Birth, death and horizontal transfer of the fumonisin biosynthetic gene cluster during the evolutionary diversification of <i><scp>F</scp>usarium</i>

Proctor, Robert H.; Hove, François Van; Susca, Antonia; Stea, Gaetano; Busman, Mark; Lee, Théo van der; Waalwijk, C.; Moretti, Antonio; Ward, Todd J.

doi:10.1111/mmi.12362

Cited by 107 publications

(100 citation statements)

References 83 publications

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“…The co-localization of divergent genetic regions and genes that are absent among related genomes is consistent with what has been reported previously for Fusarium species [4, 14, 59]. Co-localization may suggest that genes were acquired or lost as clusters; multiple gains or losses of gene clusters have been suggested for the secondary metabolite gene cluster responsible for fumonisin biosynthesis in Fusarium [60]. Lineage specific chromosomes and large scale horizontal gene transfer events, such as the transfer of an entire chromosome that have been reported in F. oxysporum , are yet to be reported for members of the F. graminearum species complex [4].…”

Section: Discussionsupporting

confidence: 87%

Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum

et al. 2016

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BackgroundThe Fusarium graminearum species complex is composed of many distinct fungal species that cause several diseases in economically important crops, including Fusarium Head Blight of wheat. Despite being closely related, these species and individuals within species have distinct phenotypic differences in toxin production and pathogenicity, with some isolates reported as non-pathogenic on certain hosts. In this report, we compare genomes and gene content of six new isolates from the species complex, including the first available genomes of F. asiaticum and F. meridionale, with four other genomes reported in previous studies.ResultsA comparison of genome structure and gene content revealed a 93–99% overlap across all ten genomes. We identified more than 700 k base pairs (kb) of single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) within common regions of the genome, which validated the species and genetic populations reported within species. We constructed a non-redundant pan gene list containing 15,297 genes from the ten genomes and among them 1827 genes or 12% were absent in at least one genome. These genes were co-localized in telomeric regions and select regions within chromosomes with a corresponding increase in SNPs and indels. Many are also predicted to encode for proteins involved in secondary metabolism and other functions associated with disease. Genes that were common between isolates contained high levels of nucleotide variation and may be pseudogenes, allelic, or under diversifying selection.ConclusionsThe genomic resources we have contributed will be useful for the identification of genes that contribute to the phenotypic variation and niche specialization that have been reported among members of the F. graminearum species complex.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3371-1) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 87%

Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum

et al. 2016

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“…This cluster occurs in the same genomic context in F. proliferatum and F. fujikuroi , at another genomic position in F. verticillioides (Proctor et al 2013), but is absent in the genomes of F. mangiferae (supplementary table S1, Supplementary Material online). F. oxysporum O-1819 has an intact cluster, whereas the cluster is absent in 12 other sequenced F. oxysporum strains (Proctor et al 2013). Recently, it has been shown that Aspergillus niger has an intact fumonisin gene cluster (Frisvad et al 2007).…”

Section: Resultsmentioning

confidence: 98%

Comparative “Omics” of theFusarium fujikuroiSpecies Complex Highlights Differences in Genetic Potential and Metabolite Synthesis

et al. 2016

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Species of the Fusarium fujikuroi species complex (FFC) cause a wide spectrum of often devastating diseases on diverse agricultural crops, including coffee, fig, mango, maize, rice, and sugarcane. Although species within the FFC are difficult to distinguish by morphology, and their genes often share 90% sequence similarity, they can differ in host plant specificity and life style. FFC species can also produce structurally diverse secondary metabolites (SMs), including the mycotoxins fumonisins, fusarins, fusaric acid, and beauvericin, and the phytohormones gibberellins, auxins, and cytokinins. The spectrum of SMs produced can differ among closely related species, suggesting that SMs might be determinants of host specificity. To date, genomes of only a limited number of FFC species have been sequenced. Here, we provide draft genome sequences of three more members of the FFC: a single isolate of F. mangiferae, the cause of mango malformation, and two isolates of F. proliferatum, one a pathogen of maize and the other an orchid endophyte. We compared these genomes to publicly available genome sequences of three other FFC species. The comparisons revealed species-specific and isolate-specific differences in the composition and expression (in vitro and in planta) of genes involved in SM production including those for phytohormome biosynthesis. Such differences have the potential to impact host specificity and, as in the case of F. proliferatum, the pathogenic versus endophytic life style.

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“…An alternative explanation could be the presence of horizontal gene transfer, already detected in other Geosmithia hydrophobin proteins (Bettini et al 2014), that will better explain the presence of very similar or even identical nucleotide sequences in different species. Such a model of evolution, involving either multiple horizontal transfer events and/or birth-and-death, was recently proposed in Fusarium for the fumonisin biosynthetic gene cluster (Proctor et al 2013).…”

Section: Resultsmentioning

confidence: 99%

Interspecific variability of class II hydrophobin GEO1 in the genus Geosmithia

et al. 2014

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a b s t r a c tThe genus Geosmithia Pitt (Ascomycota: Hypocreales) comprises cosmopolite fungi living in the galleries built by phloeophagous insects. Following the characterization in Geosmithia species 5 of the class II hydrophobin GEO1 and of the corresponding gene, the presence of the geo1 gene was investigated in 26 strains derived from different host plants and geographic locations and representing the whole phylogenetic diversity of the genus. The geo1 gene was de-tected in all the species tested where it maintained the general organization shown in Geosmithia species 5, comprising three exons and two introns. Size variations were found in both introns and in the first exon, the latter being due to the presence of an intragenic tandem repeat sequence corresponding to a stretch of glycine residues in the deduced proteins.At the amino acid level the deduced proteins had 44.6 % identity and no major differences in the biochemical parameters (pI, GRAVY index, hydropathy plots) were found. GEO1 release in the fungal culture medium was also assessed by turbidimetric assay and SDS-PAGE, and showed high variability between species. The phylogeny based on the geo1 sequences did not correspond to that generated from a neutral marker (ITS rDNA), suggesting that sequence similarities could be influenced by other factors than phylogenetic relatedness, such as the intimacy of the symbiosis with insect vectors. The hypothesis of a strong selection pressure on the geo1 gene was sustained by the low values (<1) of non synonymous to synonymous nucleotide substitutions ratios (Ka/Ks), which suggest that purifying selection might act on this gene. These results are compatible with either a birth-and-death evolution scenario or horizontal transfer of the gene between Geosmithia species.

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Birth, death and horizontal transfer of the fumonisin biosynthetic gene cluster during the evolutionary diversification of Fusarium

Cited by 107 publications

References 83 publications

Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum

Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum

Comparative “Omics” of theFusarium fujikuroiSpecies Complex Highlights Differences in Genetic Potential and Metabolite Synthesis

Interspecific variability of class II hydrophobin GEO1 in the genus Geosmithia

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