Comparative Genome Analysis of “CandidatusPhytoplasma australiense” (Subgrouptuf-Australia I;rp-A) and “Ca. Phytoplasma asteris” Strains OY-M and AY-WB

Abstract

The chromosome sequence of “Candidatus Phytoplasma australiense” (subgroup tuf-Australia I; rp-A), associated with dieback in papaya, Australian grapevine yellows in grapevine, and several other important plant diseases, was determined. The circular chromosome is represented by 879,324 nucleotides, a GC content of 27%, and 839 protein-coding genes. Five hundred two of these protein-coding genes were functionally assigned, while 337 genes were hypothetical proteins with unknown function. Potential mobile units (PMUs) containing clusters of DNA repeats comprised 12.1% of the genome. These PMUs encoded genes involved in DNA replication, repair, and recombination; nucleotide transport and metabolism; translation; and ribosomal structure. Elements with similarities to phage integrases found in these mobile units were difficult to classify, as they were similar to both insertion sequences and bacteriophages. Comparative analysis of “Ca. Phytoplasma australiense” with “Ca. Phytoplasma asteris” strains OY-M and AY-WB showed that the gene order was more conserved between the closely related “Ca. Phytoplasma asteris” strains than to “Ca. Phytoplasma australiense.” Differences observed between “Ca. Phytoplasma australiense” and “Ca. Phytoplasma asteris” strains included the chromosome size (18,693 bp larger than OY-M), a larger number of genes with assigned function, and hypothetical proteins with unknown function.

Multilocus sequence analysis reveals the genetic diversity of European fruit tree phytoplasmas and supports the existence of inter-species recombination

“…The possibility that hypo-virulent isolates are impaired in carbon metabolism can be envisaged. Glycolysis is a pathway essential for phytoplasmas which have a reduced physiology as shown by the analysis of their small genome content (Bai et al, 2006;Oshima et al, 2004;Tran-Nguyen et al, 2008). This pathway is only partially present in 'Ca.…”

“…secY is involved in protein secretion and its sequence was kindly provided by the 'Ca. P. mali' genome sequence consortium (Kube et al, 2008). imp encodes the immunodominant surface protein and had been sequenced for the three species members of the 16SrX group (Morton et al, 2003).…”

“…P. mali' was recently investigated by singlestrand conformation polymorphism and sequence analyses of the hflB gene (Schneider & Seemüller, 2009) as an outcome of the 'Ca. P. mali' genome sequencing (Kube et al, 2008). However, little is known about the genetic diversity of 'Ca.…”

Exploring the phytoplasmas, plant pathogenic bacteria

“…In 2004, the complete genomic sequence of OY-M was determined (Oshima et al 2004). To date, the complete genomic sequences of three other phytoplasmas have been reported (Bai et al 2006;Tran-Nguyen et al 2008;Kube et al 2008).…”

“…The genes encoding SecA, SecY, and SecE, required for protein translocation in Escherichia coli (Economou 1999), were identified in strain OY-M of 'Ca. P. asteris ' (Kakizawa et al 2001' (Kakizawa et al , 2004 and in three other phytoplasma genomes (Bai et al 2006;Kube et al 2008;Tran-Nguyen et al 2008). In addition, SecA protein was expressed in plants infected with five respective phytoplasma species (Wei et al 2004a).…”