogen that causes dieback of grapevines in South Africa. Little is known regarding the reproductive strategy of the pathogen. Sexual reproduction could lead to a better adaptation of the pathogen to disease management strategies by combining alleles through recombination.

Strong phylogenetic congruence between Tulasnella fungi and their associated Drakaeinae orchids.

The study of congruency between phylogenies of interacting species can provide a powerful approach for understanding the evolutionary history of symbiotic associations. Orchid mycorrhizal fungi can survive independently of orchids making cospeciation unlikely, leading us to predict that any congruence would arise from host-switches to closely related fungal species. The Australasian orchid subtribe Drakaeinae is an iconic group of sexually deceptive orchids that consists of approximately 66 species.

Cryptostylis species (Orchidaceae) from a broad geographic and habitat range associate with a phylogenetically narrow lineage of Tulasnellaceae fungi.

While many Australian terrestrial orchids have highly specialized mycorrhizal associations, we tested the hypothesis that the geographically widespread orchid genus Cryptostylis associates with a diversity of fungal species. Using fungal isolation and molecular approaches, we investigated the mycorrhizal associations of five Australian Cryptostylis species (27 sites sampled) and included limited sampling from three Asiatic Cryptostylis species (two sites). Like related orchid genera, Tulasnellaceae formed the main fungal associations of the Cryptostylis species we sampled, although some ectomycorrhizal, ericoid and saprotrophic fungi were detected infrequently.

New species of associated with Australian terrestrial orchids in the subtribes Megastylidinae and Thelymitrinae.

(Tulasnellaceae) is a genus of fungus that can form mycorrhizal associations with orchids (Orchidaceae). Here we used molecular phylogenetic analyses and morphological characteristics of pure cultures across four different media to support the description of five new species associated with commonly occurring and endangered Australian orchids. associates with with and respectively.

Seven new species associated with Australian terrestrial orchids.

is one of the main fungal genera that form mutualistic associations with species of orchids (Orchidaceae). Here, seven new species associated with various Australian orchid genera are described. These species were originally characterized by multilocus DNA sequence species delimitation analyses (three mtDNA and four nuclear genes) and confirmed as distinct with addition of further isolates and reanalysis of nuc rDNA internal transcribed spacer region ITS1-5.

Continental-scale distribution and diversity of Ceratobasidium orchid mycorrhizal fungi in Australia.

Background And Aims: Mycorrhizal fungi are a critical component of the ecological niche of most plants and can potentially constrain their geographical range. Unlike other types of mycorrhizal fungi, the distributions of orchid mycorrhizal fungi (OMF) at large spatial scales are not well understood. Here, we investigate the distribution and diversity of Ceratobasidium OMF in orchids and soils across the Australian continent.

A multitiered sequence capture strategy spanning broad evolutionary scales: Application for phylogenetic and phylogeographic studies of orchids.

With over 25,000 species, the drivers of diversity in the Orchidaceae remain to be fully understood. Here, we outline a multitiered sequence capture strategy aimed at capturing hundreds of loci to enable phylogenetic resolution from subtribe to subspecific levels in orchids of the tribe Diurideae. For the probe design, we mined subsets of 18 transcriptomes, to give five target sequence sets aimed at the tribe (Sets 1 & 2), subtribe (Set 3), and within subtribe levels (Sets 4 & 5).

Spatial and Temporal Genetic Analyses of in Two Lemon Orchards in South Africa Reveal a Role of Asexual Reproduction Within Sexually Reproducing Populations.

Citrus black spot (CBS), caused by , is a disease that affects citrus worldwide. In different regions of the world where both mating types occur, reports differ as to whether asexually produced pycnidiospores play an important role in the epidemiology of CBS and fruit infections. Therefore, we investigated the potential role of pycnidiospores in two lemon orchards in South Africa by using microsatellite-based analysis of fruit populations over time (two seasons) and space (distance).

New species of associated with Australian terrestrial orchids in the Cryptostylidinae and Drakaeinae.

Many orchids have an obligate relationship with mycorrhizal fungi for seed germination and support into adulthood. Despite the importance of as mycorrhizal partners, many species remain undescribed. Here, we use multiple sequence locus phylogenetic analyses to delimit and describe six new species associated with Australian terrestrial orchids from the subtribes Cryptostylidinae and Drakaeinae.

Specific mycorrhizal associations involving the same fungal taxa in common and threatened Caladenia (Orchidaceae): implications for conservation.

Background And Aims: In orchid conservation, quantifying the specificity of mycorrhizal associations, and establishing which orchid species use the same fungal taxa, is important for sourcing suitable fungi for symbiotic propagation and selecting sites for conservation translocation. For Caladenia subgenus Calonema (Orchidaceae), which contains 58 threatened species, we ask the following questions. (1) How many taxa of Serendipita mycorrhizal fungi do threatened species of Caladenia associate with? (2) Do threatened Caladenia share orchid mycorrhizal fungi with common Caladenia? (3) How geographically widespread are mycorrhizal fungi associated with Caladenia?

Methods: Fungi were isolated from 127 Caladenia species followed by DNA sequencing of the internal transcibed spacer (ITS) sequence locus.

Host specialisation and disparate evolution of Pyrenophora teres f. teres on barley and barley grass.

