The analysis of 'Candidatus Phytoplasma fraxini' illustrates the small core genome of phytoplasmas

The taxon 'Candidatus Phytoplasma' (Mycoplasmatota) is characterised by intracellular bacteria that colonise the plant phloem and are transmitted by sap-sucking insect vectors. Infection of these nutrient-rich environments is reflected in reduced genome sizes <1 Mb, but they are blown up by mobile elements. The obligate parasitic lifestyle suggests even smaller genomes. However, some phylogenetic branches have not yet been covered by complete genome sequences, raising the question whether the conserved gene core may be even smaller than expected or, as recently shown [1], encoding additional metabolic functions.

We analysed the complete genome of 'Candidatus Phytoplasma fraxini', the first member of the ash yellows group, and performed a pangenome analysis.

The genome was determined by SMRT sequencing and assembled by Canu [2]. Consistency in annotation was ensured by re-annotating all genomes using RAST [3]. Orthologs were determined and used as previously described [1].

Themodel organisms such as genome of 'Ca. P. fraxini' is 598 kb in size, encoding 552 CDS. It lacks lactate metabolism, separating it from the closely related elm yellows group but shares a gene set of 242 genes limited to the basic functions of replication, protein biosynthesis, membrane transport, lipid and carbohydrate metabolism. Effector proteins involved in disease pathogenesis are not part of the shared genome. The phytoplasma gene set is not covered by Mycoplasma genitalium and Bacillus subtilis.

The analysis supports the additional evolutionary pathway of phytoplasmas, characterised by simplified parasitism and adapted pathogen-host interactions.

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