Comparative genomics of plant pathogenic Botrytis species with distinct host specificity
Valero-Jiménez, Claudio A. ; Veloso, Javier ; Staats, Martijn ; Kan, Jan A.L. van - \ 2019
BMC Genomics 20 (2019)1. - ISSN 1471-2164
Effector - Grey mould - Necrotroph - Secondary metabolite - Secretome
Background: Fungi of the genus Botrytis (presently containing ~ 35 species) are able to infect more than 1400 different plant species and cause losses in a wide range of crops of economic importance. The best studied species is B. cinerea, which has a broad host range and is one of the best studied necrotrophic plant pathogenic fungi. Most other Botrytis spp. have a narrow host range and have been studied in less detail. To characterize genomic variation among different representatives of Botrytis spp., we sequenced and annotated the draft genomes of nine Botrytis species: B. calthae, B. convoluta, B. elliptica, B. galanthina, B. hyacinthi, B. narcissicola, B. paeoniae, B. porri and B. tulipae. Results: Bioinformatics and comparative genomics tools were applied to determine a core of 7668 shared protein families in all Botrytis species, which grouped them in two distinct phylogenetic clades. The secretome of all nine Botrytis spp. was similar in number (ranging from 716 to 784 predicted proteins). A detailed analysis of the molecular functions of the secretome revealed that shared activities were highly similar. Orthologs to effectors functionally studied in B. cinerea were also present in the other Botrytis species. A complex pattern of presence/absence of secondary metabolite biosynthetic key enzymes was observed. Conclusions: Comparative genomics of Botrytis show that overall, species share the main signatures and protein families in the secreted proteins, and of known effectors. Our study provides leads to study host range determinants in the genus Botrytis and provides a stepping stone to elucidate the roles of effector candidates in the infection process of these species.
Spatio-temporal patterns of genetic variation in Arbacia lixula, a thermophilous sea urchin in expansion in the Mediterranean
Pérez-Portela, Rocío ; Wangensteen, Owen S. ; Garcia-Cisneros, Alex ; Valero-Jiménez, Claudio ; Palacín, Cruz ; Turon, Xavier - \ 2019
Heredity 122 (2019)2. - ISSN 0018-067X - p. 244 - 259.
The genetic structure of 13 populations of the amphiatlantic sea urchin Arbacia lixula, as well as temporal genetic changes in three of these localities, were assessed using ten hypervariable microsatellite loci. This thermophilous sea urchin is an important engineer species triggering the formation of barren grounds through its grazing activity. Its abundance seems to be increasing in most parts of the Mediterranean, probably favoured by warming conditions. Significant genetic differentiation was found both spatially and temporally. The main break corresponded to the separation of western Atlantic populations from those in eastern Atlantic and the Mediterranean Sea. A less marked, but significant differentiation was also found between Macaronesia (eastern Atlantic) and the Mediterranean. In the latter area, a signal of differentiation between the transitional area (Alboran Sea) and the rest of the Mediterranean was detected. However, no genetic structure is found within the Mediterranean (excluding Alboran) across the Siculo-Tunisian Strait, resulting from either enough gene flow to homogenize distance areas or/and a recent evolutionary history marked by demographic expansion in this basin. Genetic temporal variation at the Alboran Sea is as important as spatial variation, suggesting that temporal changes in hydrological features can affect the genetic composition of the populations. A picture of genetic homogeneity in the Mediterranean emerges, implying that the potential expansion of this keystone species will not be limited by intraspecific genetic features and/or potential impact of postulated barriers to gene flow in the region.
The obligate alkalophilic soda-lake fungus Sodiomyces alkalinus has shifted to a protein diet
Grum-Grzhimaylo, A. ; Falkoski, D.L. ; Heuvel, Joost van den; Valero Jimenez, C.A. ; Min, B. ; Choi, I.G. ; Lipzen, A. ; Daum, C.G. ; Aanen, D.K. ; Tsang, A. ; Henrissat, B. ; Bilanenko, E.N. ; Vries, R.P. de; Kan, J.A.L. van; Grigoriev, I.V. ; Debets, A.J.M. - \ 2018
Molecular Ecology 27 (2018)23. - ISSN 0962-1083 - p. 4808 - 4819.
