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

Infiltration of purified protein of the putative effector gene <i>PfAvr4</i> from <i>Pseudocercospora fijiensis</i> into leaves of banana and tomato.

<p>A: Infiltrations into leaves of resistant and susceptible banana varieties. B: Infiltrations into leaves of tomato with or without the <i>Cf4</i> resistance gene known to interact with PfAVR4. Experiments were done with crude fermentor product and concentrated or diluted product. Fermentor medium alone and water were used as controls.</p

The repeat-induced point mutation (RIP) index calculated as (CpA+TpG)/(ApC+GpT) for genes^a and repeats^a 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">^a</a> and repeats<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005876#t002fn001" target="_blank">^a</a> in AT-poor and–rich regions of the <i>Pseudocercospora fijiensis</i> genome.</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

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

Electrophoretic karyotypes of two strains of <i>Pseudocercospora fijiensis</i>.

<p>A) Bands separated with conditions for small chromosomes. Lane 1, chromosomes from <i>Saccharomyces cerevisiae</i> as high-molecular-weight (HMW) marker; lane 2, strain CIRAD86; lane 3, strain E22. B) Bands separated under conditions to resolve medium and large chromosomes. Lane 1, chromosomes from <i>Schizosaccharomyces pombe</i> as HMW marker for large chromosomes; lane 2, strain CIRAD86; lane 3, strain E22; lane 4, chromosomes from <i>Hansenula wingei</i> as HMW marker for medium chromosomes in size. Marker sizes are in Kb.</p

Comparison of the amount of repeat-induced point mutation (RIP) between AT-rich blocks and more GC-rich regions of the <i>Pseudocercospora fijiensis</i> genome as measured by the RIP index (CpA+TpG)/(ApC+GpT).

<p>(A) AT-rich blocks have a lower RIP index indicating a depletion of RIP-susceptible sites due to a higher frequency of RIP compared to (B) an AT-poor region (higher GC) of the genome, which has a higher RIP index reflecting very little RIP. Four AT-rich blocks are shown along with one AT-poor region for comparison. Length of each block in kilobases is shown along the x-axis and the RIP index (CpA+TpG)/(ApC+GpT) is shown on the y-axis.</p

Comparison of repeat classes among <i>Zymoseptoria tritici</i>, the only Dothideomycete with a completely sequenced genome, <i>Pseudocercospora fijiensis</i> and <i>Cladosporium fulvum</i>, the only other Dothideomycete known to have a transposon-expanded genome.

<p>Comparison of repeat classes among <i>Zymoseptoria tritici</i>, the only Dothideomycete with a completely sequenced genome, <i>Pseudocercospora fijiensis</i> and <i>Cladosporium fulvum</i>, the only other Dothideomycete known to have a transposon-expanded genome.</p

Repeat-induced point mutation (RIP) dinucleotide bias in <i>Pseudocercospora fijiensis</i> genome.

<p>A clear CA <-> TA dinucleotide bias is observed in <i>P</i>. <i>fijiensis</i> repetitive families, indicating that RIP likely occurs and mutates CA nucleotide pairs to CT.</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