Molecular phylogenetic studies on Armillaria with specific reference to Southern Hemisphere species

Please read the Summary in the section 00front of this documentThesis (PhD)--University of Pretoria, 2005.GeneticsUnrestricte

Phylogenetic relationships among species of Ganoderma (Ganodermataceae, Basigiomycota) from Cameroon

Ganoderma is an important genus of the Polyporales in the tropics. Identification of tropical species has mainly been based on morphology, which has led to misidentification. This study aimed to elucidate the diversity and phylogenetic relationships of Ganoderma isolates from different hosts in Cameroon using morphological and molecular techniques. Analyses of basidiocarp morphology and the internal transcribed spacer and mitochondria small subunit were undertaken for 28 isolates from five plant species. The results show that the isolates belong to eight species. Three of the species were identified to species level; of these only G. ryvardense has been previously described from Cameroon while G. cupreum and G. weberianum are new records. The five remaining species did not match with any previously described species and have been designated as Ganoderma with different species affinities.Laboratory work for this research was funded by the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa under the Tree Protection Co-operative Program (TPCP) and Centre for Excellence in Tree Health Biotechnology (CTHB). Fieldwork and equipment were sponsored by the Rufford Small Grant for Nature Conservation and Idea Wild Grant.http://www.publish.csiro.au/nid/65.htmhb2017Forestry and Agricultural Biotechnology Institute (FABI)Genetic

Ganoderma species, including new taxa associated with root rot of the iconic Jacaranda mimosifolia in Pretoria, South Africa

Jacaranda mimosifolia trees have been progressively dying due to Ganoderma root and butt rot disease in Pretoria (the “City of Jacarandas”) for many years. Ganoderma austroafricanum was described from these trees previously but this was based on a single collection. This study treats a substantially expanded collection of isolates of Ganoderma made from all dying trees where basidiomes were present in a Pretoria suburb. DNA sequences were obtained from the ITS and LSU region for the isolates and compared against sequences on GenBank. Phylogenetic analyses were used to compare sequences with those for other Ganoderma species. Based on sequence comparisons and morphological characters, two new Ganoderma species were discovered and these are described here as G. enigmaticum and G. destructans spp. nov. Interestingly, the previously described G. austroafricanum was not found, G. enigmaticum was found on only one Ceratonia siliqua tree and G. destructans was found on all other trees sampled. The latter species appears to be the primary cause of root rot of J. mimosifolia in the area sampled.The Department of Science and Technology (DST) – National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology (CTHB).http://www.imafungus.orgam201

Evidence of low levels of genetic diversity for the Phytophthora austrocedrae population in Patagonia, Argentina

Phytophthora austrocedrae is a recently discovered pathogen that causes severe mortality of Austrocedrus chilensis in Patagonia. The high level of susceptibility of the host tree, together with the distribution pattern of the pathogen, have led to the hypothesis that P. austrocedrae was introduced into Argentina. The aim of this study was to assess the population structure of P. austrocedrae isolates from Argentina in order to gain an understanding of the origin and spread of the pathogen. Genetic diversity was determined based on amplified fragment length polymorphisms (AFLPs). In total, 48 isolates of P. austrocedrae were obtained from infected A. chilensis trees, representing the geographical range of the host. Four primer combinations were used for the AFLP analysis. Of the 332 scored bands, 12% were polymorphic. Gene diversity (h) ranged from 0 01 to 0 03; the Shannon index (I) ranged from 0 01 to 0 04. A high degree of genetic similarity was observed among the isolates (pairwise S values = 0 958–1; 0 993 0 009, mean SD). A frequency histogram showed that most of the isolate pairs were identical. Principal coordinate analysis using three-dimensional plots did not group any of the isolates based on their geographical origin. The low genetic diversity (within and between sites) and absence of population structure linked to geographic origin, together with the aggressiveness of the pathogen and the disease progression pattern, suggest that P. austrocedrae might have been introduced into Argentina.The Tree Protection Co-operative Programme (TPCP) and the NRF/DST Centre of Excellence in Tree Health Biotechnology (CTHB), South Africa.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-30592015-02-27hb201

Application of chloroplast phylogenomics to resolve species relationships within the plant genus Amaranthus

Amaranthus species are an emerging and promising nutritious traditional vegetable food source. Morphological plasticity and poorly resolved dendrograms have led to the need for well resolved species phylogenies. We hypothesized that whole chloroplast phylogenomics would result in more reliable differentiation between closely related amaranth species. The aims of the study were therefore: to construct a fully assembled, annotated chloroplast genome sequence of Amaranthus tricolor; to characterize Amaranthus accessions phylogenetically by comparing barcoding genes (matK, rbcL, ITS) with whole chloroplast sequencing; and to use whole chloroplast phylogenomics to resolve deeper phylogenetic relationships. We generated a complete A. tricolor chloroplast sequence of 150,027 bp. The three barcoding genes revealed poor inter- and intra-species resolution with low bootstrap support. Whole chloroplast phylogenomics of 59 Amaranthus accessions increased the number of parsimoniously informative sites from 92 to 481 compared to the barcoding genes, allowing improved separation of amaranth species. Our results support previous findings that two geographically independent domestication events of Amaranthus hybridus likely gave rise to several species within the Hybridus complex, namely Amaranthus dubius, Amaranthus quitensis, Amaranthus caudatus, Amaranthus cruentus and Amaranthus hypochondriacus. Poor resolution of species within the Hybridus complex supports the recent and ongoing domestication within the complex, and highlights the limitation of chloroplast data for resolving recent evolution. The weedy Amaranthus retroflexus and Amaranthus powellii was found to share a common ancestor with the Hybridus complex. Leafy amaranth, Amaranthus tricolor, Amaranthus blitum, Amaranthus viridis and Amaranthus graecizans formed a stable sister lineage to the aforementioned species across the phylogenetic trees. This study demonstrates the power of next-generation sequencing data and reference-based assemblies to resolve phylogenies, and also facilitated the identification of unknown Amaranthus accessions from a local genebank. The informative phylogeny of the Amaranthus genus will aid in selecting accessions for breeding advanced genotypes to satisfy global food demand.The Department of Science and Technology of South Africa, the National Research Foundation and the Professional Development Program of the Agricultural Research Council (ARC) in South Africa.https://link.springer.com/journal/2392019-04-01hj2018Forestry and Agricultural Biotechnology Institute (FABI)GeneticsPlant Production and Soil Scienc

Phylogenetic relationships among biological species of Armillaria from China

Fourteen Chinese Biological Species (CBS) of Armillaria were previously identified in a collection of Chinese isolates. CBS C, F, G, H, J, L, N and O remained unnamed, while the remaining isolates included A. borealis, A. cepistipes, A. gallica, A. mellea, A. sinapina and A. tabescens. CBS F was suggested to represent A. singula based on basidiocarp morphology. In this study, phylogenetic relationships between Chinese Armillaria isolates and those from other parts of the world were determined based on DNA sequence data. Results of this study suggest that CBS F might not represent A. singula, and that A. monadelpha (a name applied to the North American form of A. tabescens by some authors) and A. tabescens should be treated as a single species. Four main phylogenetic lineages, referred to as the A. ostoyae, A. gallica, A. tabescens and A. mellea clusters, were identified on the phylogenetic trees. The unnamed biological species grouped within the “A. gallica cluster” and were phylogenetically closely related. The results of this study contribute to our current understanding of the systematics of Armillaria from South East Asia where these fungi are relatively poorly known.Tree Protection Co-operative Programme (TPCP), the National Research Foundation (NRF), the THRIP initiative of the Department of Trade and Industry and the DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB) South Africa.http://www.elsevier.com/locate/myc2017-09-30hb2016Genetic

Phenolic degradation by catechol dioxygenases is associated with pathogenic fungi with a necrotrophic lifestyle in the Ceratocystidaceae

DATA AVAILABILITY : The datasets used and/or analyzed in this study are available in the NCBI Database (https://www.ncbi.nlm.nih.gov/nucleotide/). Accession numbers are detailed in Table 1.Fungal species of the Ceratocystidaceae grow on their host plants using a variety of different lifestyles, from saprophytic to highly pathogenic. Although many genomes of fungi in the Ceratocystidaceae are publicly available, it is not known how the genes that encode catechol dioxygenases (CDOs), enzymes involved in the degradation of phenolic plant defense compounds, differ among members of the Ceratocystidaceae. The aim of this study was therefore to identify and characterize the genes encoding CDOs in the genomes of Ceratocystidaceae representatives. We found that genes encoding CDOs are more abundant in pathogenic necrotrophic species of the Ceratocystidaceae and less abundant in saprophytic species. The loss of the CDO genes and the associated 3-oxoadipate catabolic pathway appears to have occurred in a lineage-specific manner. Taken together, this study revealed a positive association between CDO gene copy number and fungal lifestyle in Ceratocystidaceae representatives.The National Research Foundation and the Max Planck Society.http://www.g3journal.orgam2023BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyZoology and Entomolog