Sodiomyces alkalinus is one of the very few alkalophilic fungi, adapted to grow optimally at high pH. It is widely distributed at the plant‐deprived edges of extremely alkaline lakes and locally abundant. We sequenced the genome of S. alkalinus and reconstructed evolution of catabolic enzymes, using a phylogenomic comparison. We found that the genome of S. alkalinus is larger, but its predicted proteome is smaller and heavily depleted of both plant‐degrading enzymes and proteinases, when compared to its closest plant‐pathogenic relatives. Interestingly, despite overall losses, S. alkalinus has retained many proteinases families and acquired bacterial cell wall‐degrading enzymes, some of them via horizontal gene transfer from bacteria. This fungus has very potent proteolytic activity at high pH values, but slowly induced low activity of cellulases and hemicellulases. Our experimental and in silico data suggest that plant biomass, a common food source for most fungi, is not a preferred substrate for S. alkalinus in its natural environment. We conclude that the fungus has abandoned the ancestral plant‐based diet and has become specialized in a more protein‐rich food, abundantly available in soda lakes in the form of prokaryotes and small crustaceans.
Draft genomes of nine plant pathogenic Botrytis species
Valero Jimenez, Claudio ; Veloso, Javier ; Staats, Martijn ; Kan, Jan van - \ 2017
PRJNA401386 - Botrytis
The aim of the project is to compare the genomes of nine species of plant pathogens in the genus Botrytis with distinct host specificity, in order to identify genes involved in host range determination. Six of the nine fungal species infect ornamental bulb flower crops.
Experimental evolution to increase the efficacy of the entomopathogenic fungus Beauveria bassiana against malaria mosquitoes: Effects on mycelial growth and virulence
Valero-Jiménez, Claudio A. ; Kan, Jan A.L. van; Koenraadt, Constantianus J.M. ; Zwaan, Bas J. ; Schoustra, Sijmen E. - \ 2017
Evolutionary Applications 10 (2017)5. - ISSN 1752-4571 - p. 433 - 443.
Entomopathogenic fungi such as Beauveria bassiana are currently considered as a potential control agent for malaria mosquitoes. The success of such strategies depends among others on the efficacy of the fungus to kill its hosts. As B. bassiana can use various resources for growth and reproduction, increasing the dependency on mosquitoes as a nutritional source may be instrumental for reaching this goal. Passage of entomopathogenic fungi through an insect host has been shown to increase its virulence. We evaluated the virulence, fungal outgrowth, mycelial growth rate, and sporulation rate of two B. bassiana isolates (Bb1520 and Bb8028) that underwent 10 consecutive selection cycles through malaria mosquitoes (Anopheles coluzzii) using an experimental evolution approach. This cycling resulted in an altered capacity of evolved B. Bassiana lineages to grow on different substrates while maintaining the ability to kill insects. Notably, however, there were no significant changes in virulence or speed of outgrowth when comparing the evolved lineages against their unevolved ancestors. These results suggest that fungal growth and sporulation evolved through successive and exclusive use of an insect host as a nutritional resource. We discuss the results in light of biocontrol and provide suggestions to increase fungal virulence.
