Understanding the global population genetics of Diplodia pinea and its life cycle in plantation pines

This study has significantly broadened and deepened the understanding of ecological aspects related to the spread and reproduction of Diplodia pinea as an endophyte, latent pathogen and causal agent of serious disease problems in plantations of Pinus spp. Analyses of genetic diversity in populations using microsatellite data has revealed very high levels of genetic diversity of populations of the pathogen at different spatial levels, ranging from within a single asymptomatic tree to within and between plantations over large geographic areas and in different countries where the fungus has been introduced. Analysis of the structure of the distribution of genotypes and the association of alleles within populations, suggest that sexual recombination is occurring in most environments in the Southern Hemisphere D. pinea populations. This indicates the presence of a cryptic sexual state in this fungus. The genetic diversity was structured and differentiated for regions separated by as little as 65 km to a country and continental scale. The diversity and likely sexual reproduction of D. pinea must complicate control strategies such as selection and breeding for resistance. It is thus essential to strengthen quarantine services aimed at minimizing the risk of introducing additional genotypes of D. pinea. In this regard, understanding the infection and spread between regions is essential. Results of this study demonstrate that this fungus infects seeds, but only at low levels, and is not transmitted vertically via seeds to seedlings. Diplodia pinea was also not isolated from seedlings in three commercial nurseries and open fields in South Africa. These results provide strong evidence that neither seeds nor seedlings are the primary sources of inoculum, but that the pathogen is mainly transmitted horizontally from mature trees and debris left in plantations. Finally extensive sampling conducted as part of this study led to the discovery of the sibling species, D. scrobiculata in South Africa and outside the Northern Hemisphere for the first time.Thesis (PhD)--University of Pretoria, 2011.GeneticsUnrestricte

Draft genome sequence of Alternaria alternata isolated from onion leaves in South Africa

Alternaria alternata (Fr.) Keissler strain PPRI 21032 was isolated from onion leaves collected in Roodeplaat, Pretoria, South Africa. The whole genome of this strain was sequenced and produced a total of 33.12 Mb with a GC content of 50.9%. The whole genome comprises 11,701 predicted coding sequences.The Agricultural Research Council (ARC) of South Africa and the World Vegetable Center core donors [Republic of China (Taiwan), UK Department for International Development (DFID), United States Agency for International Development (USAID), Australian Centre for International Agricultural Research (ACIAR), Germany, Thailand, Philippines, Korea, and Japan].http://genomea.asm.orgam2017Forestry and Agricultural Biotechnology Institute (FABI)Microbiology and Plant Patholog

High levels of genetic diversity and cryptic recombination is widespread in introduced Diplodia pinea populations

Introduced populations of organisms typically have reduced diversity compared to those that are native. It is, therefore, unusual that introduced populations of the fungal tree pathogen Diplodia pinea have been shown to have high levels of genetic diversity, even surpassing diversity in some native regions. This is thought to be due to multiple introductions over time or the existence of a cryptic and yet undiscovered sexual cycle. In this study, we consider whether populations of D. pinea in Southern Hemisphere countries have similar patterns of diversity, share some level of genetic identity and how they might be influenced by sexual recombination. A total of 173 isolates from Argentina, Australia, Ethiopia and South Africa were characterized using 12 microsatellite markers. The results show that all these populations have high gene and genotype diversities, with the Australian population having the lowest diversity. Very few private alleles were found, suggesting that isolates from different countries might share a source of introduction. However, based on allele distribution and frequency, each of the populations appeared to be evolving independently. The results showed that in all but the Australian population, alleles are randomly associated, suggesting that widespread sexual recombination has influenced population structure.The DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB), members of the Tree Protection Co-operative Program (TPCP) and the International Foundation for Sciences, Stockholm, Sweden, through a grant to Wubetu Bihon.http://link.springer.com/journal/13313hb2017Geography, Geoinformatics and MeteorologyGeolog

MAT gene idiomorphs suggest a heterothallic sexual cycle in a predominantly asexual and important pine pathogen

Diplodia pinea (=Sphaeropsis sapinea) is a well-known and economically important latent pathogen of Pinus spp. in many parts of the world. Despite intensive scrutiny, its sexual state has never been observed and the fungus has thus been considered exclusively asexual. It was, therefore, surprising that a recent population genetics study showed high genotypic diversity and random association of alleles in a number of populations, suggesting that the pathogen has a cryptic sexual stage. Using the genome sequence of two individual D. pinea isolates, we interrogated the structure of the MAT locus in this fungus. The results suggested that D. pinea is heterothallic (self-sterile) with complete and apparently functional copies of the MAT genes containing the a-1 and HMG domains present in different isolates. In addition to the MAT1-2-1 and MAT1-1-1 genes, we found a MAT1-1-4 gene in the MAT1-1 idiomorph and a novel MAT1-2-5 gene in the MAT1-2 idiomorph. Importantly, the frequencies of occurrence of both idiomorphs in populations examined were not significantly different from a 1:1 ratio, which would be expected in sexually reproducing populations. Although the sexual state has never been observed, the results strongly suggest that D. pinea has a cryptic, heterothallic sexual cycle.Department of Science and Technology (DST)/National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology, members of the Tree Protection Cooperative Program (TPCP) and Genomics Research Institute (University of Pretoria Institutional Research Theme).Claude Leon Foundation.http://www.elsevier.com/locate/yfgbihb201

