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Comparison of the complete genome sequence of two closely related isolates of 'Candidatus Phytoplasma australiense' reveals genome plasticity.

Andersen MT, Liefting LW, Havukkala I, Beever RE - BMC Genomics (2013)

Bottom Line: A putative methylase (xorIIM) found in 'Ca.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand. Mark.Andersen@plantandfood.co.nz

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.

Results: The 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.

Conclusions: Comparison 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.

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Related in: MedlinePlus

Graphic representation of linearised genome sequences of ‘Candidatus Phytoplasma australiense’ isolates PAa and SLY. Coloured blocks represent unambiguous orthologous Open Reading Frames (ORFs) using PAa as the reference strain. Seventeen junctions where the two sequences diverged either by insertions, deletions or rearrangements are labelled below the representation of the PAa genome.
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Figure 2: Graphic representation of linearised genome sequences of ‘Candidatus Phytoplasma australiense’ isolates PAa and SLY. Coloured blocks represent unambiguous orthologous Open Reading Frames (ORFs) using PAa as the reference strain. Seventeen junctions where the two sequences diverged either by insertions, deletions or rearrangements are labelled below the representation of the PAa genome.

Mentions: Although the housekeeping genes were >99% similar at a nucleotide level, gene order differed between the two isolates. A comparison of ORFs not associated with PMUs revealed syntenic variation between SLY and PAa (Figure 2 and Table 3). The blocks have been labelled “A” to “N”, with PAa used as the reference strain. The most obvious differences were that in SLY the blocks labelled “C” to “E” were located between blocks “F” and “L”. Block “F” in SLY appeared after block “K” and was a single unit, but in PAa this cluster was divided into “F1” and “F2” as a result of a 30 kbp INDEL (PMU insertion). Block “J” was divided into 5, as there were several areas of differences within an otherwise ostensibly syntenous region. We note that two examples of the “PAa-PMU5” were situated either side of block “H” in PAa, whereas this type of PMU was not found in SLY.


Comparison of the complete genome sequence of two closely related isolates of 'Candidatus Phytoplasma australiense' reveals genome plasticity.

Andersen MT, Liefting LW, Havukkala I, Beever RE - BMC Genomics (2013)

Graphic representation of linearised genome sequences of ‘Candidatus Phytoplasma australiense’ isolates PAa and SLY. Coloured blocks represent unambiguous orthologous Open Reading Frames (ORFs) using PAa as the reference strain. Seventeen junctions where the two sequences diverged either by insertions, deletions or rearrangements are labelled below the representation of the PAa genome.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750655&req=5

Figure 2: Graphic representation of linearised genome sequences of ‘Candidatus Phytoplasma australiense’ isolates PAa and SLY. Coloured blocks represent unambiguous orthologous Open Reading Frames (ORFs) using PAa as the reference strain. Seventeen junctions where the two sequences diverged either by insertions, deletions or rearrangements are labelled below the representation of the PAa genome.
Mentions: Although the housekeeping genes were >99% similar at a nucleotide level, gene order differed between the two isolates. A comparison of ORFs not associated with PMUs revealed syntenic variation between SLY and PAa (Figure 2 and Table 3). The blocks have been labelled “A” to “N”, with PAa used as the reference strain. The most obvious differences were that in SLY the blocks labelled “C” to “E” were located between blocks “F” and “L”. Block “F” in SLY appeared after block “K” and was a single unit, but in PAa this cluster was divided into “F1” and “F2” as a result of a 30 kbp INDEL (PMU insertion). Block “J” was divided into 5, as there were several areas of differences within an otherwise ostensibly syntenous region. We note that two examples of the “PAa-PMU5” were situated either side of block “H” in PAa, whereas this type of PMU was not found in SLY.

Bottom Line: A putative methylase (xorIIM) found in 'Ca.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand. Mark.Andersen@plantandfood.co.nz

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.

Results: The 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.

Conclusions: Comparison 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.

Show MeSH
Related in: MedlinePlus