Evidence for a Common Toolbox Based on Necrotrophy in a Fungal Lineage Spanning Necrotrophs, Biotrophs, Endophytes, Host Generalists and Specialists

The Sclerotiniaceae (Ascomycotina, Leotiomycetes) is a relatively recently evolved lineage of necrotrophic host generalists, and necrotrophic or biotrophic host specialists, some latent or symptomless. We hypothesized that they inherited a basic toolbox of genes for plant symbiosis from their common ancestor. Maintenance and evolutionary diversification of symbiosis could require selection on toolbox genes or on timing and magnitude of gene expression. The genes studied were chosen because their products have been previously investigated as pathogenicity factors in the Sclerotiniaceae. They encode proteins associated with cell wall degradation: acid protease 1 (acp1), aspartyl protease (asps), and polygalacturonases (pg1, pg3, pg5, pg6), and the oxalic acid (OA) pathway: a zinc finger transcription factor (pac1), and oxaloacetate acetylhydrolase (oah), catalyst in OA production, essential for full symptom production in Sclerotinia sclerotiorum. Site-specific likelihood analyses provided evidence for purifying selection in all 8 pathogenicity-related genes. Consistent with an evolutionary arms race model, positive selection was detected in 5 of 8 genes. Only generalists produced large, proliferating disease lesions on excised Arabidopsis thaliana leaves and oxalic acid by 72 hours in vitro. In planta expression of oah was 10–300 times greater among the necrotrophic host generalists than necrotrophic and biotrophic host specialists; pac1 was not differentially expressed. Ability to amplify 6/8 pathogenicity related genes and produce oxalic acid in all genera are consistent with the common toolbox hypothesis for this gene sample. That our data did not distinguish biotrophs from necrotrophs is consistent with 1) a common toolbox based on necrotrophy and 2) the most conservative interpretation of the 3-locus housekeeping gene phylogeny – a baseline of necrotrophy from which forms of biotrophy emerged at least twice. Early oah overexpression likely expands the host range of necrotrophic generalists in the Sclerotiniaceae, while specialists and biotrophs deploy oah, or other as-yet-unknown toolbox genes, differently

Evolutionary analysis of endopolygalacturonase encoding genes of Botrytis cinerea

Sequence analysis of five of the six endopolygalacturonase-encoding genes (Bcpg1, Bcpg2, Bcpg3, Bcpg4, Bcpg5) from 32 strains of Botrytis cinerea showed marked gene to gene differences in the amount of among-strains diversity. Bcpg4 was almost invariable in all strains; Bcpg3 and Bcpg5 showed a moderate variability, similar to that of non-pathogenicity-associated genes examined in other studies. Conversely, Bcpg1 and Bcpg2 were highly variable and were shown to be under positive selection based on the McDonald-Kreitman test and likelihood ratio test. The evolution of the five endopolygalacturonase genes is explained by their different ecophysiological role. Diversification and balancing selection, as detected in Bcpg1 and Bcpg2, can be used by the pathogen to escape recognition by the host and delay plant reaction in the early phases of infection. The analysis of the polymorphisms and the location of the sites with high probability of being positively selected highlighted the relevance of variability of the BcPG1 and BcPG2 proteins at their C-terminal end. By contrast, the absence of variability in Bcpg4 suggests that the efficiency of the product of this gene is critical for B. cinerea growth in late phases of infection or during intraspecific competition, thus markedly affecting strain fitness

On the apple proliferation symptom display and the canopy colonization pattern of \u201cCandidatus Phytoplasma mali\u201d in apple trees

Notwithstanding the availability of several different real time PCR protocols for "Candidatus Phytoplasma mali", it is still unclear how informative is the estimation of the concentration of phytoplasma cells in the leaves of apple proliferation infected trees, and how the reliability of the estimations may be affected by an erratic and uneven distribution of the pathogen in the host. Here we investigated these issues systematically and showed that phytoplasma concentration varies significantly among seasons, but not between two cultivars that appeared to have different degree of susceptibility on the basis of the symptoms displayed. In fully symptomatic trees sampled at the end of the season the phytoplasmas were detectable in most leaves, but in more than half of the leaves at low concentrations. Both the pattern of colonization of the canopy and the amount of phytoplasmas varied greatly in trees that show symptom remission, although a direct relation between symptom severity and colonization could not be established. The sampling of the apple canopy for the purpose of evaluation of concentration of "Candidatus Phytoplasma mali" should take into consideration the complex pattern of colonization and seasonal variation

Assessment of genetic diversity in different accessions of Jatropha curcas

The aim of this work was to estimate the genetic diversity among 273 Jatropha curcas L. accessions and to develop a new SNP-based multi-allelic marker assay (Intra-. Locus SNP Haplotype, or LSH) to enhance the genetic discriminatory power of the SNP marker system. The accessions were collected in 15 countries of 3 continents (Africa, Asia and America) and analyzed with SSR, EST-SSR and SNP markers. Cluster analysis revealed the presence of two main genetic groups with an extreme high genetic uniformity and homozygosity of accessions grown in all countries of Africa, Asia, South America, and in some states of Mexico. Differently, an increased genetic variability and heterozygosity was observed in other states of Mexico and Guatemala. The newly developed LSH assay successfully identifies multiple alleles at the same locus and increased the average polymorphic information content of the SNP system. These results confirm the general idea recognizing the Central America region as the center of origin of the species and the genetic homogeneity of the world-wide cultivated accessions, and propose a new powerful SNP-based multi-allelic marker assay for enhancing genetic diversity analysis and selection methods in breeding programs. © 2015 Elsevier B.V

On the alleged origin of geminiviruses from extrachromosomal DNAs of phytoplasmas

<p>Abstract</p> <p>Background</p> <p>Several phytoplasmas, wall-less phloem limited plant pathogenic bacteria, have been shown to contain extrachromosomal DNA (EcDNA) molecules encoding a replication associated protein (Rep) similar to that of geminiviruses, a major group of single stranded (ss) DNA plant viruses. On the basis of that observation and of structural similarities between the capsid proteins of geminiviruses and the <it>Satellite tobacco necrosis virus</it>, it has been recently proposed that geminiviruses evolved from phytoplasmal EcDNAs by acquiring a capsid protein coding gene from a co-invading plant RNA virus.</p> <p>Results</p> <p>Here we show that this hypothesis has to be rejected because (i) the EcDNA encoded Rep is not of phytoplasmal origin but has been acquired by phytoplasmas through horizontal transfer from a geminivirus or its ancestor; and (ii) the evolution of geminivirus capsid protein in land plants implies missing links, while the analysis of metagenomic data suggests an alternative scenario implying a more ancient evolution in marine environments.</p> <p>Conclusion</p> <p>The hypothesis of geminiviruses evolving in plants from DNA molecules of phytoplasma origin contrasts with other findings. An alternative scenario concerning the origin and spread of Rep coding phytoplasmal EcDNA is presented and its implications on the epidemiology of phytoplasmas are discussed.</p