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Eucalyptus scab and shoot malformation is an emerging disease and a serious threat to the global plantation forestry industry. The disease appeared in North Sumatra (Indonesia) in the early 2010s and the causal agent was recently described as a novel species, Elsinoe necatrix. Nothing is known regarding its possible origin or why it emerged rapidly to cause a serious local epidemic. To investigate its population biology, we developed 15 polymorphic microsatellite markers as well as mating‐type markers using genome sequences for two E. necatrix isolates. Isolates of the pathogen were collected from different host varieties at four locations in the Lake Toba region of North Sumatra and characterized using these markers. A high level of genotypic diversity was observed for all populations with little to no genetic differentiation between sampling areas. Discriminant analysis of principal components, genotype networks and analysis of molecular variance all showed a lack of population structure and a high level of gene flow among sampling regions. Mating‐type ratios and linkage disequilibrium analyses suggest that sexual recombination is likely to be occurring, although a sexual state has not been found for the pathogen. The results of this study highlight the fact that new genotypes of E. necatrix, probably arising from cryptic sexual recombination, will challenge efforts to manage the disease, and that breeding and selection for tolerance will require substantial host genetic diversity. [ABSTRACT FROM AUTHOR]

Pitch canker on plantation‐grown Pinus species, caused by the fungal pathogen Fusarium circinatum, first appeared in the western and southern Cape regions of South Africa. However, outbreaks have subsequently been reported from the major plantation growing regions of KwaZulu‐Natal and Limpopo in the eastern, summer rainfall regions of the country. It is more than 10 years since the last detailed population genetics studies on F. circinatum in the region were conducted. To shed light on the population biology of F. circinatum in this region of South Africa, we used microsatellite markers and mating‐type assays to study a collection of 296 isolates from different nurseries and plantation sites. Our results showed that populations in the region are highly diverse, but strongly interconnected, with various genotypes shared across nursery and plantation collection sites. In contrast to nursery populations, those associated with pitch canker outbreaks were characterized by the presence of relatively small numbers of dominant genotypes that were generally widespread across the region. Opposite mating‐type individuals occurred in most of the isolate collections, but multilocus linkage disequilibrium analyses pointed towards clonality being the main reproductive mode of F. circinatum in the region. Most of the pathogen's genetic variation could probably have resulted from multiple different introductions into the country and more specifically, into the summer rainfall region. Because the spread and establishment of invasive pathogens are typically driven by aggressive clones, the results of this study provide important considerations for current and future Pinus disease management strategies. [ABSTRACT FROM AUTHOR]

Species in the Ceratocystis manginecans complex are important fungal pathogens of plantation trees globally. The most important hosts include species of Eucalyptus, Acacia, Mangifera, and Punica. Despite their relevance and widespread occurrence, little is known regarding their population genetics and how this might relate to their host associations or geographic regions in which they occur. A global collection of 491 isolates representing the C. manginecans complex, from four different plant hosts and nine countries, were genotyped using microsatellite markers. Population genetic analyses using numerous tools were conducted to interrogate how their genetic diversity and structure might be affected by host or areas of occurrence. Results of genetic diversity studies showed that when grouping isolates into populations based on their host associations, the population on Eucalyptus was most diverse, and it also has a broad global distribution. When considering countries of origin as a basis for defining populations, the gene and genotypic diversity were highest in populations from China, Indonesia, and Brazil. In contrast, populations from Oman and Pakistan collected from Mangifera had the lowest genetic diversity and were clonal. Molecular variance, population differentiation, and network and structure analyses showed that the genetic structure of isolates in the C. manginecans complex is influenced by both host association as well as geographical isolation. Furthermore, the results reflected the movement of genotypes between plant hosts and geographic regions that have implications regarding the broad global distribution of this pathogen. [ABSTRACT FROM AUTHOR]

