The majority of plant pathogens are fungi and many of these adversely affect food security. This mini-review 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.

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.

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Summary 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. Useful websites Mycobank, https://www.mycobank.org ; Publications of the Forestry and Agricultural Biotechnology Institute (FABI), https://www.fabinet.up.ac.za/index.php/journals .

Knoxdaviesia 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 (Ĝ = 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 ( = 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 long-distance dispersal by beetles plays an important part in the biology of these intriguing fungi.

The aggressive Eucalyptus leaf pathogen, Teratosphaeria destructans, causes widespread damage in tropical and subtropical Eucalyptus‐growing regions of Indonesia, China, Thailand, East Timor, Vietnam, Lao, and South Africa. Little is known regarding the origin, pathways of dispersal, or reproductive biology of this pathogen. The aim of this study was to investigate the genetic structure of a global collection of T. destructans isolates. This was achieved by developing and using polymorphic microsatellite markers. Low genotypic diversity and a limited number of private alleles were found in all investigated populations, with the highest maximum diversity of 10.7% in isolates from South Sumatra. This supports the hypothesis that T. destructans was introduced to these regions. High levels of clonality were common in all populations, especially in isolates sampled from the recent disease outbreak in South Africa, which were all identical. The global collection of isolates grouped into three distinct clusters, corresponding largely to their sampled regions. Low levels of genotypic diversity, high levels of clonality, and strong geographic structure suggest independent introductions into all the sampled areas from an unknown source. The results imply that strict biosecurity measures are needed to avoid introductions of additional genotypes in these areas.

Knoxdaviesia proteae is one of the first native ophiostomatoid fungi discovered in South Africa, where it consistently occurs in the infructescences of the iconic Cape Biome plant, Protea repens. Although numerous studies have been undertaken to better understand the ecology of K. proteae, many questions remain to be answered, particularly given its unique niche and association with arthropods for dispersal. We describe the development and distribution of microsatellite markers in K. proteae through Interspersed Simple Seqeunce Repeat-Polymerase Chain Reaction (ISSR-PCR) enrichment and pyrosequencing. A large proportion of the 31492 sequences obtained from sequencing the enriched genomic DNA were characterized by microsatellites consisting of short tandem repeats and di-and trinucleotide motifs. Seventeen percent of these microsatellites contained flanking regions 2 sufficient for primer design. Twenty-three primer pairs were tested, of which 13 amplified and 12 generated polymorphic fragments in K. proteae. Half of these could be transferred to the sister species, K. capensis. The developed markers will be used to investigate the reproductive strategy, genetic diversity and dispersal strategies of K.proteae.

The Fynbos Biome in the Core Cape Subregion of South Africa is prone to recurrent fires that can clear vast areas of vegetation. Between periods of fire, ophiostomatoid fungi colonize the fruiting structures of serotinous Protea species through arthropod-mediated dispersal. Using microsatellite markers, this study considered the process whereby a Protea-associated ophiostomatoid fungus, Knoxdaviesia proteae, recolonizes a burnt area. The genetic diversity, composition and structure of fungal populations from young P. repens plants in a recently burnt area were compared to populations from the adjacent, unburnt Protea population. The only difference between K. proteae populations from the two areas was found in the number of private alleles, which was significantly higher in the unburnt population. The population structure, although weak, indicated that most K. proteae 1 individuals from recently burnt areas originated from the unburnt population. However, individuals from unsampled source populations were also detected. This, together with the lack of isolation-by-distance across the landscape, suggested that long-distance dispersal is important for K. proteae to recolonize burnt areas. Similarly, the high level of gene flow and low differentiation observed between two distantly separated K. proteae populations also supported the existence of long-distance dispersal. The genetic cohesiveness of populations over long distances and the genetic diversity within populations could be attributed to frequent multiple fungal migration events mediated primarily by arthropods but, potentially, also by birds.