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The Pectobacterium complex : diversity and phylogeny

Valérie Hélias: French Federation of Seed Potato Growers

<div><em>Pectobacterium</em> is one of the two bacterial genera responsible for blackleg and tuber soft rot on potato. <em>Pectobacterium </em>contains today eight species, namely <em>P. atrosepticum, P. carotovorum, P. betavasculorum, P. wasabiae, P. parmentieri</em>, <em>P. polaris</em>, <em>P. cacticida,</em> and<em> P. aroidearum </em>after recent new assignments. Field surveys conducted annually in France since 2003, coupled with diversity studies of the resulting strain collections, showed that blackleg symptoms are associated with a much larger range of species than the one (<em>P. atrosepticum</em>) historically almost exclusively held responsible for these symptoms in Europe. We thus aimed at analyzing more deeply the diversity and the phylogeny of <em>Pectobacterium, </em>particularly strains isolated from field symptoms on potato, and at evaluating changes within the <em>P. carotovorum (P.c.)</em> group during the last decades. Refining the taxonomy of the <em>Pectobacterium</em> groups was needed to develop specific detection tools, useful for testing and certifying seed lots. A MLSA was performed using <em>recA</em>, <em>dnaX</em> and <em>leuS</em> genes on 384 strains from the FN3PT and the CIRM-CFBP collections; 53 <em>Pectobacterium</em> sequences from databases were used as supplementary data. The already described species including the recently described <em>P. polaris</em> and the subspecies <em>P. c. odoriferum</em>, <em>P. c. brasiliense</em>, <em>P. c. actinidiae</em> were clearly defined by the MLSA results. In contrast, strains from <em>P.</em> <em>carotovorum </em>subsp. <em>carotovorum</em> showed a high genetic diversity in accordance with the earlier sequencing work on <em>PelY</em>. Our results showed that <em>P. carotovorum </em>subsp.<em> carotovorum</em> strains were distributed in several groups, all not being previously described.</div>