The Eucalyptus foliar pathogen Teratosphaeria destructans causes severe and widespread damage in South‐East Asian and South African plantations. In 2016, leaf blight symptoms resembling those caused by T. destructans were observed in a plantation of a Eucalyptus grandis × E. urophylla hybrid in Sabah, Malaysia. The aims of this study were to confirm the identity of the causal agent as T. destructans and to investigate the genetic structure of isolates associated with this newly detected disease outbreak. Using sequence data of three gene regions, the identity of the pathogen was confirmed as T. destructans. The mating type and microsatellite genotypes of 41 isolates from this Malaysian population were identified and compared with those from previously characterized populations in South‐East Asia and South Africa. The Malaysian population had the highest genotypic diversity of any T. destructans population thus far investigated. Both the mating types were found in the collection of isolates, and these were in approximately equal proportions. Although structures linked to a sexual state of the fungus have not been found, sexual reproduction is theoretically possible and could explain the high genetic diversity in the pathogen that must have been accidentally introduced into Malaysia. This is the first record of T. destructans in Sabah and, to the best of our knowledge, in also other parts of Borneo. [ABSTRACT FROM AUTHOR]

Teratosphaeria foliar pathogens cause leaf and shoot blight on Eucalyptus trees in many parts of the world. Among them, T. destructans is one of the most aggressive pathogens causing defoliation of young Eucalyptus trees in tropic regions. Identification of T. destructans to species level is currently not possible based solely on morphological characteristics or ITS sequence data. The aim of this study was to assess T. destructans microsatellites and a newly developed T. epicoccoides microsatellite as a diagnostic tool to differentiate among T. destructans and several closely related foliar pathogens. Based on the number of markers that amplified, the T. destructans microsatellites allowed for the differentiation of T. destructans, T. epicoccoides,T. eucalypti,T. nubilosa,T. pseudoeucalypti and T. viscidus. These microsatellites provide a rapid and cost‐effective diagnostic tool that will enable the identification of a large number of isolates important in disease surveys and inoculation trials. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Draft genome sequences of five Calonectria species [including Calonectria aciculata, C. crousiana, C. fujianensis, C. honghensis and C. pseudoturangicola], Celoporthe dispersa, Sporothrix phasma and Alectoria sarmentosa are presented. Species of Calonectria are the causal agents of Eucalyptus leaf blight disease, threatening the growth and sustainability of Eucalyptus plantations in China. Celoporthe dispersa is the causal agent of stem canker in native Syzygium cordatum and exotic Tibouchina granulosa in South Africa. Sporothrix phasma was first discovered in the infructescences of Protea laurifolia and Protea neriifolia in South Africa. Alectoria sarmentosa is fruticose lichen belongs to the alectorioid clade of the family Parmeliaceae. The availability of these genome sequences will facilitate future studies on the systematics, population genetics, and genomics of these fungi. [ABSTRACT FROM AUTHOR]

Sirex noctilio is an economically important invasive pest of commercial pine forestry in the Southern Hemisphere. Newly established invasive populations of this woodwasp are characterized by highly male‐biased sex ratios that subsequently revert to those seen in the native range. This trend was not observed in the population of S. noctilio from the summer rainfall regions in South Africa, which remained highly male‐biased for almost a decade. The aim of this study was to determine the cause of this persistent male bias. As an explanation for this pattern, we test hypotheses related to mating success, female investment in male versus female offspring, and genetic diversity affecting diploid male production due to complementary sex determination. We found that 61% of females in a newly established S. noctilio population were mated. Microsatellite data analysis showed that populations of S. noctilio from the summer rainfall regions in South Africa are far less genetically diverse than those from the winter rainfall region, with mean Nei's unbiased gene diversity indexes of 0.056 and 0.273, respectively. These data also identified diploid males at low frequencies in both the winter (5%) and summer (2%) rainfall regions. The results suggest the presence of a complementary sex determination mechanism in S. noctilio, but imply that reduced genetic diversity is not the main driver of the male bias observed in the summer rainfall region. Among all the factors considered, selective investment in sons appears to have the most significant influence on male bias in S. noctilio populations. Why this investment remains different in frontier or early invasive populations is not clear but could be influenced by females laying unfertilized eggs to avoid diploid male production in populations with a high genetic relatedness. [ABSTRACT FROM AUTHOR]