Growing apple (Malus domestica) under tropical mountain climate conditions in Northern Ethiopia

Lack of effective chilling during the dormant season is one of the major problems when apples are growing under a tropical climate. We evaluated the response of different apple cultivars (Golden Delicious, Gala, Fuji, Granny Smith and Jonagold) grown on M9 rootstock with different dormancy-management practices. The trials were carried out between 2004 and 2006 in a tropical mountain area (Tigray, Ethiopia), where chilling conditions are poor with the aim of improving and synchronizing the bud break and the blossoming period of these apple cultivars. Two-year-old well-feathered trees were planted in two experimental trial sites in it randomized complete block design. Trees were subjected to the following treatments in two sets of experiments: one defoliation per year only; two defoliations per year, one defoliation followed by 1% hydrogen cyanamide (Dormex) treatment; one defoliation followed by 2% Dormex treatment; one defoliation followed by 40% winter oil; one defoliation followed by 0.5% Dormex and 2% winter oil; and a control with no defoliation or dormancy breaking treatments. The result show positive effects of the dormancy breaking agents oil the productivity of the trees after defoliation, with comparable results for the effectiveness of both Dormex and winter oil. There were On statistically significant differences between the Dormex closes. The defoliation treatment alone Was not sufficient to break dormancy for the cultivars Golden Delicious, Granny Smith or Gala but showed promising results with dormancy breaking Jonagold. Yields increased as a result of better flowering time synchronization within a tree but even with the dormancy treatments the length of the flowering period was still spread over five weeks, where under it more temperate climate it lasted two to three weeks. The average fruit weight of Jonagold and Granny Smith can be considered as it good fruit quality while the fruit of other diploid cultivars like Golden, Gala and Fuji were rather small, which indicates chat fruit thinning by hand will be it necessity For these cultivars. Red colouration of the apples oil the cultivars Gala and Jonagold was excellent and meets the standards necessary for commercialization of these fruits. The sugar concentration of the fruits and the fruit firmness at harvest was high. The results of these first trials indicate that it is possible to develop new apple production in the mountain region of Tigray, Ethiopia

Assessment of pesticide residues in vegetables produced in central and eastern Ethiopia

Background: In Ethiopia, pesticides are widely used in vegetable production. However, if used incorrectly they may harm consumers of vegetables contaminated with pesticide residues, as well as producers handling the pesticides and lead to ecological damage. We performed a cross-sectional survey to assess pesticide residues in vegetables produced in central and eastern Ethiopia. Methods: A total of 232 vegetable samples (91 tomatoes, 106 cabbages and 35 Swiss chard) were collected from fields and retail markets, and were screened for 35 pesticides (16 organochlorine, 11 organophosphate, 3 pyrethroids, 2 carbamates and 3 other agrochemicals) using GC–MS analysis. Results: Pesticides residues were detected in 60% of Swiss chard, 47% of cabbage and 45% of tomato samples. Two or more pesticides were detected in 20% of cabbages, 13% of tomatoes and over half of Swiss chard samples. Bendiocarb, diazinon, endrin, piperonyl butoxide, profenofos and propargite were detected, but only diazinon, propargite and profenofos had residual values above EU Maximum Residue Level (MRL), with diazinon commonly detected at relatively high levels. About 15% of the total analyzed samples, 10% of cabbages and tomatoes, and nearly half of Swiss chard samples had pesticide concentration exceeding EU MRL. However, none of the tested samples had residues exceeding Codex Alimentarius Commission (Codex) MRLs. Conclusion: This study showed widespread contamination of vegetables with pesticides, mainly organophosphates. We recommend monitoring and regulation of pesticides usage, with promotion of good agricultural practices

Draft genome sequences of Diplodia sapinea, Ceratocystis manginecans, and Ceratocystis moniliformis

