Botryosphaeria dothidea: a latent pathogen of global importance to woody plant health
TL;DR: This pathogen profile synthesizes the current understanding of B. dothidea pertaining to its distribution, host associations and role as a pathogen in managed and natural woody environments, as well as elucidating previously unknown aspects of the species, including mating and host infection strategies.
Abstract: The National Research Foundation (NRF) of South Africa and members of the Tree Protection Co-operative Programme (TPCP).
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Charles University in Prague1, Academy of Sciences of the Czech Republic2, Stellenbosch University3, Canterbury of New Zealand4, University of Tennessee5, University of Fribourg6, University College London7, Zoological Society of London8, Williams College9, Durham University10, University of Vienna11, South African National Parks12, International Union for Conservation of Nature and Natural Resources13, Free University of Berlin14, Leibniz Association15, Helmholtz Centre for Environmental Research - UFZ16, Martin Luther University of Halle-Wittenberg17, Czech University of Life Sciences Prague18, United States Forest Service19, University of Toronto20, University of Rhode Island21, University of Concepción22, Taizhou University23, University of Konstanz24, University of Seville25, Spanish National Research Council26, University of Pretoria27
TL;DR: Improved international cooperation is crucial to reduce the impacts of invasive alien species on biodiversity, ecosystem services, and human livelihoods, as synergies with other global changes are exacerbating current invasions and facilitating new ones, thereby escalating the extent and impacts of invaders.
Abstract: Biological invasions are a global consequence of an increasingly connected world and the rise in human population size The numbers of invasive alien species – the subset of alien species that spread widely in areas where they are not native, affecting the environment or human livelihoods – are increasing Synergies with other global changes are exacerbating current invasions and facilitating new ones, thereby escalating the extent and impacts of invaders Invasions have complex and often immense long‐term direct and indirect impacts In many cases, such impacts become apparent or problematic only when invaders are well established and have large ranges Invasive alien species break down biogeographic realms, affect native species richness and abundance, increase the risk of native species extinction, affect the genetic composition of native populations, change native animal behaviour, alter phylogenetic diversity across communities, and modify trophic networks Many invasive alien species also change ecosystem functioning and the delivery of ecosystem services by altering nutrient and contaminant cycling, hydrology, habitat structure, and disturbance regimes These biodiversity and ecosystem impacts are accelerating and will increase further in the future Scientific evidence has identified policy strategies to reduce future invasions, but these strategies are often insufficiently implemented For some nations, notably Australia and New Zealand, biosecurity has become a national priority There have been long‐term successes, such as eradication of rats and cats on increasingly large islands and biological control of weeds across continental areas However, in many countries, invasions receive little attention Improved international cooperation is crucial to reduce the impacts of invasive alien species on biodiversity, ecosystem services, and human livelihoods Countries can strengthen their biosecurity regulations to implement and enforce more effective management strategies that should also address other global changes that interact with invasions
677 citations
Cites background from "Botryosphaeria dothidea: a latent p..."
...This pathway of introduction has only recently been recognized through the emergence of metagenomic technologies and is particularly relevant for microbial invasives (Marsberg et al., 2017)....
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TL;DR: A well defined natural classification and an extensive collection of tools to study the Botryosphaeriaceae, including a growing number of genomes, now provide a springboard for a much deeper exploration of their biology, biogeography and host associations.
71 citations
Cites background from "Botryosphaeria dothidea: a latent p..."
...have been studied, they illustrate a group of fungi uniquely interactingwith their hosts (Marsberg et al. 2017)....
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...Southern Africa, amongst many other hosts around the world (Marsberg et al. 2017)....
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...Yet, the genomes of those species that have been analysed clearly show that they have a well developed arsenal of potential pathogenicity genes and virulence factors with which to overcome host defences and cause serious disease (Islam et al. 2012; Blanco-Ulate et al. 2013; Morales-Cruz et al. 2015; Marsberg et al. 2017; Massonnet et al. 2017)....
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...In contrast, B. dothidea, for which a sexual cycle is known, appears to be homothallic (Marsberg et al. 2017)....
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...also increasing evidence that these pathogens are being spread around the world with little constraint, and apparently with increasing frequency associated with globalization (Sakalidis et al. 2013; Burgess et al. 2017; Marsberg et al. 2017)....
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TL;DR: This article used all published records with available sequence data of the Botryosphaeriaceae in Australia to examine the distribution and host range of these taxa.
Abstract: The Botryosphaeriales, and in particular the Botryosphaeriaceae, are a well-studied group of fungi best known for the canker diseases they cause on woody hosts especially in stressed or damaged trees. Australian Plant Pathology herbaria contain many records for this group, but due to considerable taxonomic changes over the past decade, many of the species names have since been reclassified. In this article we used all published records with available sequence data of the Botryosphaeriaceae in Australia to examine the distribution and host range of these taxa. There are 24 genera encompassing 222 species in the Botryosphaeriaceae; 9 genera and 62 species have been recorded in Australia. Some genera such as Neoscytalidium are only found in warm, humid climates while Dothiorella species are more common in temperate climates. There were species, such as Lasiodiplodia theobromae, Neofusicoccum parvum and Botryosphaeria dothidea, which had a wide host range with many records. However, there were also several species found only in one location on a single host. While systematic data collection is still required, the information presented here provides a baseline of species present in Australia and will underpin future studies into this group of important pathogens.
