Abstract
Background‘Candidatus Phytoplasma australiense’ is associated with at least nine diseases in Australia and New Zealand. The impact of this phytoplasma is considerable, both economically and environmentally. The genome of a NZ isolate was sequenced in an effort to understand its pathogenicity and ecology. Comparison with a closely related Australian isolate enabled us to examine mechanisms of genomic rearrangement.ResultsThe complete genome sequence of a strawberry lethal yellows (SLY) isolate of ‘Candidatus Phytoplasma australiense’ was determined. It is a circular genome of 959,779 base pairs with 1126 predicted open reading frames. Despite being 80 kbp larger than another ‘Ca. Phytoplasma australiense’ isolate PAa, the variation between housekeeping genes was generally less than 1% at a nucleotide level. The difference in size between the two isolates was largely due to the number and size of potential mobile units (PMUs), which contributed to some changes in gene order. Comparison of the genomes of the two isolates revealed that the highly conserved 5′ UTR of a putative DNA-directed RNA polymerase seems to be associated with insertion and rearrangement events. Two types of PMUs have been identified on the basis of the order of three to four conserved genes, with both PMUs appearing to have been present in the last common ancestor of ‘Ca. Phytoplasma asteris’ and ‘Ca. Phytoplasma australiense’. Comparison with other phytoplasma genomes showed that modification methylases were, in general, species-specific. A putative methylase (xorIIM) found in ‘Ca. Phytoplasma australiense’ appeared to have no analogue in any other firmicute, and we believe has been introduced by way of lateral gene transfer. A putative retrostransposon (ltrA) analogous to that found in OY-M was present in both isolates, although all examples in PAa appear to be fragments. Comparative analysis identified highly conserved 5′ and 3′ UTR regions of ltrA, which may indicate how the gene is excised and inserted.ConclusionsComparison of two assembled ‘Ca. Phytoplasma australiense’ genomes has shown they possess a high level of plasticity. This comparative analysis has yielded clues as to how rearrangements occur, and the identification of sets of genes that appear to be associated with these events.
Highlights
Phytoplasmas are pathogenic bacteria associated with diseases of several hundred plant species, with many newly emerging diseases being reported [1]
When we further examined the composition of these gene clusters, we discovered that within each Potential Mobile Units (PMUs) there is an arrangement of three Open Reading Frame (ORF), consisting of a DNA helicase, a thymidylate kinase, and a conserved hypothetical protein that appears to be associated with tmk-a (CHPtap), which extends the identification of conserved PMU genes by Arashida et al [25]
One mechanism for ltrA to operate requires a functional recA, which might indicate that the recA gene, which in strawberry lethal yellows (SLY) is fragmented by two INDELs, might produce a functional protein by a mechanism such as ribosomal slippage
Summary
Phytoplasmas are pathogenic bacteria associated with diseases of several hundred plant species, with many newly emerging diseases being reported [1]. Phormium yellow leaf (PYL) was first reported in 1908, but was only determined to be a phytoplasma-associated disease in 1969 [6]. Since the late 1970s, this phytoplasma has been discovered associated with diseases in New Zealand of Cordyline, Coprosma, strawberry, and more recently potato [7,8,9,10,11]. ‘Ca. Phytoplasma australiense’ is associated with at least five diseases in Australia [12,13,14]. That ‘Ca. Phytoplasma australiense’ is being detected in increasing numbers of plant species has heightened the need to devise effective methods to control or manage the pathogen
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