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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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Graphical depiction of xorIIM and CHPxap in SLY. Graphical depiction of genes and fragments of xorIIM and CHPxap from three locations on the SLY genome. SLY164 and SLY575 are truncations with the Open Reading Frames interrupted by putative phage related protein (gepA).
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Figure 5: Graphical depiction of xorIIM and CHPxap in SLY. Graphical depiction of genes and fragments of xorIIM and CHPxap from three locations on the SLY genome. SLY164 and SLY575 are truncations with the Open Reading Frames interrupted by putative phage related protein (gepA).

Mentions: There are ten ORFs in SLY that are annotated as xorIIM. Five copies consist of a 418 amino acid protein and five ORFs that are fragments. This gene is very highly conserved, with the full-length copies differing at only 3/1257 nucleotides, which results in two amino acid changes (99.5% identity). It is annotated as a putative methylase, and the predicted protein has 46% identity to that of Helicobacter acinonychis str. Sheeba (YP_664125). Another ORF for which the closest match is to a Helicobacter acinonychis str. Sheeba ORF (YP_664126) is SLY008 (35% identity), coding for a conserved hypothetical protein 378 aa in length. There are two other ORFs in the SLY (SLY164 and SLY575) that are truncations of this protein, and they both also follow ORFs that code for xorIIM (SLY007 is a truncation of xorIIM) (Figure 5). Like xorIIM, the putative amino acid sequence for this CHP is very highly conserved, and differs at only 1 out of 125 aa residues (at the N-terminus), and the two fragments are identical to each other at a protein level. The 3′ end of SLY007 (xorIIM fragment) overlaps the 5′ end of SLY008 by 24 nucleotides, which suggests that these two genes were possibly part of an operon. Subsequently we have termed SLY008 and paralogues: CHPxap (for xorIIM-associated conserved hypothetical protein). Two fragments of xorIIM are present in PAa (PA0003 and PA0004) as consecutive ORFs, which together cover the amino and carboxy termini of the putative complete gene. CHPxap occurs as ORF PA0005. PA0005 is truncated when compared with the SLY orthologue (334 aa v. 378 aa), and differs by only 1 aa over that length. The two truncations of CHPxap in SLY are part of an exact (presumably recent) duplication. In SLY it seems as though xorIIM has been duplicated by being incorporated into a PMU. The accompanying ORF CHPxap has only become partially incorporated and as a result the complete ORF has not been successfully duplicated. Because xorIIM and CHPxap are highly conserved in SLY and PAa, and these genes have not been reported in any other firmicute, the possibility that these genes have been acquired by lateral (horizontal) gene transfer after the divergence of ‘Ca. Phytoplasma australiense’ and ‘Ca. Phytoplasma asteris’ is discussed below.


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)

Graphical depiction of xorIIM and CHPxap in SLY. Graphical depiction of genes and fragments of xorIIM and CHPxap from three locations on the SLY genome. SLY164 and SLY575 are truncations with the Open Reading Frames interrupted by putative phage related protein (gepA).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Graphical depiction of xorIIM and CHPxap in SLY. Graphical depiction of genes and fragments of xorIIM and CHPxap from three locations on the SLY genome. SLY164 and SLY575 are truncations with the Open Reading Frames interrupted by putative phage related protein (gepA).
Mentions: There are ten ORFs in SLY that are annotated as xorIIM. Five copies consist of a 418 amino acid protein and five ORFs that are fragments. This gene is very highly conserved, with the full-length copies differing at only 3/1257 nucleotides, which results in two amino acid changes (99.5% identity). It is annotated as a putative methylase, and the predicted protein has 46% identity to that of Helicobacter acinonychis str. Sheeba (YP_664125). Another ORF for which the closest match is to a Helicobacter acinonychis str. Sheeba ORF (YP_664126) is SLY008 (35% identity), coding for a conserved hypothetical protein 378 aa in length. There are two other ORFs in the SLY (SLY164 and SLY575) that are truncations of this protein, and they both also follow ORFs that code for xorIIM (SLY007 is a truncation of xorIIM) (Figure 5). Like xorIIM, the putative amino acid sequence for this CHP is very highly conserved, and differs at only 1 out of 125 aa residues (at the N-terminus), and the two fragments are identical to each other at a protein level. The 3′ end of SLY007 (xorIIM fragment) overlaps the 5′ end of SLY008 by 24 nucleotides, which suggests that these two genes were possibly part of an operon. Subsequently we have termed SLY008 and paralogues: CHPxap (for xorIIM-associated conserved hypothetical protein). Two fragments of xorIIM are present in PAa (PA0003 and PA0004) as consecutive ORFs, which together cover the amino and carboxy termini of the putative complete gene. CHPxap occurs as ORF PA0005. PA0005 is truncated when compared with the SLY orthologue (334 aa v. 378 aa), and differs by only 1 aa over that length. The two truncations of CHPxap in SLY are part of an exact (presumably recent) duplication. In SLY it seems as though xorIIM has been duplicated by being incorporated into a PMU. The accompanying ORF CHPxap has only become partially incorporated and as a result the complete ORF has not been successfully duplicated. Because xorIIM and CHPxap are highly conserved in SLY and PAa, and these genes have not been reported in any other firmicute, the possibility that these genes have been acquired by lateral (horizontal) gene transfer after the divergence of ‘Ca. Phytoplasma australiense’ and ‘Ca. Phytoplasma asteris’ is discussed below.

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