Open access
15 October 2015

Draft Genome Sequence of “Candidatus Phytoplasma pruni” Strain CX, a Plant-Pathogenic Bacterium


Candidatus Phytoplasma pruni” strain CX, belonging to subgroup 16SrIII-A, is a plant-pathogenic bacterium causing economically important diseases in many fruit crops. Here, we report the draft genome sequence, which consists of 598,508 bases, with a G+C content of 27.21 mol%.


Phytoplasmas are cell wall-less plant-pathogenic prokaryotes, which inhabit both insects (e.g., leafhoppers, planthoppers, and psyllids) and >1,000 plant species (13), causing numerous economically important diseases worldwide. In nature, insects serve as vectors that transmit phytoplasmas and spread diseases among plants. There are a vast number of diverse phytoplasma strains that are distributed on all continents. Phylogenetic analysis based on 16S rRNA gene sequences has indicated that phytoplasmas form a large discreet monophyletic clade paraphyletic to the genus Acholeplasma in the class Mollicutes (4). Because of the inability to readily cultivate phytoplasmas in cell-free medium, the provisional genus “Candidatus Phytoplasma” and also “Candidatus Phytoplasma spp.” were proposed to accommodate their classification (5). For finer classification of phytoplasmas, a scheme was proposed based on restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA sequence that thus far includes 32 16S ribosomal (16Sr) groups and >200 subgroups (6, 7). Group 16SrIII represents one of the most diverse groups (810). “Candidatus Phytoplasma pruni” strain CX belongs to subgroup 16SrIII-A; strains in this subgroup cause severe disease of decline in many stone fruit trees (10). In order to understand the pathogenic nature of phytoplasmas, genomic sequencing has been the focus. Thus far, five phytoplasma genomes (belonging to 16SrI, 16SrX, and 16SrXII groups) have been fully sequenced (1115). Draft genome sequences of four phytoplasmas belonging to 16SrIII-B (Italian clover phyllody, “Candidatus Phytoplasma” strain MA), 16SrIII-F (milkweed witches’ broom, “Candidatus Phytoplasma” strain MW1 and Vaccinium witches’ broom “Candidatus Phytoplasma” strain VAC), and 16SrIII-H (poinsettia branch-inducing “Candidatus Phytoplasma” strain JR1 = PoiBI), were published recently (16). Here, we report the draft genome sequence of “Ca. Phytoplasma pruni” strain CX.
Candidatus Phytoplasma pruni” strain CX DNA was extracted from preparations of sieve cells isolated from infected periwinkle plants (Catharanthus roseus), as previously described (17), with the addition of RNase A digestion prior to the final phenol-chloroform extraction. Whole-genome paired-end sequencing was performed using the 454-GS Junior system (Roche Diagnostics, Indianapolis, IN). The original 177,537 reads were filtered using the BLAST(p/n). The reads were searched against custom BLAST databases containing “Candidatus Phytoplasma” sequences. This resulted in 132,205 reads that were assembled using the Newbler Assembler 2.9. The number of aligned reads was 130,704, and the number of aligned bases was 43,684,964. The average read coverage was 65×. The assembly resulted in 46 contigs >534 bp, with a total base value of 598,508 bases, which is in agreement with the sizes of other published group 16SrIII “Candidatus Phytoplasma” partial genomes (583 to 670 kb) (16, 18). The G+C content was 27.21 mol%. The N50 was 38,825 bases, and the largest contig was 93,855 bases. Use of the gene finder GeneMark.hmm on the largest 46 contigs resulted in the identification of 602 protein-coding genes.
The availability of the 16SrIII-A CX draft genome sequence combined with the other existing four draft genome sequences of group 16SrIII strains will facilitate the identification of specific genomic features of this group that may be responsible for the pathogeneses inflicted by various 16SrIII group “Candidatus Phytoplasma” strains. All five strains exhibit characteristic symptoms in their common host, C. roseus.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under accession no. LHCF00000000. The version described in this paper is the first version, LHCF01000000.


Funding for this project was provided by the U.S. Government.


