Genomic analysis and biology of a novel variant of Xylella fastidiosa subspecies multiplex infecting different host plants in Tuscany, Italy

An increasing number of Xylella fastidiosa outbreaks associated with strains of the
subspecies multiplex has been reported in southern Europe, currently the most common strains being
detected in Corsica, the Balearic Islands, the province of Alicante (Spain) and, more recently, reported
for the first time in Portugal and in the region of Tuscany (northen Italy). The Tuscany outbreak raised
major concerns, being associated with a new variant of X. fastidiosa subsp. multiplex, characterised
as sequence type ST87, capable of infecting, among the others, almond. Although this sequence type
is closely related to the more common ST6 and ST7 variants, remarkable differences were recorded
when culturing the ST87 isolates on different media as well as when comparing their draft genomes. In
contrast to the majority of the strains of the subspecies multiplex, the ST87 isolates grow on PD3 solid
medium, a peculiar feature described for a few and highly virulent strains associated with almond leaf
scorch disease in North America (Almeida and Purcell, 2003). Analyses based on core genome
alignments and single nucleotide polymorphisms of currently available Xylella genomes show they are
genetically related to strains previously characterised in North America, but in a separate clade from
strains of the subspecies multiplex previously sequenced in Europe, supporting the hyphothesis that
they originate from a distinct introduction that occured in Europe. Pathogenicity tests on Prunus spp.
and grapes are ongoing to assess the virulence and the host range of this newly discovered variant of
X. fastidiosa.