The disease known as pitch canker results from infection of Pinus species by the fungus Fusarium circinatum. This fungus also causes a serious root disease of Pinus seedlings and cuttings in forestry nurseries. Pinus radiata and P. patula are especially susceptible to the pathogen, but there are no records of pitch canker on P. patula in established plantations. To date, only planting material of this tree species in nurseries or in plantations at the time of establishment have been infected by F. circinatum. Symptoms of pitch canker have recently emerged in an established P. patula plantation in South Africa and this study sought to determine whether the symptoms were caused by F. circinatum. Isolates from cankers were identified as F. circinatum using morphology and DNA-based diagnostic markers. Microsatellite markers were then used to determine the genetic diversity of a collection of 52 isolates. The entire population included 17 genotypes representing 30 alleles, with a greater number of genotypes collected from younger (three- to six-year-old) than older (12- to 19-year-old) trees. Both mating types of F. circinatum were present, but no evidence of sexual recombination was inferred from population genetic analyses. This is the first record globally of pitch canker on P. patula trees in managed plantations. It is of significant concern to South Africa, where P. patula is the most important Pinus species utilised for plantation forestry. [ABSTRACT FROM AUTHOR]

Deladenus siricidicola is the primary biocontrol agent of the invasive woodwasp, Sirex noctilio. The nematode is mass-reared in culture on the S. noctilio symbiotic fungus, A. areolatum, but can also be induced to convert into its infective form in culture. The aim of this study was to explore the level of variation among a collection of D. siricidicola strains to convert into the infective form in culture. In addition, we measured variation in growth of the nematode on a strain of A. areolatum that is commonly used for laboratory rearing. Both traits could influence laboratory rearing and efficiency in the field. The 22 strains from three countries showed significant variation in the frequency of conversion into the infective form in culture. Even genetically uniform strains from South Africa displayed a range of variation in this trait. There was also significant variation in the growth of D. siricidicola on A. areolatum. These results emphasise the importance of considering variation in traits in D. siricidicola that could influence a biological control program. They also provide tools that could be used to screen larger collections of D. siricidicola for variation in traits linked to virulence and reproduction. [ABSTRACT FROM AUTHOR]

Exotic forest insects and their symbionts pose an increasing threat to forest health. This is apparently true for the red turpentine beetle ( Dendroctonus valens), which was unintentionally introduced to China, where the beetle has killed millions of healthy native pine trees. Previous population genetics studies that used cytochrome oxidase I as a marker concluded that the source of D. valens in China was western North America. In contrast, surveys of fungi associated with D. valens demonstrated that more fungal species are shared between China and eastern North America than between China and western North America, suggesting that the source population of D. valens could be eastern North America. In this study, we used microsatellite markers to determine population structure of D. valens in North America as well as the source population of the beetle in China. The analyses revealed that four genetically distinct populations (herein named the West, Central, Northeast and Mexico) represent the native range of D. valens. Clustering analyses and a simulation-based approximate Bayesian computation (ABC) approach supported the hypothesis that western North America is the source of the invasive D. valens population. This study provides a demonstration of non-congruence between patterns inferred by studies on population genetics and symbiont assemblages in an invasive bark beetle. [ABSTRACT FROM AUTHOR]

Abstract: Dothistroma septosporum is a haploid fungal pathogen that causes a serious needle blight disease of pines, particularly as an invasive alien species on Pinus radiata in the Southern Hemisphere. During the course of the last two decades, the pathogen has also incited unexpected epidemics on native and non‐native pine hosts in the Northern Hemisphere. Although the biology and ecology of the pathogen has been well documented, there is a distinct lack of knowledge regarding its movement or genetic diversity in many of the countries where it is found. In this study we determined the global population diversity and structure of 458 isolates of D. septosporum from 14 countries on six continents using microsatellite markers. Populations of the pathogen in the Northern Hemisphere, where pines are native, displayed high genetic diversities and included both mating types. Most of the populations from Europe showed evidence for random mating, little population differentiation and gene flow between countries. Populations in North America (USA) and Asia (Bhutan) were genetically distinct but migration between these continents and Europe was evident. In the Southern Hemisphere, the population structure and diversity of D. septosporum reflected the anthropogenic history of the introduction and establishment of plantation forestry, particularly with Pinus radiata. Three introductory lineages in the Southern Hemisphere were observed. Countries in Africa, that have had the longest history of pine introductions, displayed the greatest diversity in the pathogen population, indicating multiple introductions. More recent introductions have occurred separately in South America and Australasia where the pathogen population is currently reproducing clonally due to the presence of only one mating type. [ABSTRACT FROM AUTHOR]

