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Background  Almond witches’-broom (AlmWB), a devastating disease of almond, peach and nectarine in Lebanon, is associated with ‘ Candidatus  Phytoplasma phoenicium’. In the present study, we generated a draft genome sequence of ‘ Ca . P. phoenicium’ strain SA213, representative of phytoplasma strain populations from different host plants, and determined the genetic diversity among phytoplasma strain populations by phylogenetic analyses of  16S rRNA ,  groEL ,  tufB  and  inmp  gene sequences.    Results  Sequence-based typing and phylogenetic analysis of the gene  inmp , coding an integral membrane protein, distinguished AlmWB-associated phytoplasma strains originating from diverse host plants, whereas their  16S rRNA ,  tufB  and  groEL  genes shared 100 % sequence identity. Moreover, dN/dS analysis indicated positive selection acting on  inmp  gene. Additionally, the analysis of ‘ Ca . P. phoenicium’ draft genome revealed the presence of integral membrane proteins and effector-like proteins and potential candidates for interaction with hosts. One of the integral membrane proteins was predicted as BI-1, an inhibitor of apoptosis-promoting Bax factor. Bioinformatics analyses revealed the presence of putative BI-1 in draft and complete genomes of other ‘ Ca . Phytoplasma’ species.    Conclusion  The genetic diversity within ‘ Ca . P. phoenicium’ strain populations in Lebanon suggested that AlmWB disease could be associated with phytoplasma strains derived from the adaptation of an original strain to diverse hosts. Moreover, the identification of a putative inhibitor of apoptosis-promoting Bax factor (BI-1) in ‘ Ca . P. phoenicium’ draft genome and within genomes of other ‘ Ca . Phytoplasma’ species suggested its potential role as a phytoplasma fitness-increasing factor by modification of the host-defense response.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-015-0487-4) contains supplementary material, which is available to authorized users.

‘Candidatus Phytoplasma phoenicium’ associated with almond witches’-broom disease: from draft genome to genetic diversity among strain populations