title: 'Candidatus Phytoplasma phoenicium' associated with almond witches'-broom disease: from draft genome to genetic diversity among strain populations.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, via Celoria 2, 20133, Milan, Italy. fabio.quaglino@unimi.it.
authors.forename: Fabio
authors.initials: F
authors.lastname: Quaglino
authors.affiliation: Division Phytomedicine, Thaer-Institute, Humboldt-Universität zu Berlin, Berlin, Germany. michael.kube@agrar.hu-berlin.de.
authors.forename: Michael
authors.initials: M
authors.lastname: Kube
authors.affiliation: Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut, Lebanon. maanjawhari@gmail.com.
authors.forename: Maan
authors.initials: M
authors.lastname: Jawhari
authors.affiliation: Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut, Lebanon. abujawyf@aub.edu.lb.
authors.forename: Yusuf
authors.initials: Y
authors.lastname: Abou-Jawdah
authors.affiliation: Division Phytomedicine, Thaer-Institute, Humboldt-Universität zu Berlin, Berlin, Germany. christin.siewert@agrar.hu-berlin.de.
authors.forename: Christin
authors.initials: C
authors.lastname: Siewert
authors.affiliation: Department of Plant Protection, Lebanese Agricultural Research Institute, Tal Amara, Lebanon. echoueiri@lari.gov.lb.
authors.forename: Elia
authors.initials: E
authors.lastname: Choueiri
authors.affiliation: Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut, Lebanon. hs05@aub.edu.lb.
authors.forename: Hana
authors.initials: H
authors.lastname: Sobh
authors.affiliation: Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, via Celoria 2, 20133, Milan, Italy. paola.casati@unimi.it.
authors.forename: Paola
authors.initials: P
authors.lastname: Casati
authors.affiliation: Department of Agricultural, Forest and Food Sciences, Università degli Studi di Torino, Grugliasco (TO), Italy. rosemarie.tedeschi@unito.it.
authors.forename: Rosemarie
authors.initials: R
authors.lastname: Tedeschi
authors.affiliation: AVSI Foundation, Jounieh, Ghadir, Lebanon. marina.molinolova@avsi.org.
authors.forename: Marina Molino
authors.initials: MM
authors.lastname: Lova
authors.affiliation: Department of Agricultural, Forest and Food Sciences, Università degli Studi di Torino, Grugliasco (TO), Italy. alberto.alma@unito.it.
authors.forename: Alberto
authors.initials: A
authors.lastname: Alma
authors.affiliation: Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, via Celoria 2, 20133, Milan, Italy. piero.bianco@unimi.it.
authors.forename: Piero Attilio
authors.initials: PA
authors.lastname: Bianco
mesh_terms: D000129:Acholeplasmataceae; D001426:Bacterial Proteins / Q000235:genetics; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D007861:Lebanon; D008969:Molecular Sequence Data; D058889:Molecular Typing; D010802:Phylogeny; D045582:Phytoplasma / Q000145:classification* / Q000302:isolation & purification*; D010935:Plant Diseases / Q000382:microbiology*; D000068181:Prunus dulcis / Q000382:microbiology*; D000068239:Prunus persica / Q000382:microbiology; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S