Data from: Experimental evolution to increase the efficacy of the entomopathogenic fungus Beauveria bassiana against malaria mosquitoes: effects on mycelial growth and virulence
Valero Jimenez, C.A. ; Kan, J.A.L. van; Koenraadt, C.J.M. ; Zwaan, B.J. ; Schoustra, S.E. - \ 2016
experimental evolution - biocontrol - malaria
Entomopathogenic fungi such as Beauveria bassiana are currently considered as a potential control agent for malaria mosquitoes. The success of such strategies depends among others on the efficacy of the fungus to kill its hosts. As B. bassiana can use various resources for growth and reproduction, increasing the dependency on mosquitoes as a nutritional source may be instrumental for reaching this goal. Passage of entomopathogenic fungi through an insect host has been shown to increase its virulence. We evaluated the virulence, fungal outgrowth, mycelial growth rate, and sporulation rate of two B. bassiana isolates (Bb1520 and Bb8028) that underwent 10 consecutive selection cycles through malaria mosquitoes (Anopheles coluzzii) using an experimental evolution approach. This cycling resulted in an altered capacity of evolved B. Bassiana lineages to grow on different substrates while maintaining the ability to kill insects. Notably, however, there were no significant changes in virulence or speed of outgrowth when comparing the evolved lineages against their un-evolved ancestors. These results suggest that fungal growth and sporulation evolved through successive and exclusive use of an insect host as a nutritional resource. We discuss the results in the light of biocontrol and provide suggestions to increase fungal virulence.
Beauveria bassiana Genome sequencing and assembly
Valero Jimenez, C.A. ; Faino, L. ; Spring in 'T Veld, Daphne ; Smit, S. ; Zwaan, B.J. ; Kan, J.A.L. van - \ 2016
Beauveria bassiana - PRJNA260878
The virulence of the entompathogenic fungus, Beauveria bassiana, is being studied by comparative genomics of five isolates.
Comparative genomics of Beauveria bassiana : Uncovering signatures of virulence against mosquitoes
Valero-Jiménez, Claudio A. ; Faino, Luigi ; Spring in 'T Veld, Daphne ; Smit, Sandra ; Zwaan, Bas J. ; Kan, Jan A.L. van - \ 2016
BMC Genomics 17 (2016). - ISSN 1471-2164
Beauveria bassiana - Comparative genomics - Genome sequencing - Virulence
Background: Entomopathogenic fungi such as Beauveria bassiana are promising biological agents for control of malaria mosquitoes. Indeed, infection with B. bassiana reduces the lifespan of mosquitoes in the laboratory and in the field. Natural isolates of B. bassiana show up to 10-fold differences in virulence between the most and the least virulent isolate. In this study, we sequenced the genomes of five isolates representing the extremes of low/high virulence and three RNA libraries, and applied a genome comparison approach to uncover genetic mechanisms underpinning virulence. Results: A high-quality, near-complete genome assembly was achieved for the highly virulent isolate Bb8028, which was compared to the assemblies of the four other isolates. Whole genome analysis showed a high level of genetic diversity between the five isolates (2.85-16.8 SNPs/kb), which grouped into two distinct phylogenetic clusters. Mating type gene analysis revealed the presence of either the MAT1-1-1 or the MAT1-2-1 gene. Moreover, a putative new MAT gene (MAT1-2-8) was detected in the MAT1-2 locus. Comparative genome analysis revealed that Bb8028 contains 163 genes exclusive for this isolate. These unique genes have a tendency to cluster in the genome and to be often located near the telomeres. Among the genes unique to Bb8028 are a Non-Ribosomal Peptide Synthetase (NRPS) secondary metabolite gene cluster, a polyketide synthase (PKS) gene, and five genes with homology to bacterial toxins. A survey of candidate virulence genes for B. bassiana is presented. Conclusions: Our results indicate several genes and molecular processes that may underpin virulence towards mosquitoes. Thus, the genome sequences of five isolates of B. bassiana provide a better understanding of the natural variation in virulence and will offer a major resource for future research on this important biological control agent.