Human-associated introduction of pathogens and consequent invasions is very evident in areas where no related organisms existed before. In areas where related but distinct populations or closely related cryptic species already exist, the invasion process is much harder to unravel. In this study, the population structure of the Eucalyptus leaf pathogen Teratosphaeria nubilosa was studied within its native range in Australia, including both commercial plantations and native forests. A collection of 521 isolates from across its distribution was characterized using eight microsatellite loci, resulting in 112 multilocus haplotypes (MLHs). Multivariate and Bayesian analyses of the population conducted in structure revealed three genetically isolated groups (A, B and C), with no evidence for recombination or hybridization among groups, even when they co-occur in the same plantation. DNA sequence data of the ITS ( n = 32), β-tubulin ( n = 32) and 27 anonymous loci ( n = 16) were consistent with microsatellite data in suggesting that T. nubilosa should be considered as a species complex. Patterns of genetic diversity provided evidence of biological invasions by the pathogen within Australia in the states of Western Australia and New South Wales and helped unravel the pattern of invasion beyond Australia into New Zealand, Brazil and Uruguay. No significant genetic differences in pathogen populations collected in native forests and commercial plantations were observed. This emphasizes the importance of sanitation in the acquisition of nursery stock for the establishment of commercial plantations. [ABSTRACT FROM AUTHOR]

Sexual reproduction in fungi involves either a single individual (selfing) or two individuals (outcrossing). To investigate the roles that these two strategies play in the establishment of an invasive alien pathogen, the Eucalyptus leaf-infecting fungus, Teratosphaeria ( Mycosphaerella) nubilosa was studied. Specifically, the genetic diversity of the pathogen was investigated at micro and macrospatial scales. Interestingly, while data obtained at microspatial scales show clearly that selfing is the main reproductive strategy, at macrospatial scales the population genetic structure was consistent with a genetically outcrossing organism. Additional analyses were performed to explore these apparently discordant results at different spatial scales and to quantify the contribution of selfing vs. outcrossing to the genotypic diversity. The results clearly show that the fungus has a mixed mating strategy. While selfing is the predominant form of mating, outcrosses must have occurred in the pathogen that increased the genotypic diversity of the fungus over time. This mating strategy, coupled with the high levels of geneflow between distant populations of the pathogen, has created an even distribution of maximum diversity from the smallest (leaf) to largest scales (>500 km), which will make breeding for resistance difficult. These data illustrate the evolutionary potential and danger of the introduction of multiple genotypes of a potentially outcrossing pathogen, especially when it has a high dispersal potential. [ABSTRACT FROM AUTHOR]

Ophiostoma ips is a common fungal associate of various conifer-infesting bark beetles in their native ranges and has been introduced into non-native pine plantations in the Southern Hemisphere. In this study, we used 10 microsatellite markers to investigate the population biology of O. ips in native (Cuba, France, Morocco and USA) and non-native (Australia, Chile and South Africa) areas to characterize host specificity, reproductive behaviour, and the potential origin as well as patterns of spread of the fungus and its insect vectors. The markers resolved a total of 41 alleles and 75 haplotypes. Higher genetic diversity was found in the native populations than in the introduced populations. Based on the origin of the insect vectors, the populations of O. ips in Australia would be expected to reflect a North American origin, and those in Chile and South Africa to reflect a European origin. However, most alleles observed in the native European population were also found in the native North American population; only the allele frequencies among the populations varied. This admixture made it impossible to confirm the origin of the introduced Southern Hemisphere (SH) populations of O. ips. There was also no evidence for specificity of the fungus to particular bark beetle vectors or hosts. Although O. ips is thought to be mainly self-fertilizing, evidence for recombination was found in the four native populations surveyed. The higher genetic diversity in the North American than in the European population suggests that North America could be the possible source region of O. ips. [ABSTRACT FROM AUTHOR]

