16 research outputs found
7.Econ.concorrenza e regolazione_AeGI 2015_2016_2 PP
<div><p>Black Sigatoka or black leaf streak disease, caused by the Dothideomycete fungus <i>Pseudocercospora fijiensis</i> (previously: <i>Mycosphaerella fijiensis</i>), is the most significant foliar disease of banana worldwide. Due to the lack of effective host resistance, management of this disease requires frequent fungicide applications, which greatly increase the economic and environmental costs to produce banana. Weekly applications in most banana plantations lead to rapid evolution of fungicide-resistant strains within populations causing disease-control failures throughout the world. Given its extremely high economic importance, two strains of <i>P</i>. <i>fijiensis</i> were sequenced and assembled with the aid of a new genetic linkage map. The 74-Mb genome of <i>P</i>. <i>fijiensis</i> is massively expanded by LTR retrotransposons, making it the largest genome within the Dothideomycetes. Melting-curve assays suggest that the genomes of two closely related members of the Sigatoka disease complex, <i>P</i>. <i>eumusae</i> and <i>P</i>. <i>musae</i>, also are expanded. Electrophoretic karyotyping and analyses of molecular markers in <i>P</i>. <i>fijiensis</i> field populations showed chromosome-length polymorphisms and high genetic diversity. Genetic differentiation was also detected using neutral markers, suggesting strong selection with limited gene flow at the studied geographic scale. Frequencies of fungicide resistance in fungicide-treated plantations were much higher than those in untreated wild-type <i>P</i>. <i>fijiensis</i> populations. A homologue of the <i>Cladosporium fulvum Avr4</i> effector, <i>PfAvr4</i>, was identified in the <i>P</i>. <i>fijiensis</i> genome. Infiltration of the purified PfAVR4 protein into leaves of the resistant banana variety Calcutta 4 resulted in a hypersensitive-like response. This result suggests that Calcutta 4 could carry an unknown resistance gene recognizing PfAVR4. Besides adding to our understanding of the overall Dothideomycete genome structures, the <i>P</i>. <i>fijiensis</i> genome will aid in developing fungicide treatment schedules to combat this pathogen and in improving the efficiency of banana breeding programs.</p></div
Comparison of selected gene families with potential roles in pathogenicity among five Dothideomycete fungi and the saprotrophic Sordariomycete <i>Neurospora crassa</i>.
<p>Comparison of selected gene families with potential roles in pathogenicity among five Dothideomycete fungi and the saprotrophic Sordariomycete <i>Neurospora crassa</i>.</p
Comparative genome statistics of the version 2 assembly of <i>Pseudocercospora fijiensis</i>, and several other sequenced fungi in the order Capnodiales.
<p>Comparative genome statistics of the version 2 assembly of <i>Pseudocercospora fijiensis</i>, and several other sequenced fungi in the order Capnodiales.</p
Genetic linkage map of <i>Pseudocercospora fijiensis</i> constructed from segregation data at 322 loci (233 DArT, 86 SSR and 3 minisatellite markers) among 135 individuals of a cross between the sequenced isolates CIRAD86 and CIRAD139A.
<p>The Diversity Arrays Technology (DArT) markers were named according to the output of proprietary DArT analysis software. For each of the 19 linkage groups (listed on top) the cumulative map distances (cM) as calculated using the Haldane mapping function are shown to the left.</p
Genome-wide nucleotide comparison between <i>Zymoseptoria tritici</i> (lower half of the circle) and <i>Pseudocercospora fijiensis</i> (upper half of the circle).
<p>The longest 28 scaffolds from <i>P</i>. <i>fijiensis</i> are shown. Gene content is conserved but is scattered among different chromosomes between these two fungi. There were no significant hits to dispensable chromosomes of <i>Z</i>. <i>tritici</i> (14–21). The 12 major scaffolds of <i>P</i>. <i>fijiensis</i> showing synteny are labeled in dark blue-green and the other 16 scaffolds are labeled in orange.</p
First-derivative graphs of melting curves of four different Dothideomycetes.
<p>Examples of first-derivative graphs of melting curves obtained for <i>Zymoseptoria tritici</i> (A), <i>Pseudocercospora fijiensis</i> (B), <i>P</i>. <i>eumusae</i> (C) and <i>P</i>. <i>musae</i> (D). E: A plot of G+C contents from sequence reads of <i>P</i>. <i>fijiensis</i>. This graph is very similar to the melting-curve analyses showing the difference in G+C content between the genomes of <i>P</i>. <i>fijiensis</i> and the other banana pathogens versus the <i>Z</i>. <i>tritici</i> genome.</p
The numbers of long terminal repeat (LTR) retrotransposons in hypothetical age bins from less than one to more than 20 million years.
<p>Estimated age of each transposon was calculated using the number of differences between its left and right repeats. These are considered identical at the time of insertion so all changes are likely due to mutations that occurred after transposition. All transition mutations were excluded to minimize the effects of repeat-induced point mutation.</p
Dot plot showing mesosynteny between the scaffolds of <i>Pseudocercospora fijiensis</i> and <i>Dothistroma septosporum</i>.
<p>Dot plot showing mesosynteny between the scaffolds of <i>Pseudocercospora fijiensis</i> and <i>Dothistroma septosporum</i>.</p
Phylogenetic analysis showing the placement of Dothideomycete species within the Capnodiales with expanded genomes.
<p>At least two genome expansions may have taken place; one leading to the banana pathogen <i>Pseudocercospora fijiensis</i> and one that contributed to its close relative the tomato pathogen <i>Cladosporium fulvum</i>. Genome sizes and percentages of the genome containing repeat elements are indicated in parentheses.</p
The repeat-induced point mutation (RIP) index calculated as (CpA+TpG)/(ApC+GpT) for genes<sup>a</sup> and repeats<sup>a</sup> in AT-poor and–rich regions of the <i>Pseudocercospora fijiensis</i> genome.
<p>The repeat-induced point mutation (RIP) index calculated as (CpA+TpG)/(ApC+GpT) for genes<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005876#t002fn001" target="_blank"><sup>a</sup></a> and repeats<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005876#t002fn001" target="_blank"><sup>a</sup></a> in AT-poor and–rich regions of the <i>Pseudocercospora fijiensis</i> genome.</p