46 citations
Cites result from "Botryosphaeria dothidea: a latent p..."
...Recent studies on Botryosphaeria dothidea (Marsberg et al. 2017), L. theobromae (Mehl et al. 2017) and N. parvum (Sakalidis et al. 2013) did not find a phylogeographic pattern for these species....
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TL;DR: This commentary highlights four emerging issues that need to be considered regarding the invasions by fungal pathogens of trees and it emphasizes opportunities to better understand their relevance and impacts on natural and planted forests.
Abstract: The DST/NRF Centre of Excellence in Tree Health Biotechnology, the National Research Foundation (South Africa) and the Tree Protection Cooperative Programme (TPCP)
33 citations
Cites background from "Botryosphaeria dothidea: a latent p..."
...But there are also examples where the fungi are moved via traded plants or plant material to new environments where they become invasive aliens in their own right (Anderson et al. 2004; Santini et al. 2013; Marsberg et al. 2017)....
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...they become invasive aliens in their own right (Anderson et al. 2004; Santini et al. 2013; Marsberg et al. 2017)....
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...Some endophytes, such as members of the Botryosphaeriaceae, are well known latent pathogens, existing for long periods of time in asymptomatic tissue, but able to cause disease under conditions of stress (Slippers and Wingfield 2007; Marsberg et al. 2017)....
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01 Jul 2018
TL;DR: Comparing the genomes of Botryosphaeria dothidea and B. kuwatsukai will be instrumental in understanding how both phytopathogens interact with their plant hosts and in designing efficient strategies for disease control and molecular breeding to help ensure global apple production and food security.
Abstract: Ring rot, one of the most destructive diseases of apple worldwide, is caused primarily by Botryosphaeria dothidea and 8. kuwatsukai. Here, we sequenced the genomes of 8. dothidea strain PG45 (44.3 Mb with 5.12 % repeat rate) and 8. kuwatsukai epitype strain PG2 (48.0 Mb with 13.02 % repeat rate), and conducted a comparative analysis of these two genomes, as well as other sequenced fungal genomes, in order to understand speciation and distinctive patterns of evolution of pathogenicity-related genes. Pair-wise genome alignments revealed that the two species are highly syntenic (96.74 % average sequence identity). Both species encode a significant number of pathogenicity-related genes, e.g.carbohydrateactive enzymes (CAZYs), plant cell wall degrading enzymes (PCWDEs), secondary metabolites (SMs) biosynthetic enzymes, cytochrome P450 enzymes (CYPs), and secreted peptidases, in comparison to all additional sequenced fungal species involved in various life-styles. The number of pathogenicity-related genes in 8. dothidea and 8. kuwatsukai is higher than other genomes of Botryosphaeriaceae pathogens (Macrophomina phaseolina and Neofusicoccum parvum), suggesting a secondary round of Botryosphaeria-lineage expansion in the family. There were, however, also significant differences in the genomes of the two Botryosphaeria species. Botryosphaeria kuwatsukai, which infects only apple and pear, apparently lost a set of SMs genes, CAZYs and PCWDEs, possibly as a result of host specialization. Botryosphaeria kuwatsukai contained significantly more transposable elements and higher value of repeat induced point (RIP) index than B. dothidea. Our results will be instrumental in understanding how both phytopathogens interact with their plant hosts and in designing efficient strategies for disease control and molecular breeding to help ensure global apple production and food security.
32 citations
References
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Journal Article•
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Abstract: Copyright (©) 1999–2012 R Foundation for Statistical Computing. Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this manual under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this manual into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the R Core Team.
272,030 citations
"Botryosphaeria dothidea: a latent p..." refers background in this paper
...1.3 (R Core Team, 2015)....
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TL;DR: This version of MAFFT has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update.
Abstract: We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
27,771 citations
Additional excerpts
...215 (Katoh et al., 2002, Katoh & Standley, 2013) using the L-INS-I option....
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TL;DR: This work presents some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees.
Abstract: Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting postanalyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU
23,838 citations
"Botryosphaeria dothidea: a latent p..." refers methods in this paper
...1.22 (Stamatakis, 2014) invoking the GTRGAMMA option and a rapid bootstrap with 100 replications....
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TL;DR: A simplified scoring system is proposed that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length.
Abstract: A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homologous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
12,003 citations
Additional excerpts
...215 (Katoh et al., 2002, Katoh & Standley, 2013) using the L-INS-I option....
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TL;DR: It is hypothesized that the endophytes, in contrast to known pathogens, generally have far greater phenotypic plasticity and thus more options than pathogens: infection, local but also extensive colonisation, latency, virulence, pathogenity and (or) saprophytism.
1,323 citations
"Botryosphaeria dothidea: a latent p..." refers background in this paper
...This is true for many pathogens that have a latent phase during a part of their lifecycle (Hyde & Soytong, 2008, Rai & Agarkar, 2014, Schulz & Boyle, 2005)....
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