Thielaviopsis basicola is a soil-borne fungal pathogen affecting many important agricultural crops. Little is known regarding the population biology or origin of this pathogen. Polymorphic markers developed for Ceratocystis fimbriata, a species complex phylogenetically closely related to T. basicola, were tested and found not to be useful for T. basicola. In this study 14 primer pairs, seven of which resulted in the amplification of single polymorphic fragments in T. basicola were developed. These primers will enable further studies on this economically important pathogen, and will result in an enhanced understanding of its population structure in different parts of the world. [ABSTRACT FROM AUTHOR]

Population genetic studies play an integral role in understanding the ecology and management of fungal plant pathogens. Such studies for species of Botryosphaeriaceae are hampered by a lack of available markers. Genomic sequences are available for multiple species in this family and they provide excellent resources for the development of population genetic markers. Here we describe highly transferable microsatellite or simple sequence repeat (SSR) markers for species in Lasiodiplodia and Neofusicoccum ; two important and globally distributed members of the Botryosphaeriaceae. These were developed by extracting SSR-containing sequences from available genomes. Seventy-seven markers were developed for Lasiodiplodia and 32 markers were developed for Neofusicoccum. Most of these markers were transferable between species within a genus. Twelve markers tested for fragment length polymorphism in 20 isolates of Lasiodiplodia mahajangana identified between two and nine alleles and gene diversities between 0.18 and 0.83. Eleven markers indicated between two and five alleles for 20 isolates of Neofusicoccum parvum and gene diversities between 0.26 and 0.57. The large number and high transferability of the developed markers will facilitate population studies of a wide range of Lasiodiplodia and Neofusicoccum species associated with tree diseases globally. • 72 and 32 SSR markers were developed for Lasiodiplodia and Neofusicoccum. • Most of the markers were transferable across species in these genera. • A subset of markers were shown to be polymorphic within sample populations. • Transferable SSR markers broadly enable molecular ecology studies in these genera. [ABSTRACT FROM AUTHOR]

Amylostereum areolatum is a wood‐decaying homobasidiomycete fungal symbiont of Sirex noctilio. Together, they cause serious damage to pine plantations in the Southern Hemisphere. The fungus reproduces asexually and is vertically transmitted by S. noctilio females, which results in extensive spread of clones. Specific A. areolatum clones are often dominant in areas invaded by the wasp. This is in contrast with the high diversity and complex invasion pattern of S. noctilio in most of these regions. In South Africa, for example, nuclear and mitochondrial ribosomal loci and vegetative compatibility group (VCG) markers on a small number of isolates have shown that only one genotype is present in the country. The aim of this study was to develop microsatellite markers for A. areolatum and determine the genetic diversity and structure of a relatively large collection of isolates of the fungus in South Africa. From five sequenced A. areolatum genomes, a total of 233 microsatellite primer pairs were designed, of which 57 were polymorphic among the genomes. Eleven of these polymorphic markers were then used in a population genetics study including 55 South African isolates. In a surprising manner, nine multilocus genotypes were found among these isolates, and with no population structure among different regions across South Africa. The single VCG previously identified for isolates from the country clearly do not correspond to a clone. The detected A. areolatum variation has relevance for the biology of the Sirex‐Amylostereum symbiosis, its introduction history into South Africa and its management through biocontrol. The microsatellite primers and data emerging from them also provide powerful tools for the study of A. areolatum populations in other parts of the world. [ABSTRACT FROM AUTHOR]

