Draft whole-genome sequence of the Diaporthe helianthi 7/96 strain, causal agent of sunflower stem canker

Baroncelli, Riccardo; Scala, F.; Vergara, Mariarosaira; Thon, Michael R.; Ruocco, Michelina

doi:10.1016/j.gdata.2016.11.005

Cited by 20 publications

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“…In the present study we generated a draft genome of the highly virulent isolate D. helianthi 7/96 and annotated 40 genes coding for putative PKSs [ 29 ]. By using the Pathogen-Host Interaction database (PHI-base) ( http://www.phi-base.org ) [ 30 ], orthologs of genes known to be involved in biosynthesizing PKs, which are virulence factors in other fungal species, were identified.…”

Section: Introductionmentioning

confidence: 99%

Polyketide synthases of Diaporthe helianthi and involvement of DhPKS1 in virulence on sunflower

et al. 2018

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BackgroundThe early phases of Diaporthe helianthi pathogenesis on sunflower are characterized by the production of phytotoxins that may play a role in host colonisation. In previous studies, phytotoxins of a polyketidic nature were isolated and purified from culture filtrates of virulent strains of D. helianthi isolated from sunflower. A highly aggressive isolate (7/96) from France contained a gene fragment of a putative nonaketide synthase (lovB) which was conserved in a virulent D. helianthi population.ResultsIn order to investigate the role of polyketide synthases in D. helianthi 7/96, a draft genome of this isolate was examined. We were able to find and phylogenetically analyse 40 genes putatively coding for polyketide synthases (PKSs). Analysis of their domains revealed that most PKS genes of D. helianthi are reducing PKSs, whereas only eight lacked reducing domains. Most of the identified PKSs have orthologs shown to be virulence factors or genetic determinants for toxin production in other pathogenic fungi. One of the genes (DhPKS1) corresponded to the previously cloned D. helianthi lovB gene fragment and clustered with a nonribosomal peptide synthetase (NRPS) -PKS hybrid/lovastatin nonaketide like A. nidulans LovB. We used DhPKS1 as a case study and carried out its disruption through Agrobacterium-mediated transformation in the isolate 7/96. D. helianthi DhPKS1 deleted mutants were less virulent to sunflower compared to the wild type, indicating a role for this gene in the pathogenesis of the fungus.ConclusionThe PKS sequences analysed and reported here constitute a new genomic resource that will be useful for further research on the biology, ecology and evolution of D. helianthi and generally of fungal plant pathogens.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-4405-z) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Polyketide synthases of Diaporthe helianthi and involvement of DhPKS1 in virulence on sunflower

et al. 2018

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“…This type of genome wide phylogeny reconstruction is impossible for organisms that have not had their genomes fully sequenced and annotated. This is the case for the genus Diaporthe, for which the first genome sequencing project started in 2013 (GOLD project Gp0038530) and until now only Diaporthe species have their genome sequenced ( Phomopsis longicolla , Diaporthe aspalathi , Diaporthe ampelina and Diaporthe helianthi ) (Li et al, 2015; Baroncelli et al, 2016; Li et al, 2016; Savitha, Bhargavi & Praveen, 2016). …”

Section: Introductionmentioning

confidence: 99%

Evaluating multi-locus phylogenies for species boundaries determination in the genusDiaporthe

Santos

Alves

2017

PeerJ

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BackgroundSpecies identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem.MethodsHere we addressed that problem by identifying five loci that have been sequenced in 142 Diaporthe isolates representing 96 species: TEF1, TUB, CAL, HIS and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees.ResultsAs expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the TEF1-TUB-CAL-HIS 4-loci tree as almost equivalent to the 5-loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus.DiscussionOur results question the current use of the ITS locus for DNA barcoding in the genus Diaporthe and suggest that TEF1 might be a better choice if one locus barcoding needs to be done.

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“…All sequenced species in Diaporthales (one genome per species for 12 species) were used. These species include: Cryphonectria parasitica (jgi.doe.gov), Chrysoporthe cubensis [14], Chrysoporthe deuterocubensis [14], Chrysoporthe austroafricana [15], Valsa mali [12], Valsa pyri [12], Diaporthe ampelina [16], Diaporthe aspalathi [17], Diaporthe longicolla [18], Diaporthe helianthi [19], and Melanconium sp. The outgroups used were Neurospora crassa [20] and Magnaporthe grisea [21].…”

Section: Resultsmentioning

confidence: 99%

“…Genome sequences were deposited at ncbi.nlm.nih.gov under Bioproject number PRJNA434132. Gene annotation was performed using the MAKER2 pipeline [31] in an iterative manner as is described in [32], with protein evidence from related species of Melanconium sp., Cryphonectria parasitica , Diaporthe ampelina , (from jgi.doe.gov) and Diaporthe helianthi [19], for a total of three iterations. PFAM domains were identified in all the genomes using hmmscan with trusted cutoff [33].…”

Section: Methodsmentioning

confidence: 99%

The genome of the butternut canker pathogen, Ophiognomonia clavigignenti-juglandacearum shows an elevated number of genes associated with secondary metabolism and protection from host resistance responses in comparison with other members of the Diaporthales

Schuelke

Broders

2019

Preprint

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Ophiognomonia clavigignentijuglandacearum (Oc-j) is a plant pathogenic fungus that causes canker and branch dieback diseases in the hardwood tree butternut, Juglans cinerea. Oc-j is a member of the order of Diaporthales, which includes many other plant pathogenic species, several of which also infect hardwood tree species. In this study, we sequenced the genome of Oc-j and achieved a high-quality assembly and delineated the phylogeny of Oc-j within the Diaporthales order using a genome-wide multi-gene approach. We also further examined multiple gene families that might be involved in plant pathogenicity and degradation of complex biomass, which are relevant to a pathogenic life-style in a tree host. We found that the Oc-j genome contains a greater number of genes in these gene families compared to other species in Diaporthales. These gene families include secreted CAZymes, kinases, cytochrome P450, efflux pumps, and secondary metabolism gene clusters. The large numbers of these genes provide Oc-j with an arsenal to cope with the specific ecological niche as a pathogen of the butternut tree.

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Draft whole-genome sequence of the Diaporthe helianthi 7/96 strain, causal agent of sunflower stem canker

Cited by 20 publications

References 11 publications

Polyketide synthases of Diaporthe helianthi and involvement of DhPKS1 in virulence on sunflower

Polyketide synthases of Diaporthe helianthi and involvement of DhPKS1 in virulence on sunflower

Evaluating multi-locus phylogenies for species boundaries determination in the genusDiaporthe

The genome of the butternut canker pathogen, Ophiognomonia clavigignenti-juglandacearum shows an elevated number of genes associated with secondary metabolism and protection from host resistance responses in comparison with other members of the Diaporthales

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