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Background  Phytoplasmas are insect-transmitted, uncultivable bacterial plant pathogens that cause diseases in hundreds of economically important plants. They represent a monophyletic group within the class  Mollicutes  (trivial name mycoplasmas) and are characterized by a small genome with a low GC content, and the lack of a firm cell wall. All mycoplasmas, including strains of ' Candidatus (Ca.)  Phytoplasma asteris' and ' Ca . P. australiense', examined so far have circular chromosomes, as is the case for almost all walled bacteria.    Results  Our work has shown that ' Ca . Phytoplasma mali', the causative agent of apple proliferation disease, has a linear chromosome. Linear chromosomes were also identified in the closely related provisional species ' Ca . P. pyri' and ' Ca . P. prunorum'. The chromosome of ' Ca . P. mali' strain AT is 601,943 bp in size and has a GC content of 21.4%. The chromosome is further characterized by large terminal inverted repeats and covalently closed hairpin ends. Analysis of the protein-coding genes revealed that glycolysis, the major energy-yielding pathway supposed for ' Ca . P. asteris', is incomplete in ' Ca . P. mali'. Due to the apparent lack of other metabolic pathways present in mycoplasmas, it is proposed that maltose and malate are utilized as carbon and energy sources. However, complete ATP-yielding pathways were not identified. ' Ca . P. mali' also differs from ' Ca . P. asteris' by a smaller genome, a lower GC content, a lower number of paralogous genes, fewer insertions of potential mobile DNA elements, and a strongly reduced number of ABC transporters for amino acids. In contrast, ' Ca . P. mali' has an extended set of genes for homologous recombination, excision repair and SOS response than ' Ca . P. asteris'.    Conclusion  The small linear chromosome with large terminal inverted repeats and covalently closed hairpin ends, the extremely low GC content and the limited metabolic capabilities reflect unique features of ' Ca . P. mali', not only within phytoplasmas, but all mycoplasmas. It is expected that the genome information obtained here will contribute to a better understanding of the reduced metabolism of phytoplasmas, their fastidious nutrition requirements that prevented axenic cultivation, and the mechanisms involved in pathogenicity.

The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'