Bertaccini A. 2007. Phytoplasmas: diversity, taxonomy, and epidemiology. Front Biosci 12:673–689.
Hogenhout SA, Oshima K, Ammar E, Kakizawa S, Kingdom HN, Namba S. 2008. Phytoplasmas: bacteria that manipulate plants and insects. Mol Plant Pathol 9:403–423.
Lee I, Davis RE, Gundersen-Rindal DE. 2000. Phytoplasma: phytopathogenic Mollicutes. Annu Rev Microbiol 54:221–255.
Gundersen DE, Lee I.-M, Rehner SA, Davis RE, Kingsbury DT. 1994. Phylogeny of mycoplasmalike organisms (phytoplasmas): a basis for their classification. J Bacteriol 176:5244–5254.
IRPCM Phytoplasma/Spiroplasma Working Team--Phytoplasma Taxonomy Group. 2004. ‘Candidatus Phytoplasma’, a taxon for the wall-less, non-helical prokaryotes that colonize plant phloem and insects. Int J Syst Evol Microbiol 54:1243–1255.
Lee I.-M, Gundersen-Rindal DE, Davis RE, Bartoszyk IM. 1998. Revised classification scheme of phytoplasmas based on RFLP analyses of 16S rRNA and ribosomal protein gene sequences. Int J Syst Evol Microbiol 48:1153–1169.
Nejat N, Vadamalai G, Davis RE, Harrison NA, Sijam K, Dickinson M, Abdullah SNA, Zhao Y. 2013. “Candidatus Phytoplasma malaysianum”, a novel taxon associated with virescence and phyllody of Madagascar periwinkle (Catharanthus roseus). Int J Syst Evol Microbiol 63:540–548.
Wei W, Davis RE, Lee I.-M, Zhao Y. 2007. Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups. Int J Syst Evol Microbiol 57:1855–1867.
Zhao Y, Wei W, Lee I.-M, Shao J, Suo X, Davis RE. 2009. Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII). Int J Syst Evol Microbiol 59:2582–2593.
Davis RE, Zhao Y, Dally EL, Lee I.-M, Jomantiene R, Douglas SM. 2013. “Candidatus Phytoplasma pruni”, a novel taxon associated with X-disease of stone fruits, Prunus spp.: multilocus characterization based on 16S rRNA, secY, and ribosomal protein genes. Int J Syst Evol Microbiol 63:766–776.
Oshima K, Kakizawa S, Nishigawa H, Jung H, Wei W, Suzuki S, Arashida R, Nakata D, Miyata S, Ugaki M, Namba S. 2004. Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma. Nat Genet 36:27–29.
Bai X, Zhang J, Ewing A, Miller SA, Jancso Radek A, Shevchenko DV, Tsukerman K, Walunas T, Lapidus A, Campbell JW, Hogenhout SA. 2006. Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts. J Bacteriol 188:3682–3696.
Tran-Nguyen LTT, Kube M, Schneider B, Reinhardt R, Gibb KS. 2008. Comparative genome analysis of “Candidatus Phytoplasma australiense” (subgroup tuf-Australia I; rp-A) and “Ca. Phytoplasma asteris” strains OY-M and AY-WB. J Bacteriol 190:3979–3991.
Kube M, Schneider B, Kuhl H, Dandekar T, Heitmann K, Migdoll AM, Reinhardt R, Seemüller E. 2008. The linear chromosome of the plant-pathogenic mycoplasma “Candidatus Phytoplasma mali”. BMC Genomics 9:306.
Andersen MT, Liefting LW, Havukkala I, Beever RE. 2013. Comparison of the complete genome sequence of two closely related isolates of “Candidatus Phytoplasma australiense” reveals genome plasticity. BMC Genomics 14:529.
Saccardo F, Martini M, Palmano S, Ermacora P, Scortichini M, Loi N, Firrao G. 2012. Genome drafts of four phytoplasma strains of the ribosomal group 16SrIII. Microbiology 158:2805–2814.
Lee I.-M, Davis RE. 1988. Detection and investigation of genetic relatedness among aster yellows and other mycoplasmalike organisms by using cloned DNA and RNA probes. Mol Plant Microbe Interact 1:303–310.
Marcone C, Neimark H, Ragozzino A, Lauer U, Seemüller E. 1999. Chromosome sizes of phytoplasmas composing major phylogenetic groups and subgroups. Phytopathology 89:805–810.

Information & Contributors


Published In

cover image Genome Announcements
Genome Announcements
Volume 3Number 529 October 2015
eLocator: 10.1128/genomea.01117-15


Received: 14 August 2015
Accepted: 11 September 2015
Published online: 15 October 2015



I.-M. Lee
Molecular Plant Pathology Laboratory, U.S. Department of Agriculture, Beltsville, Maryland, USA
J. Shao
Molecular Plant Pathology Laboratory, U.S. Department of Agriculture, Beltsville, Maryland, USA
K. D. Bottner-Parker
Molecular Plant Pathology Laboratory, U.S. Department of Agriculture, Beltsville, Maryland, USA
D. E. Gundersen-Rindal
Invasive Insect Biocontrol and Behavior Laboratory, U.S. Department of Agriculture, Beltsville, Maryland, USA
Y. Zhao
Molecular Plant Pathology Laboratory, U.S. Department of Agriculture, Beltsville, Maryland, USA
R. E. Davis
Molecular Plant Pathology Laboratory, U.S. Department of Agriculture, Beltsville, Maryland, USA


Address correspondence to I.-M. Lee, [email protected].

Metrics & Citations


Note: There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.

Citation counts come from the Crossref Cited by service.


If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download.

View Options

Figures and Media






Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy