Browsing by Author "Aylward, Janneke"
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- ItemComparative genomics of Knoxdaviesia species in the Core Cape Subregion(Stellenbosch : Stellenbosch University, 2017-03) Aylward, Janneke; Dreyer, L. L.; Roets, Francois; Steenkamp, Emma T.; Wingfield, Brenda D.; Wingfield, Michael J.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: Knoxdaviesia capensis and K. proteae are saprotrophic fungi that inhabit the seed cones (infructescences) of Protea plants in the Core Cape Subregion (CCR) of South Africa. Arthropods, implicated in the pollination of Protea species, disperse these native fungi from infructescences to young flower heads (inflorescences). Knoxdaviesia proteae is a specialist restricted to one Protea species, while the generalist K. capensis occupies a range of Protea species. Within young flower heads, Knoxdaviesia species grow vegetatively, but switch to sexual reproduction once flower heads mature into enclosed infructescences. Nectar becomes depleted and infructescences are colonised by numerous other organisms, including the arthropod vectors of the fungi. The aim of this dissertation was to study the ecology of K. capensis and K. proteae by making use of their genome sequences. Knoxdaviesia belongs to the family Gondwanamycetaceae, for which no genomes were available at the start of this study. Using Illumina technology, we determined the genome sequences of both CCR Knoxdaviesia species and applied them to investigate reproduction, substrate use and tolerance to competition. Population genetic studies on K. capensis and K. proteae have revealed massive diversity, suggesting an outcrossing reproductive strategy. To determine the genetic basis for this diversity, we used the genomes to identify and characterise their mating type (MAT) loci. Each species contained only a single MAT idiomorph per isolate, indicating that they require an individual of the opposite mating type for sexual reproduction. The MAT loci of the two Knoxdaviesia species were almost identical, reflecting their phylogenetic relatedness. The features of the Knoxdaviesia MAT1-2-7 gene also suggested a historic recombination event between the MAT1-1 and MAT1-2 idiomorphs. The carbon resources that Knoxdaviesia species utilise were investigated with phenome assays and compared to the carbon usage profile of a Protea pathogen, Ceratocystis albifundus. Knoxdaviesia capensis, the generalist, utilised the widest range of substrates, whereas the pathogen utilised the least. The Knoxdaviesia species were able to grow on all monosaccharides that occur in Protea nectar. The predicted proteins in the Knoxdaviesia and C. albifundus genomes suggested that cell wall degradation is important to the nutrition of Knoxdaviesia species in infructescences, whereas the pathogen prefers plant storage polysaccharides. Overall, carbon metabolism in three ecologically different, but related fungi reflected their ecological adaptations. Knoxdaviesia species appear to be effective competitors in infructescences. Few secondary metabolite biosynthesis clusters were, however, detected from the K. capensis and K. proteae genomes. This may suggest that it is the antimicrobial products of Streptomyces bacteria that rid infructescences of fungal competitors. The few secondary metabolite clusters of the Knoxdaviesia species likely produce compounds that enable them to tolerate these bacteria and arthropod and nematode predation. Proteins involved in cell defence were also detected among the predicted secreted proteins of K. capensis and K. proteae. Knoxdaviesia proteae appears to have some non-functional secondary metabolite clusters and secretes less cell defence proteins than K. capensis, suggesting that its specialisation on a single host has resulted in the loss of some functions.
- ItemDiversity and dispersal of the ophiostomatoid fungus, Knoxdaviesia proteae, within Protea repens infructescences(Stellenbosch : Stellenbosch University, 2014-04) Aylward, Janneke; Roets, Francois; Dreyer, L. L.; Steenkamp, Emma T.; Wingfield, Michael J.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: Two genera of ophiostomatoid fungi occur in the seed-bearing structures of serotinous Protea species in the Cape Floristic Region. These fungi are dispersed by arthropods, including mites and beetles that visit the Protea host plants. Although the vectors of Proteaassociated ophiostomatoid fungi are known, their dispersal patterns remain unknown – especially the manner in which recently burnt fynbos vegetation is recolonized. Additionally, their reproduction strategy has not previously been investigated. The focus of this study was, therefore, to determine the extent of within- and between-plant dispersal of Proteaassociated ophiostomatoid fungi at the population level and to investigate their reproductive strategy. One Protea-associated ophiostomatoid fungus, Knoxdaviesia proteae, is found exclusively in the fruiting structures of P. repens and was the focus of this study. In order to interrogate natural populations of this fungus, 12 polymorphic microsatellite markers specific to K. proteae were developed with an ISSR-PCR enrichment strategy and pyrosequencing. These markers were amplified in two distantly separated populations of K. proteae. The genetic and genotypic diversities of both populations were exceptionally high and neither showed significant population differentiation. The lack of population structure in both populations implies that K. proteae individuals within a P. repens stand are in panmixia. As one of the sampling sites had burnt recently, the process whereby young fynbos is recolonized could be investigated. Compared to the adjacent, unburnt area, K. proteae individuals in the burnt area of this population had significantly less private alleles, suggestive of a young population that had experienced a genetic bottleneck. Knoxdaviesia proteae individuals that did not originate from the adjacent unburnt area were encountered within the burnt site and, additionally, isolation-by-distance could not be detected. The parsimony-based haplotype networks and the tests for linkage disequilibrium indicated that recombination is taking place within as well as between the two distantly separated populations. The observed panmixia in P. repens stands, widespread recolonization and the high genetic similarity and number of migrants between the two populations emphasizes long-distance dispersal and therefore the role of beetles in the movement of K. proteae. This cohesive genetic structure and connection across large distances is likely a result of multiple migration events facilitated by beetles carrying numerous phoretic mites.
- ItemGenome sequences of Knoxdaviesia capensis and K. proteae (Fungi: Ascomycota) from Protea trees in South Africa(BioMed Central, 2016) Aylward, Janneke; Steenkamp, Emma T.; Dreyer, Leanne L.; Roets, Francois; Wingfield, Brenda D.; Wingfield, Michael J.Two closely related ophiostomatoid fungi, Knoxdaviesia capensis and K. proteae, inhabit the fruiting structures of certain Protea species indigenous to southern Africa. Although K. capensis occurs in several Protea hosts, K. proteae is confined to P. repens. In this study, the genomes of K. capensis CBS139037 and K. proteae CBS140089 are determined. The genome of K. capensis consists of 35,537,816 bp assembled into 29 scaffolds and 7940 predicted protein-coding genes of which 6192 (77.98 %) could be functionally classified. K. proteae has a similar genome size of 35,489,142 bp that is comprised of 133 scaffolds. A total of 8173 protein-coding genes were predicted for K. proteae and 6093 (74.55 %) of these have functional annotations. The GC-content of both genomes is 52.8 %.
- ItemIMA Genome - F13 : Draft genome sequences of Ambrosiella cleistominuta, Cercospora brassicicola, C. citrullina, Physcia stellaris, and Teratosphaeria pseudoeucalypti(BMC (part of Springer Nature), 2020-09-24) Wilken, P. Markus; Aylward, Janneke; Chand, Ramesh; Grewe, Felix; Lane, Frances A.; Sinha, Shagun; Ametrano, Claudio; Distefano, Isabel; Divakar, Pradeep K.; Duong, Tuan A.; Huhndorf, Sabine; Kharwar, Ravindra N.; Lumbsch, P. Markus; Navathe, Sudhir; Pérez, Carlos A.; Ramírez-Berrutti, Nazaret; Sharma, Rohit; Sun, Yukun; Wingfield, Brenda D.; Wingfield, Michael J.Draft genomes of the fungal species Ambrosiella cleistominuta, Cercospora brassicicola, C. citrullina, Physcia stellaris, and Teratosphaeria pseudoeucalypti are presented. Physcia stellaris is an important lichen forming fungus and Ambrosiella cleistominuta is an ambrosia beetle symbiont. Cercospora brassicicola and C. citrullina are agriculturally relevant plant pathogens that cause leaf-spots in brassicaceous vegetables and cucurbits respectively. Teratosphaeria pseudoeucalypti causes severe leaf blight and defoliation of Eucalyptus trees. These genomes provide a valuable resource for understanding the molecular processes in these economically important fungi.
- ItemIMA Genome-F 11: Draft genome sequences of Fusarium xylarioides, Teratosphaeria gauchensis and T. zuluensis and genome annotation for Ceratocystis fimbriata(BMC (part of Springer Nature), 2019-09-13) Wingfield, Brenda D.; Fourie, Arista; Simpson, Melissa C.; Bushula-Njah, Vuyiswa S.; Aylward, Janneke; Barnes, Irene; Coetzee, Martin P. A.; Dreyer, Leanne L.; Duong, Tuan A.; Geiser, David M.; Roets, Francois; Steenkamp, E. T.; Van Der Nest, Magriet A.; van Heerden, Carel J.; Wingfield, Michael J.ENGLISH ABSTRACT: Draft genomes of the fungal species Fusarium xylarioides, Teratosphaeria gauchensis and T. zuluensis are presented. In addition an annotation of the genome of Ceratocystis fimbriata is presented. Overall these genomes provide a valuable resource for understanding the molecular processes underlying pathogenicity and potential management strategies of these economically important fungi.
- ItemKnoxdaviesia proteae is not the only Knoxdaviesia-symbiont of Protea repens(International Mycological Association, 2015-11-10) Aylward, Janneke; Dreyer, Leanne L.; Steenkamp, Emma T.; Wingfield, Michael J.; Roets, FrancoisTwo polyphyletic genera of ophiostomatoid fungi are symbionts of Proteaceae in southern Africa. One of these, Knoxdaviesia, includes two closely related species, K. proteae and K. capensis, that have overlapping geographical distributions, but are not known to share Protea host species. Knoxdaviesia capensis appears to be a generalist that occupies numerous hosts, but has never been found in P. repens, the only known host of K. proteae. In this study, extensive collections were made from P. repens and isolates were identified using DNA sequence comparisons. This led to the surprising discovery of K. capensis from P. repens for the first time. The fungus was encountered at a low frequency, suggesting that P. repens is not its preferred host, which may explain why it has not previously been found on this plant. The basis for the specialisation of K. proteae and K. capensis on different Protea species remains unknown.
- ItemNine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphila, and C. cf. spartinae, pseudomolecules for the pitch canker pathogen Fusarium circinatum, draft genome of Davidsoniella eucalypti, Grosmannia galeiformis, Quambalaria eucalypti, and Teratosphaeria destructans(International Mycological Association, 2018-12-01) Wingfield, Brenda D.; Liu, Miao; Nguyen, Hai D. T.; Lane, Frances A.; Morgan, Seamus W.; De Vos, Lieschen; Wilken, P. M.; Duong, Tuan A.; Aylward, Janneke; Coetzee, Martin P. A.; Dadej, Kasia; De Beer, Z. W.; Findlay, Wendy; Havenga, Minette; Kolarik, Miroslav; Menzies, Jim G.; Naidoo, Kershney; Pochopski, Olivia; Shoukouhi, Parivash; Santana, Quentin C.; Seifert, Keith A.; Soal, Nicole; Steenkamp, Emma T.; Tatham, Catherine T.; Van Der Nest, Margriet A.; Wingfield, Michael J.This genome announcement includes draft genomes from Claviceps purpurea s.lat., including C. arundinis, C. humidiphila and C. cf. spartinae. The draft genomes of Davidsoniella eucalypti, Quambalaria eucalypti and Teratosphaeria destructans, all three important eucalyptus pathogens, are presented. The insect associate Grosmannia galeiformis is also described. The pine pathogen genome of Fusarium circinatum has been assembled into pseudomolecules, based on additional sequence data and by harnessing the known synteny within the Fusarium fujikuroi species complex. This new assembly of the F. circinatum genome provides 12 pseudomolecules that correspond to the haploid chromosome number of F. circinatum. These are comparable to other chromosomal assemblies within the FFSC and will enable more robust genomic comparisons within this species complex.
- ItemPanmixia defines the genetic diversity of a unique arthropod-dispersed fungus specific to Protea flowers(Wiley Open Access, 2014-09) Aylward, Janneke; Dreyer, Leanne L.; Steenkamp, Emma T.; Wingfield, Michael J.; Roets, FrancoisKnoxdaviesia proteae, a fungus specific to the floral structures of the iconic Cape Floral Kingdom plant, Protea repens, is dispersed by mites phoretic on beetles that pollinate these flowers. Although the vectors of K. proteae have been identified, little is known regarding its patterns of distribution. Seed bearing infructescences of P. repens were sampled from current and previous flowering seasons, from which K. proteae individuals were isolated and cultured. The genotypes of K. proteae isolates were determined using 12 microsatellite markers specific to this species. Genetic diversity indices showed a high level of similarity between K. proteae isolates from the two different infructescence age classes. The heterozygosity of the population was high (0.74 +- 0.04), and exceptional genotypic diversity was encountered (^G = 97.87%). Population differentiation was negligible, owing to the numerous migrants between the infructescence age classes (Nm = 47.83) and between P. repens trees (Nm = 2.96). Parsimony analysis revealed interconnected genotypes, indicative of recombination and homoplasies, and the index of linkage disequilibrium confirmed that outcrossing is prevalent in K. proteae (rd = 0.0067; P = 0.132). The high diversity and panmixia in this population is likely a result of regular gene flow and an outcrossing reproductive strategy. The lack of genetic cohesion between individuals from a single P. repens tree suggests that K. proteae dispersal does not primarily occur over short distances via mites as hypothesized, but rather that longdistance dispersal by beetles plays an important part in the biology of these intriguing fungi.
- ItemA plant pathology perspective of fungal genome sequencing(International Mycological Association, 2017) Aylward, Janneke; Steenkamp, Emma T.; Dreyer, Leanne L.; Roets, Francois; Wingfield, Brenda D.; Wingfield, Michael J.The majority of plant pathogens are fungi and many of these adversely affect food security. This minireview aims to provide an analysis of the plant pathogenic fungi for which genome sequences are publically available, to assess their general genome characteristics, and to consider how genomics has impacted plant pathology. A list of sequenced fungal species was assembled, the taxonomy of all species verified, and the potential reason for sequencing each of the species considered. The genomes of 1090 fungal species are currently (October 2016) in the public domain and this number is rapidly rising. Pathogenic species comprised the largest category (35.5 %) and, amongst these, plant pathogens are predominant. Of the 191 plant pathogenic fungal species with available genomes, 61.3 % cause diseases on food crops, more than half of which are staple crops. The genomes of plant pathogens are slightly larger than those of other fungal species sequenced to date and they contain fewer coding sequences in relation to their genome size. Both of these factors can be attributed to the expansion of repeat elements. Sequenced genomes of plant pathogens provide blueprints from which potential virulence factors were identified and from which genes associated with different pathogenic strategies could be predicted. Genome sequences have also made it possible to evaluate adaptability of pathogen genomes and genomic regions that experience selection pressures. Some genomic patterns, however, remain poorly understood and plant pathogen genomes alone are not sufficient to unravel complex pathogen-host interactions. Genomes, therefore, cannot replace experimental studies that can be complex and tedious. Ultimately, the most promising application lies in using fungal plant pathogen genomics to inform disease management and risk assessment strategies. This will ultimately minimize the risks of future disease outbreaks and assist in preparation for emerging pathogen outbreaks.
- ItemTeratosphaeria stem canker of Eucalyptus : two pathogens, one devastating disease(British Society for Plant Pathology, 2018) Aylward, Janneke; Roets, Francois; Dreyer, Leanne L.; Wingfield, Michael J.Background: Teratosphaeria gauchensis and T. zuluensis are closely related fungi that cause Teratosphaeria (previously Coniothyrium) stem canker disease on Eucalyptus species propagated in plantations for commercial purposes. This disease is present in many countries in which Eucalyptus trees are planted, and continues to spread with the international trade of infected plant germplasm. Taxonomy: Fungi, Ascomycota, Pezizomycotina, Dothideomycetes, Dothideomycetidae, Capnodiales, Teratosphaeriaceae, Teratosphaeria. Identification: The causal agents form dark masses of pycnidia that are visible on the surface of distinct stem cankers that typically form on young green stem tissues. Accurate diagnosis of the causal agents requires DNA sequence data. Host range: Nine species of Eucalyptus are known to be affected. Of these, E. grandis and its hybrids, which include some of the most important planting stock globally, appear to be particularly vulnerable. Disease symptoms: Small necrotic lesions develop on young green stem tissue. These lesions coalesce to form large cankers that exude gum. Epicormic shoots develop below the girdling canker and, in severe cases, trees die.