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

Abstract

BackgroundAlmond 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.ResultsSequence-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.ConclusionThe 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 materialThe online version of this article (doi:10.1186/s12866-015-0487-4) contains supplementary material, which is available to authorized users.

Multilocus sequence analysis of phytoplasma strains of 16SrII group in Iran and their comparison with related strains

“…MLSA has been successfully used as a tool for characterising and defining the genetic divergence of phytoplasma strains (Casati et al, ; Davis et al, ; Duduk, Calari, Paltrinieri, Duduk, & Bertaccini, ; Lee, Bottner‐Parker, Zhao, Bertaccini, & Davis, ; Lee, Martini, Marcone, & Zhu, ; Quaglino et al, ). In this study, we applied MLSA to assess the genetic divergence among the representative phytoplasmas within the group 16SrII reported from Iran and other countries.…”

“…Inmp gene was first used in the genetic variation analysis of “ Ca . P. phoenicium” strains (16SrIX; Quaglino et al, ). In contrast to phytoplasmas of 16SrIX, inmp gene was under a negative selection pressure in phytoplasmas of 16SrII and 16SrIII groups.…”

A few sequence polymorphisms among isolates of Maize bushy stunt phytoplasma associate with organ proliferation symptoms of infected maize plants

“…To date, there are only five fully assembled genomes (Oshima et al , 2004; Bai et al , 2006; Kube et al , 2008; Tran-Nguyen et al , 2008; Andersen et al , 2013) and a further nine draft genome (contig) sequences available of phytoplasmas (Saccardo et al , 2012; Chung et al , 2013; Chen et al , 2014; Kakizawa et al , 2014; Mitrovic et al , 2014; Quaglino et al , 2015). These belong to 16Sr-I, -II, -III, -X and -XII groups of diverse clades within the phylogenetic tree (Hogenhout et al , 2008), enabling assessment of the diversity in phytoplasma genome content and organization.…”

Compilación de oligonucleótidos para la detección y clasificación de fitoplasmas

“…Phytoplasma pruni" [16SrIII] (Saccardo et al, 2012), el de "Ca. Phytoplasma phoenicium" [16SrIX] que, hasta el momento, es el genoma reportado más pequeño con 0,35 Mbp (Quaglino et al, 2015), y recientemente el genoma de "Ca. Phytoplasma aurantifolia" [16SrII] con 0,47 Mbp (Foissac y Carle, 2017) (Cuadro 1).…”