Comparative genome analysis of jujube witches'-broom Phytoplasma, an obligate pathogen that causes jujube witches'-broom disease

Abstract

Background: JWB phytoplasma is a kind of insect-transmitted and uncultivable bacterial plant pathogen causeing a destructive Jujube disease. To date, no genome information about JWB phytoplasma has been published, which hindered its characterization at genomic level. To understand its pathogenicity and ecology, the genome of a JWB phytoplasma isolate jwb-nky was sequenced and compared with other phytoplasmas enabled us to explore the mechanisms of genomic rearrangement.

Results: The complete genome sequence of JWB phytoplasma (jwb-nky) was determined, which consisting of one circular chromosome of 750,803 bp with a GC content of 23.3%. 694 protein-encoding genes, 2 operons for rRNA genes and 31 tRNA genes as well as 4 potential mobile units (PMUs) containing clusters of DNA repeats were identified. Based on PHIbaes analysis, a large number of genes were genome-specific and approximately 13% of JWB phytoplasma genes were predicted to be associated with virulence. Although transporters for maltose, dipeptides/oligopeptides, spermidine/putrescine, cobalt, Mn/Zn and methionine were identified, KEGG pathway analysis revealed the reduced metabolic capabilities of JWB phytoplasma. Comparative genome analyses between JWB phytoplasma and other phytoplasmas shows the occurrence of large-scale gene rearrangements. The low synteny with other phytoplasmas indicated that the expansion of multiple gene families/duplication probably occurred separately after differentiation.

Conclusions: In this study, the complete genome sequence of a JWB phytoplasma isolate jwb-nky that causing JWB disease was reported for the first time and a number of species-specific genes were identified in the genome. The study enhanced our understandings about genomic basis and the pathogenicity mechanism of this pathogen, which will aid in the development of improved strategies for efficient management of JWB diseases.

Keywords: Genome sequence; Phytoplasma; Potential mobile unit (PMU); Synteny.

Fig. 1

Genome map of the 750,803-bp circular chromosome of JWB phytoplasma jwb-nky. Rings from the outside to inside are as follows: ring 1, predicted ORFs on the sense strand; ring 2, predicted ORFs on the antisense strand; ring 3, fragmented genes on the sense strand; ring 4, fragmented genes on the antisense strand; ring 5, locations of rRNA genes (brown), tRNA genes (gray), and miscellaneous RNAs (black); ring 6, PMUs on the sense strand; ring 7, PMUs on the antisense strand

Fig. 2

Gene Ontology categories of Phytoplasma according to function

Fig. 3

KEGG pathway analysis of Phytoplasma

Fig. 4

The COG functional category of JWB phytoplasma genes

Fig. 5

The number of clustering genes from 6 different phytopathogens

Fig. 6

Phylogeny of phytoplasmas. The organismal phylogeny based on the concatenated alignment of 150 single-copy genes conserved among the six phytoplasma genomes

Fig. 7

Whole-genome alignment reveal the gene synteny. The chromosomes are shown in linearized form to illustrate relative gene synteny A,B,C,D,E indicated the alignment of JWB with with Ca. Phytoplasma pruni (a), Ca.Phytoplasma australiense (b), Ca. Phytoplasma mali (c), Onion yellows hytoplasma (d) and Peanut witches’-broom phytoplasma (e) respectively

Fig. 8

Potential mobile units (PMUs) from JWB phytoplasma and aster yellows-witches’ broom (AY-WB) phytoplasmas. Homologous genes between the PMUs are linked by lines. Dam, adenine-specifc DNA methyltransferase; sigF, RNA polymerase; sigma-F factor; ssb, single-stranded DNA-binding protein; himA, DNA binding protein HU; hflB, ATP-dependent Zn protease; smc, chromosome segregation ATPase-like protein; tmk, thymidylate kinase; dnaB, replicative DNA helicase; dnaG, DNA primase; tra5, putative transposase; NA, conserved hypothetical protein without assigned fuction