<i>In silico</i>prediction and characterisation of secondary metabolite clusters in the plant pathogenic fungus<i>Verticillium dahliae</i>

Shi-Kunne, Xiaoqian; Jové, Roger de Pedro; Depotter, Jasper R L; Ebert, Malaika K.; Seidl, Michael; Thomma, Bart P.H.J.

doi:10.1093/femsle/fnz081

Cited by 21 publications

(18 citation statements)

References 66 publications

(93 reference statements)

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“…Thus, some secreted CAZymes may be essential from the early infection stage, like penetration of plant tissue, to later stages such as the necrotrophic phase where the pathogen feeds from dead plant tissue [16]. Likewise, secondary metabolites are known to be involved in plant infection and contribute to virulence and the interaction with other plant-associated microorganisms [17,18]. Many of these genes can be predicted either according to their composition and known protein domains or through machine learning methods [19].…”

Section: Introductionmentioning

confidence: 99%

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria

et al. 2020

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Background: Antagonistic co-evolution can drive rapid adaptation in pathogens and shape genome architecture. Comparative genome analyses of several fungal pathogens revealed highly variable genomes, for many species characterized by specific repeat-rich genome compartments with exceptionally high sequence variability. Dynamic genome structure may enable fast adaptation to host genetics. The wheat pathogen Zymoseptoria tritici with its highly variable genome, has emerged as a model organism to study genome evolution of plant pathogens. Here, we compared genomes of Z. tritici isolates and of sister species infecting wild grasses to address the evolution of genome composition and structure. Results: Using long-read technology, we sequenced and assembled genomes of Z. ardabiliae, Z. brevis, Z. pseudotritici and Z. passerinii, together with two isolates of Z. tritici. We report a high extent of genome collinearity among Zymoseptoria species and high conservation of genomic, transcriptomic and epigenomic signatures of compartmentalization. We identify high gene content variability both within and between species. In addition, such variability is mainly limited to the accessory chromosomes and accessory compartments. Despite strong host specificity and non-overlapping host-range between species, predicted effectors are mainly shared among Zymoseptoria species, yet exhibiting a high level of presence-absence polymorphism within Z. tritici. Using in planta transcriptomic data from Z. tritici, we suggest different roles for the shared orthologs and for the accessory genes during infection of their hosts. Conclusion: Despite previous reports of high genomic plasticity in Z. tritici, we describe here a high level of conservation in genomic, epigenomic and transcriptomic composition and structure across the genus Zymoseptoria. The compartmentalized genome allows the maintenance of a functional core genome co-occurring with a highly variable accessory genome.

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Section: Introductionmentioning

confidence: 99%

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria

et al. 2020

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“…Typically, genes involved in SM biosynthesis are clustered together [ 88 ]. In V. dahliae, 25 potential secondary metabolite gene clusters have been identified and 36% of those clusters were located in sub-telomeric regions close to the chromosomal end [ 90 ]. The phylogenetic and comparative genomic analysis suggested clusters in V. dahliae are involved in the biosynthesis of two putative siderophores, ferricrocin and triacetylfusarinine C (TAFC), 1,8-dihydroxynaphthalene (DHN)-melanin and fujikurin [ 90 ].…”

Section: Current Knowledge On Verticillium Dahliae mentioning

confidence: 99%

“…In V. dahliae, 25 potential secondary metabolite gene clusters have been identified and 36% of those clusters were located in sub-telomeric regions close to the chromosomal end [ 90 ]. The phylogenetic and comparative genomic analysis suggested clusters in V. dahliae are involved in the biosynthesis of two putative siderophores, ferricrocin and triacetylfusarinine C (TAFC), 1,8-dihydroxynaphthalene (DHN)-melanin and fujikurin [ 90 ]. Melanin, a polyketide, is one of the most thoroughly studied SMs because it is directly linked to fungal cell wall stability and pathogenicity [ 75 , 81 , 91 , 92 , 93 ].…”

Section: Current Knowledge On Verticillium Dahliae mentioning

confidence: 99%

Opportunities and Challenges in Studies of Host-Pathogen Interactions and Management of Verticillium dahliae in Tomatoes

Acharya

Ingram

et al. 2020

Plants

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Tomatoes (Solanum lycopersicum L.) are a valuable horticultural crop that are grown and consumed worldwide. Optimal production is hindered by several factors, among which Verticillium dahliae, the cause of Verticillium wilt, is considered a major biological constraint in temperate production regions. V. dahliae is difficult to mitigate because it is a vascular pathogen, has a broad host range and worldwide distribution, and can persist in soil for years. Understanding pathogen virulence and genetic diversity, host resistance, and plant-pathogen interactions could ultimately inform the development of integrated strategies to manage the disease. In recent years, considerable research has focused on providing new insights into these processes, as well as the development and integration of environment-friendly management approaches. Here, we discuss the current knowledge on the race and population structure of V. dahliae, including pathogenicity factors, host genes, proteins, enzymes involved in defense, and the emergent management strategies and future research directions for managing Verticillium wilt in tomatoes.

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“…Secondary metabolism genes and gene clusters have been identified in the genome sequence of V. dahliae (Xiong et al 2016;Shi-Kunne et al 2019). According to these data, Nag1 is located in a PKS/NRPS hybrid secondary metabolism gene cluster containing genes from VDAG_07920 to VDAG_07931.…”

Section: Silencing Of Nag1 Decreases Expression Of Secondary Metabolimentioning

confidence: 99%

A novel gene from a secondary metabolism gene cluster is required for microsclerotia formation and virulence in Verticillium dahliae

2019

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Verticillum dahliae is a notorious plant pathogenic fungus, which can cause wilt disease on hundreds of plant species. The genome of V. dahliae has been sequenced and annotated, but incorrect gene annotations and unidentified transcribed regions persist. Using RNA-Seq combined with reverse-transcription PCR, we identified a novel transcribed gene, Nag1, located in a cluster of putative secondary metabolic genes whose roles remain unknown. Functional analysis of Nag1 by dsRNA-mediated gene silencing revealed that loss of Nag1 significantly decreased fungal growth and conidial production. In addition, Nag1-silenced mutants exhibited obvious defects in microsclerotia formation and fungal virulence. Consistent with the reduction in microsclerotia formation, melanin production and expression of genes involved in melanin biosynthesis were markedly reduced in Nag1-silenced mutants. Overall, our data suggest that Nag1 acts as an important regulator of fungal development, microsclerotia formation and secondary metabolism in V. dahliae.

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In silicoprediction and characterisation of secondary metabolite clusters in the plant pathogenic fungusVerticillium dahliae

Cited by 21 publications

References 66 publications

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria

Opportunities and Challenges in Studies of Host-Pathogen Interactions and Management of Verticillium dahliae in Tomatoes

A novel gene from a secondary metabolism gene cluster is required for microsclerotia formation and virulence in Verticillium dahliae

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