A multidisciplinary approach to study virulence of the entomopathogenic fungus Beauveria bassiana towards malaria mosquitoes
Valero Jimenez, C.A. - \ 2016
Wageningen University. Promotor(en): Bas Zwaan; Willem Takken, co-promotor(en): Sander Koenraadt; Jan van Kan. - Wageningen : Wageningen University - ISBN 9789462578548 - 131
beauveria bassiana - entomogenous fungi - virulence - vector control - mosquito-borne diseases - malaria - anopheles - culicidae - beauveria bassiana - entomopathogene schimmels - virulentie - vectorbestrijding - ziekten overgebracht door muskieten - malaria - anopheles - culicidae
Although globally malaria mortality rates have fallen by 48% between 2000 and 2015, malaria is still killing an estimated 438,000 people each year. An effective way to alleviate the burden of malaria is to control its vector (malaria mosquitoes) using insecticides. This can be achieved either with insecticide-treated bed nets (ITNs) or through indoor residual spraying of insecticides (IRS). However, because of rapidly expanding insecticide resistance, there is a need to find alternatives to control the mosquitoes. Entomopathogenic fungi (EPF) could constitute an effective biological control tool, as is able to reduce malaria transmission under laboratory and field conditions. However, fundamental knowledge on the mechanisms and regulation of the infection process of the fungus, as well as insights into the defensive responses of the host insect to EPF, is limited. Therefore, the main goal of this thesis was to study virulence of the entomopathogenic fungus B. bassiana towards malaria mosquitoes using a multidisciplinary approach.
Chapter 2 provides an overview of existing knowledge of genes influencing virulence in EPF, with a special focus on B. bassiana. The infection cycle and virulence mechanisms are discussed, and put in a framework of novel strategies and experimental methods that are needed to better understand virulence and improve the usage of EPF as a biocontrol agent.
The study of natural variation in fungal virulence is a first step towards understanding the genetic mechanisms involved, because it reveals the extent of variation in the different components of virulence and their overall role. Chapter 3 describes the natural variation in virulence for 29 B. bassiana isolates that were tested on malaria mosquitoes. Furthermore, the phenotypic characteristics of the fungal isolates such as sporulation, spore size and growth were evaluated and their relationship with virulence analysed.
Based on the ample natural variation observed in fungal virulence, in Chapter 4, a comparative genomics analysis was performed on five selected isolates of contrasting virulence. In order to understand mechanisms underlying contrasting virulence, a comparison on gene gain/loss, single nucleotide polymorphisms (SNPs), secreted proteins, and secondary metabolites was performed. Insight is provided to the magnitude of the complexity of a trait such as virulence and suggests candidate genes that can be further studied using a functional analysis approach.
Chapter 5 focuses on an experimental evolution approach in which B. bassiana was solely using insects as a nutritional source for ten consecutive passages through malaria mosquitoes. Two isolates of B. bassiana that differed in virulence were compared to their respective ancestors, and they were assayed in virulence, fungal outgrowth, mycelial growth rate (MGR), and sporulation. Passage of the entomopathogenic fungi B. bassiana through the insect host resulted in an altered capacity to grow on different substrates while maintaining the ability to kill insects.
Chapter 6 presents a discussion on the main findings of this thesis and describes future perspectives to study virulence of the entomopathogenic fungi Beauveria bassiana in the context of biological control of malaria mosquitoes.
Genes involved in virulence of the entomopathogenic fungus Beauveria bassiana
Valero-Jiménez, Claudio A. ; Wiegers, Harm ; Zwaan, Bas J. ; Koenraadt, Constantianus J.M. ; Kan, Jan A.L. van - \ 2016
Journal of Invertebrate Pathology 133 (2016). - ISSN 0022-2011 - p. 41 - 49.
Beauveria bassiana - Entomopathogenic fungi - Virulence factors - Virulence genes
Pest insects cause severe damage to global crop production and pose a threat to human health by transmitting diseases. Traditionally, chemical pesticides (insecticides) have been used to control such pests and have proven to be effective only for a limited amount of time because of the rapid spread of genetic insecticide resistance. The basis of this resistance is mostly caused by (co)dominant mutations in single genes, which explains why insecticide use alone is an unsustainable solution. Therefore, robust solutions for insect pest control need to be sought in alternative methods such as biological control agents for which single-gene resistance is less likely to evolve. The entomopathogenic fungus Beauveria bassiana has shown potential as a biological control agent of insects, and insight into the mechanisms of virulence is essential to show the robustness of its use. With the recent availability of the whole genome sequence of B. bassiana, progress in understanding the genetics that constitute virulence toward insects can be made more quickly. In this review we divide the infection process into distinct steps and provide an overview of what is currently known about genes and mechanisms influencing virulence in B. bassiana. We also discuss the need for novel strategies and experimental methods to better understand the infection mechanisms deployed by entomopathogenic fungi. Such knowledge can help improve biocontrol agents, not only by selecting the most virulent genotypes, but also by selecting the genotypes that use combinations of virulence mechanisms for which resistance in the insect host is least likely to develop.
