Multilocus sequence analysis reveals the genetic diversity of European fruit tree phytoplasmas and supports the existence of inter-species recombination

Abstract

The genetic diversity of three temperate fruit tree phytoplasmas 'Candidatus Phytoplasma prunorum', 'Ca. P. mali' and 'Ca. P. pyri' has been established by multilocus sequence analysis. Among the four genetic loci used, the genes imp and aceF distinguished 30 and 24 genotypes, respectively, and showed the highest variability. Percentage of substitution for imp ranged from 50 to 68 % according to species. Percentage of substitution varied between 9 and 12 % for aceF, whereas it was between 5 and 6 % for pnp and secY. In the case of 'Ca P. prunorum' the three most prevalent aceF genotypes were detected in both plants and insect vectors, confirming that the prevalent isolates are propagated by insects. The four isolates known to be hypo-virulent had the same aceF sequence, indicating a possible monophyletic origin. Haplotype network reconstructed by eBURST revealed that among the 34 haplotypes of 'Ca. P. prunorum', the four hypo-virulent isolates also grouped together in the same clade. Genotyping of some Spanish and Azerbaijanese 'Ca. P. pyri' isolates showed that they shared some alleles with 'Ca. P. prunorum', supporting for the first time to our knowledge, the existence of inter-species recombination between these two species.

The genome biology of phytoplasma: modulators of plants and insects

“…Even though phytoplasmas are subject to most of these factors, phytoplasmas are not restricted to a single insect host and populations can consist of multiple phytoplasma strains [26, [34][35][36][37]. Particularly phytoplasmas with wide plant and insect vectors host ranges are more likely to encounter phytoplasmas and other organisms that provide sources for acquisition of genetic elements.…”

In-vineyard population structure of ‘Candidatus Phytoplasma solani’ using multilocus sequence typing analysis

“…The study of phytoplasma population genetics can be based on genotyping by multilocus sequence typing analysis (Arnaud et al, 2007;Danet et al, 2011), and on the estimation of the dN/dS ratio, which is the ratio between the non-synonymous (dN) and the synonymous (dS) substitution rates in an alignment of amino-acidcoding sequences (Nielsen, 2005). Synonymous substitutions are usually regarded as having much smaller effects on fitness than non-synonymous substitutions.…”

Molecular typing of ‘Candidatus Phytoplasma mali’ and epidemic history tracing by a combined T-RFLP/VNTR analysis approach

“…The application of these methods has helped to reveal the genetic diversity of 'Ca. P. mali' in several geographic areas (Jarausch et al 2000;Cainelli et al 2004;Martini et al 2008;Schneider and Seemüller 2009;Casati et al 2010;Danet et al 2011) and to gain insight into the pathological relevance of different strains (Seemüller and Schneider 2007;Seemüller et al 2010). These analysis procedures, however, involve several timeconsuming and labour-intensive steps, making highthroughput screening difficult.…”

“…P. mali' subtypes has been based on PCR-RFLP analysis (Jarausch et al 2000;Martini et al 2008;Casati et al 2010), SSCP analysis (Schneider and Seemüller 2009) and/or DNA sequence analysis (Schneider and Seemüller 2009;Casati et al 2010;Seemüller et al 2010;Danet et al 2011) of different genomic regions. The application of these methods has helped to reveal the genetic diversity of 'Ca.…”