The draft nuclear genomes of Diplodia sapinea, Ceratocystis moniliformis s. str., and C. manginecans are presented. Diplodia sapinea is an important shoot-blight and canker pathogen of Pinus spp., C. moniliformis is a saprobe associated with wounds on a wide range of woody angiosperms and C. manginecans is a serious wilt pathogen of mango and Acacia mangium. The genome size of D. sapinea is estimated at 36.97 Mb and contains 13 020 predicted genes. Ceratocystis moniliformis includes 25.43 Mb and is predicted to encode at least 6 832 genes. This is smaller than that reported for the mango wilt pathogen C. manginecans which is 31.71 Mb and is predicted to encode at least 7 494 genes. The latter is thus more similar to C. fimbriata s.str., the type species of the genus. The genome sequences presented here provide an important resource to resolve issues pertaining to the taxonomy, biology and evolution of these fungi.The University of Pretoria, the Department of Science and Technology (DST)/National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology, Genomics Research Institute (University of Pretoria) and Claude Leon Foundation, South Africa.http://www.imafungus.org/am201

Characterization of a novel dsRNA element in the pine endophytic fungus Diplodia scrobiculata

Diplodia scrobiculata and Diplodia pinea are endophytic fungi associated with dieback and cankers of mainly Pinus spp. in many parts of the world. These two fungi are closely related and have, in the past, been considered to represent two morphological forms (A and B morphotypes) of D. pinea. dsRNA elements are known to occur in both D. scrobiculata and D. pinea. Two dsRNA elements from D. pinea, SsRV1 and SsRV2, have been characterized previously. The aim of this study was to characterize a third dsRNA element that is most commonly associated with D. scrobiculata and to determine its phylogenetic relationship to other mycoviruses. The 5018-bp genome of this element was sequenced, and it is referred to as D. scrobiculata RNA virus 1, or DsRV1. It has two open reading frames (ORFs), one of which codes for a putative polypeptide with a high degree of similarity to proteins of the vacuolar protein-sorting (VPS) machinery, and the other for an RNA-dependent RNA polymerase (RdRp). Phylogenetic comparisons based on amino acid sequence alignments of the RdRp revealed that DsRV1 is closely related to a dsRNA element isolated from Phlebiopsis gigantea (PgV2), and they grouped separately from virus families in which mycoviruses have previously been described. Although D. pinea and D. scrobiculata are closely related, DsRV1 does not share high sequence identity with SsRV1 or SsRV2, and they probably have different recent evolutionary origins

Sources of Diplodia pinea endophytic infections in Pinus patula and P. radiata seedlings in South Africa

Diplodia pinea, an opportunistic and latent pathogen, can significantly affect Pinus productivity worldwide. Despite being studied in South Africa for almost 100 years, the source of D. pinea inoculum responsible for seedling infection is unknown. The aim of this study was to determine the role of seed in vertical transmission of D. pinea and to investigate sources of inoculum leading to horizontal transmission to pine seedlings. Surface-disinfected seeds were inoculated with spore and mycelium suspensions of D. pinea to determine its effect on germination. In addition, isolation of the fungus was performed from surface-disinfected seeds, asymptomatic seedlings collected from nurseries, plantations where pines naturally regenerate and recently established fields, to assess transmission and incidence of endophytic D. pinea infections. Inoculation of seeds with D. pinea spore suspensions affected speed and rate of germination. The fungus was isolated from surface-disinfected seeds in only a few instances (2–3%) and was not found in healthy seedlings collected from greenhouses and nurseries, suggesting that vertical transmission of the fungus does not occur or is rare. In contrast, D. pinea was isolated from 40% of seedlings obtained from the understory of mature P. patula trees showing that horizontal transmission from mature to young trees sustains the D. pinea inoculum in South African pine plantations.DST/NRF Centre of Excellence in Tree Health Biotechnology, Tree Protection Co-operative Program, International Foundation for Science through a grant to Mr Wubetu Biho

Data from: Multiple introductions from multiple sources: invasion patterns for an important eucalyptus leaf pathogen

Many population studies on invasive plant pathogens are undertaken without knowing the center of origin of the pathogen. Most leaf pathogens of Eucalyptus originate in Australia and consequently with indigenous populations available, and it is possible to study the pathways of invasion. Teratosphaeria suttonii is a commonly occurring leaf pathogen of Eucalyptus species, naturally distributed in tropical and subtropical regions of eastern Australia where it is regarded as a minor pathogen infecting older leaves; however, repeated infections, especially in exotic plantations, can result in severe defoliation and tree deaths. Nine polymorphic microsatellite markers were used to assess the genetic structure of 11 populations of T. suttonii of which four where from within its native range in eastern Australia and the remaining seven from exotic Eucalyptus plantations. Indigenous populations exhibited high allele and haplotype diversity, predominantly clonal reproduction, high population differentiation, and low gene flow. The diversity of the invasive populations varied widely, but in general, the younger the plantation industry in a country or region, the lower the diversity of T. suttonii. Historical gene flow was from Australia, and while self-recruitment was dominant in all populations, there was evidence for contemporary gene flow, with South Africa being the most common source and Uruguay the most common sink population. This points distinctly to human activities underlying long-distance spread of this pathogen, and it highlights lessons to be learned regarding quarantine