Single dominant Ganoderma species is responsible for root rot of Acacia mangium and Eucalyptus in Sumatra

Ganoderma root rot is the most serious disease affecting commercially planted Acacia mangium in plantations in Indonesia. Numerous Ganoderma spp. have been recorded from diseased trees of this species and to a lesser extent Eucalyptus, causing confusion regarding the primary cause of the disease. In this study, a large collection of Ganoderma isolates were obtained from the roots of A. mangium showing early signs of root rot in disease centres in South Sumatra plantations. Isolates were also collected from Eucalyptus roots at Lake Toba in North Sumatra showing similar symptoms as well as from sporocarps connected to these samples. Phylogenetic analyses showed that a single Ganoderma sp., identified as G. philippii, is the major causal agent of Ganoderma root rot on A. mangium. Results from this study also showed that the isolates obtained for Eucalyptus trees in North Sumatra belong to G. philippii. Isolates from roots and connected fruiting bodies together with the morphology of the fruiting structures confirmed this identification. Symptoms associated with this pathogen are obvious and it should not be confused with other diseases. Other Ganoderma spp. found in disease centres are considered to be of minor importance and management strategies for root rot should be focused on G. philippii.The Tree Protection Cooperative Programme (TPCP), the National Research Foundation (NRF), the THRIP initiative of the Department of Trade and Industry, and the DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB) South Africahttp://www.tandfonline.com/loi/tsfs20nf201

Nursery-linked plantation outbreaks and evidence for multiple introductions of the pitch canker pathogen Fusarium circinatum into South Africa

In recent years, Pinus plantation forestry has been significantly hampered by outbreaks of pitch canker caused by the fungus Fusarium circinatum. In this study we investigated the role of Pinus host, geographic origin and reproductive mode in structuring the F. circinatum populations in plantations. For this purpose, 159 isolates originating from diseased plantation trees in the Western and Eastern Cape Provinces of South Africa, were genotyped using 10 microsatellite markers. Analyses of these data revealed 30 multilocus haplotypes and that the populations were distinct based on geographic origin as well as host. However, shared haplotypes were observed between populations, showing that these populations are connected possibly through the movement of haplotypes. A second aim was to determine whether the genetic variation found in these populations of the fungus could be attributed to outbreaks of the seedling disease caused by this pathogen in Pinus nurseries. To achieve this goal, an additional set of 43 isolates originating from pine seedling nurseries were genotyped and analysed. The results showed that the populations of F. circinatum in plantations most likely originated from the nursery outbreaks that occurred prior to the plantation outbreak. Inferences regarding reproductive mode further showed that sexual reproduction has little impact on the genetic makeup of the F. circinatum populations and that they primarily reproduce asexually. Overall the results of this study showed that the F. circinatum diversity in South Africa has arisen due to multiple introductions of the pathogen and is not due to sexual reproduction.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-30592017-04-30hb2016Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Analysis of microsatellite markers in the genome of the plant pathogen Ceratocystis fimbriata

Ceratocystis fimbriata sensu lato represents a complex of cryptic and commonly plant pathogenic species that are morphologically similar. Species in this complex have been described using morphological characteristics, intersterility tests and phylogenetics. Microsatellite markers have been useful to study the population structure and origin of some species in the complex. In this study we sequenced the genome of C. fimbriata. This provided an opportunity to mine the genome for microsatellites, to develop new microsatellite markers, and map previously developed markers onto the genome. Over 6000 microsatellites were identified in the genome and their abundance and distribution was determined. Ceratocystis fimbriata has a medium level of microsatellite density and slightly smaller genome when compared with other fungi for which similar microsatellite analyses have been performed. This is the first report of a microsatellite analysis conducted on a genome sequence of a fungal species in the order Microascales. Forty-seven microsatellite markers have been published for population genetic studies, of which 35 could be mapped onto the C. fimbriata genome sequence. We developed an additional ten microsatellite markers within putative genes to differentiate between species in the C. fimbriata s.l. complex. These markers were used to distinguish between 12 species in the complex.The National Research Foundation (NRF), the South African Biosystematics Initiative (SABI), members of the Tree Protection Co-Operative Programme (TPCP), and the Department of Science and Technology (DST)/ NRF Centre of Excellence in Tree Health Biotechnology (CTHB), South Africa.http://www.elsevier.com/locate/funbiohj201