Lecanosticta acicola is a heterothallic ascomycete that causes brown spot needle blight on native and nonnative Pinus spp. in many regions of the world. In this study we investigated the origin of European L. acicola populations and estimated the level of random mating of the pathogen in affected areas. Part of the elongation factor 1-a gene was sequenced, 11 microsatellite regions were screened, and the mating type idiomorphs were determined for 201 isolates of L. acicola collected from three continents and 17 host species. The isolates from Mexico and Guatemala were unique, highly diverse and could represent cryptic species of Lecanosticta. The isolates from East Asia formed a uniform and discrete group. Two distinct populations were identified in both North America and Europe. Approximate Bayesian computation analyses strongly suggest independent introductions of two populations from North America into Europe. Microsatellite data and mating type distributions indicated random recombination in the populations of North America and Europe. Its intercontinental introduction can most likely be explained as a consequence of the movement of infected plant material. In contrast, the spread of L. acicola within Europe appears to be primarily due to conidial dispersion and probably also ascospore dissemination. [ABSTRACT FROM AUTHOR]

Highlights • The most comprehensive global study of the genetic diversity of D. siricidicola. • Three lineages associated with North America, the Southern Hemisphere and Europe. • An admixed North American and Southern Hemisphere population identified in Chile. • An opportunity exists to augment the reduced diversity in some biocontrol programs. Abstract The nematode Deladenus siricidicola is the primary biological control agent of Sirex noctilio, a globally invading woodwasp pest of Pinus species. Preliminary studies on the diversity of populations of D. siricidicola revealed very low diversity in the Southern Hemisphere where they have been introduced for the purpose of biological control. The potential to augment biocontrol efficacy by increasing genetic diversity in biocontrol programs motivated this study, which investigated the patterns of genetic diversity in D. siricidicola across eight countries, including the presumed native range (Spain), areas of accidental introduction (Canada and the USA) and countries D. siricidicola has been intentionally released (Argentina, Brazil, Chile, New Zealand and South Africa). Nematodes were screened using mitochondrial COI sequence data and twelve microsatellite markers. Analyses of these data identified three distinct lineages from North America (Lineage A), the Southern Hemisphere (Lineage B) and Spain (Lineage C). Strains from Chile were an exception as they appear to represent an admixture of lineages A and B. This suggests a common origin of populations throughout the Southern Hemisphere, with a second introduction from North America into Chile. The introduction into North America is distinct from that in the Southern Hemisphere and probably originated from Europe. It is evident that substantial genetic diversity exists in D. siricidicola globally, which could be exploited to augment the reduced diversity in some populations used in biocontrol programs. [ABSTRACT FROM AUTHOR]

Ophiostoma quercus ( Ascomycota , Ophiostomatales ) is a globally widespread, insect-vectored fungus that colonizes a wide diversity of hardwood and conifer hosts. Although the fungus is considered to be non-pathogenic, it is closely related to the fungi that cause Dutch elm disease. We examined the global diversity of O. quercus based on a ribosomal RNA marker and three unlinked gene regions. The fungus exhibited substantial morphological diversity. In addition, O. quercus had high genetic diversity in every continent from which it was collected, although the fungus was most diverse in Eurasia. There was no evidence of geographical clustering of haplotypes based on phylogenetic and network analyses. In addition, the phylogenetic trees generated based on the different markers were non-congruent. These results suggest that O. quercus has been repeatedly moved around the globe, because of trade in wood products, and that the fungal species most likely outcrosses regularly. The high genetic diversity of the fungus, as well as its ability to utilize a wide variety of arthropod vectors and colonize a tremendous diversity of tree host species makes O. quercus truly unique among ophiostomatoid fungi. [ABSTRACT FROM AUTHOR]

Abstract: This study considers the population diversity and structure of Diplodia pinea in South Africa at different spatial scales from single trees to plantations, as well as comparing infections on healthy and diseased trees. A total of 236 isolates were characterized using 13 microsatellite markers. Analysis of these markers confirmed previous results that D. pinea has a high level of gene and genotypic diversity in South Africa, with the latter values ranging from 6% to 68% for the different plantations. The data also reflect a fungus with randomly associated alleles in populations at local plantation scales and for the population as a whole. These results suggest that recombination is occurring in D. pinea and that it most likely has a cryptic sexual state. The study also reveals the sources of endophytic infection and stress related disease out-breaks as diverse infections that have occurred over a long time period. In contrast, wound-associated die-back appears to be caused by clones of the pathogen occurring in narrow time frames. [Copyright &y& Elsevier]