Background: Pathogens evolve in an arms race, frequently evolving virulence that defeats resistance genes in their hosts. Infection of multiple hosts may accelerate this virulence evolution. Theory predicts that host diversity affects pathogen diversity, with more diverse hosts expected to harbour more diverse pathogens that reproduce sexually.

Matching symbiotic associations of an endangered orchid to habitat to improve conservation outcomes.

Background And Aims: An understanding of mycorrhizal variation, orchid seed germination temperature and the effect of co-occurring plant species could be critical for optimizing conservation translocations of endangered plants with specialized mycorrhizal associations.

Methods: Focusing on the orchid Thelymitra epipactoides, we isolated mycorrhizal fungi from ten plants within each of three sites; Shallow Sands Woodland (SSW), Damp Heathland (DH) and Coastal Heathland Scrub (CHS). Twenty-seven fungal isolates were tested for symbiotic germination under three 24 h temperature cycles: 12 °C for 16 h-16 °C for 8 h, 16 °C for 16 h-24 °C for 8 h or 27 °C constant.

New species of associated with terrestrial orchids in Australia.

Recent studies using sequence data from eight sequence loci and coalescent-based species delimitation methods have revealed several species-level lineages of associated with the orchid genera and in Australia. Here we formally describe three of those species, and spp. nov.

Evidence and Consequence of a Highly Adapted Clonal Haplotype within the Australian Population.

The Australian (Pass.) Labr. (syn.

Weeds, as ancillary hosts, pose disproportionate risk for virulent pathogen transfer to crops.

Background: The outcome of the arms race between hosts and pathogens depends heavily on the interactions between their genetic diversity, population size and transmission ability. Theory predicts that genetically diverse hosts will select for higher virulence and more diverse pathogens than hosts with low genetic diversity. Cultivated hosts typically have lower genetic diversity and thus small effective population sizes, but can potentially harbour large pathogen population sizes.

Defence gene expression profiling to Ascochyta rabiei aggressiveness in chickpea.

Significant differences in defence pathway-related gene expression were observed among chickpea cultivars following A. rabiei infection. Differential gene expression is indicative of diverse resistances, a theoretical tool for selective breeding.

Continent-wide distribution in mycorrhizal fungi: implications for the biogeography of specialized orchids.

Background And Aims: Although mycorrhizal associations are predominantly generalist, specialized mycorrhizal interactions have repeatedly evolved in Orchidaceae, suggesting a potential role in limiting the geographical range of orchid species. In particular, the Australian orchid flora is characterized by high mycorrhizal specialization and short-range endemism. This study investigates the mycorrhizae used by Pheladenia deformis, one of the few orchid species to occur across the Australian continent.

Development of phylogenetic markers for Sebacina (Sebacinaceae) mycorrhizal fungi associated with Australian orchids.

Premise Of The Study: To investigate fungal species identity and diversity in mycorrhizal fungi of order Sebacinales, we developed phylogenetic markers. These new markers will enable future studies investigating species delineation and phylogenetic relationships of the fungal symbionts and facilitate investigations into evolutionary interactions among Sebacina species and their orchid hosts. •

Methods And Results: We generated partial genome sequences for a Sebacina symbiont originating from Caladenia huegelii with 454 genome sequencing and from three symbionts from Eriochilus dilatatus and one from E.

Himalayan-Tibetan plateau uplift drives divergence of polyploid poppies: Meconopsis Viguier (Papaveraceae).

Meconopsis Viguier (Papaveraceae) is an iconic genus of alpine forbs that includes medicinal and ornamental species. This study extends previous phylogenetic analyses of Meconopsis, using ITS sequences representing all the major Meconopsis clades. Phenotypic traits are also analysed for all described species.

Climate, not Aboriginal landscape burning, controlled the historical demography and distribution of fire-sensitive conifer populations across Australia.

Climate and fire are the key environmental factors that shape the distribution and demography of plant populations in Australia. Because of limited palaeoecological records in this arid continent, however, it is unclear as to which factor impacted vegetation more strongly, and what were the roles of fire regime changes owing to human activity and megafaunal extinction (since ca 50 kya). To address these questions, we analysed historical genetic, demographic and distributional changes in a widespread conifer species complex that paradoxically grows in fire-prone regions, yet is very sensitive to fire.

The host bias of three epiphytic Aeridinae orchid species is reflected, but not explained, by mycorrhizal fungal associations.

Premise Of The Study: The three co-occurring epiphytic orchid species, Sarcochilus hillii, Plectorrhiza tridentata, and Sarcochilus parviflorus vary in host specificity; all are found predominantly on the tree Backhousia myrtifolia but some also associate with a broad range of species. Despite this specialization, no fitness advantage has been detected for adult orchid plants growing on the preferred host. Therefore, we predicted that the host specialization of these orchid species is a consequence of a bias toward particular orchid mycorrhizal fungi, which are in turn biased toward particular woody plant species.

Phylogenetic and microsatellite markers for Tulasnella (Tulasnellaceae) mycorrhizal fungi associated with Australian orchids.

Premise Of The Study: Phylogenetic and microsatellite markers were developed for Tulasnella mycorrhizal fungi to investigate fungal species identity and diversity. These markers will be useful in future studies investigating the phylogenetic relationship of the fungal symbionts, specificity of orchid-mycorrhizal associations, and the role of mycorrhizae in orchid speciation within several orchid genera. •

Methods And Results: We generated partial genome sequences of two Tulasnella symbionts originating from Chiloglottis and Drakaea orchid species with 454 genome sequencing.