|Comparative genomics of virulence towards malaria mosquitoes in Beauveria bassiana
Valero Jimenez, C.A. ; Spring in 'T Veld, D. ; Smit, Sandra ; Koenraadt, C.J.M. ; Zwaan, B.J. ; Kan, J.A.L. van - \ 2015
In: Book of Abstracts 28th Fungal Genetics Conference. - - p. 162 - 162.
Entomopathogenic fungi such as Metarhizium anisopliae and Beauveria bassiana have been proposed as biological control agents to kill malaria mosquitoes. Indeed, it has been shown that these fungi successfully reduce the lifespan of mosquitoes in the laboratory and in the field. Previously, we characterized the natural variation in virulence of 29 isolates of Beauveria bassiana and showed that there were up to 10-fold differences in virulence between the most virulent isolate compared to the least virulent isolate. This natural variation can be used to uncover the genetic mechanisms underpinning virulence, which will provide essential information for (i) further improving fungi as biocontrol agents, and (ii) estimating the likelihood of resistance development in the vector, i.e. mosquitoes. In this study, we sequenced 5 isolates representing the extremes of low/high virulence for further comparative genomic analysis. The genomes were de novo assembled and the draft genome size varied from 35.02 Mb to 38.83 Mb. The predicted encoding proteins were supported with three RNA-Seq libraries, and ranged from 10,283 to 10,831 genes. The core set consisted of 8800 genes shared between all isolates. We focused on the genome differences between isolates with contrasting virulence, with special emphasis on gene gain/loss, single nucleotide polymorphisms (SNPs), and secreted proteins. Our findings are discussed in the context of other sequenced entomopathogenic fungi (Metarhizium anisopliae, M. robertsii and M. acridum) as well as plant pathogenic fungi.
Natural variation in virulence of the entomopathogenic fungus Beauveria bassiana against malaria mosquitoes
Valero Jimenez, C.A. ; Debets, A.J.M. ; Kan, J.A. van; Schoustra, S.E. ; Takken, W. ; Zwaan, B.J. ; Koenraadt, C.J.M. - \ 2014
Malaria Journal 13 (2014). - ISSN 1475-2875 - 8 p.
metarhizium-anisopliae - anopheles-gambiae - infection - agents - susceptibility - degradation - persistence - expression - resistance - behavior
Background Insecticide resistance is greatly hampering current efforts to control malaria and therefore alternative methods are needed. Entomopathogenic fungi have been proposed as an alternative with a special focus on the cosmopolitan species Beauveria bassiana. However, few studies have analysed the effects of natural variation within fungal isolates on mosquito survival, and the implications and possible exploitation for malaria control. Methods Laboratory bioassays were performed on adult female mosquitoes (Anopheles coluzzii) with spores from 29 isolates of B. bassiana, originating from different parts of the world. In addition, phenotypic characteristics of the fungal isolates such as sporulation, spore size and growth rate were studied to explore their relationship with virulence. Results All tested isolates of B. bassiana killed An. coluzzii mosquitoes, and the rate at which this happened differed significantly among the isolates. The risk of mosquitoes dying was around ten times higher when they were exposed to the most virulent as compared to the least virulent isolate. There was significant variation among isolates in spore size, growth rate and sporulation, but none of these morphological characteristics were correlated, and thus predictive, for the ability of the fungal isolate to kill malaria mosquitoes. Conclusions This study shows that there is a wide natural variation in virulence of isolates of B. bassiana, and that selecting an appropriate fungal isolate is highly relevant in killing and thus controlling malaria mosquitoes, particularly if used as part of an integrated vector management strategy. Also, the wide variation observed in virulence offers the opportunity to better understand the molecular and genetic mechanisms that drive this variation and thus to address the potential development of resistance against entomopathogenic fungi