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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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5′ UTR of rpoD. DNA sequence alignments of the 5′ Untranslated Region (UTR) of (A)rpoD Group A and (B)rpoD Group B genes found in ‘Ca. Phytoplasma australiense’. (C) Alignment of 5′ UTR region of Group B without SLY256. Although SLY256 has the best match with Group B, its protein sequence indicates that it is the most divergent of examples within that group. There is greater conservation of the 5′ UTR regions of the remaining members of Group B, although they seem to be more divergent that those of Group A. Yellow colouring indicates exact nucleotide match and blue colouring is greatest consensus match.
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Figure 4: 5′ UTR of rpoD. DNA sequence alignments of the 5′ Untranslated Region (UTR) of (A)rpoD Group A and (B)rpoD Group B genes found in ‘Ca. Phytoplasma australiense’. (C) Alignment of 5′ UTR region of Group B without SLY256. Although SLY256 has the best match with Group B, its protein sequence indicates that it is the most divergent of examples within that group. There is greater conservation of the 5′ UTR regions of the remaining members of Group B, although they seem to be more divergent that those of Group A. Yellow colouring indicates exact nucleotide match and blue colouring is greatest consensus match.

Mentions: There are 20 ORFs in the SLY genome that are annotated as rpoD - DNA-dependent RNA polymerase. Those ORFs annotated as rpoD are all associated with PMUs and are quite distinct from the DNA-dependent RNA polymerase not associated with a PMU (SLY419), which is annotated as sigA. In PAa there are five ORFs annotated as fliA (DNA-directed RNA polymerase, specialized sigma subunit). They are PA0316, PA0409, PA0723, PA0790 and PA0815. There are also two ORFs (PA0127 and PA0258) annotated as “RNA polymerase sigma factor”. In SLY the ORFs characterised as DNA-dependent RNA polymerase can be divided into four groups: sigA, rpoA, rpoB, rpoC, and rpoD. The ORFs annotated as rpoD can be further divided into Group A and Group B. The rpoD A &B groupings are complex because the protein sequences appear to be a mix of motifs that may be shared between otherwise distant sequences and not present in those seemingly more closely related. The groupings are more distinct when the 5′ UTR regions are compared, as the regions of c. 140 bp (GpA) and c. 150 bp (GpB) are highly conserved (Figure 4). Our assessment is that PAa ORFs annotated as fliA are orthologous to rpoD Group B, whereas PA0127 and PA0258 are orthologous to rpoD Group A (see Additional file5).


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)

5′ UTR of rpoD. DNA sequence alignments of the 5′ Untranslated Region (UTR) of (A)rpoD Group A and (B)rpoD Group B genes found in ‘Ca. Phytoplasma australiense’. (C) Alignment of 5′ UTR region of Group B without SLY256. Although SLY256 has the best match with Group B, its protein sequence indicates that it is the most divergent of examples within that group. There is greater conservation of the 5′ UTR regions of the remaining members of Group B, although they seem to be more divergent that those of Group A. Yellow colouring indicates exact nucleotide match and blue colouring is greatest consensus match.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: 5′ UTR of rpoD. DNA sequence alignments of the 5′ Untranslated Region (UTR) of (A)rpoD Group A and (B)rpoD Group B genes found in ‘Ca. Phytoplasma australiense’. (C) Alignment of 5′ UTR region of Group B without SLY256. Although SLY256 has the best match with Group B, its protein sequence indicates that it is the most divergent of examples within that group. There is greater conservation of the 5′ UTR regions of the remaining members of Group B, although they seem to be more divergent that those of Group A. Yellow colouring indicates exact nucleotide match and blue colouring is greatest consensus match.
Mentions: There are 20 ORFs in the SLY genome that are annotated as rpoD - DNA-dependent RNA polymerase. Those ORFs annotated as rpoD are all associated with PMUs and are quite distinct from the DNA-dependent RNA polymerase not associated with a PMU (SLY419), which is annotated as sigA. In PAa there are five ORFs annotated as fliA (DNA-directed RNA polymerase, specialized sigma subunit). They are PA0316, PA0409, PA0723, PA0790 and PA0815. There are also two ORFs (PA0127 and PA0258) annotated as “RNA polymerase sigma factor”. In SLY the ORFs characterised as DNA-dependent RNA polymerase can be divided into four groups: sigA, rpoA, rpoB, rpoC, and rpoD. The ORFs annotated as rpoD can be further divided into Group A and Group B. The rpoD A &B groupings are complex because the protein sequences appear to be a mix of motifs that may be shared between otherwise distant sequences and not present in those seemingly more closely related. The groupings are more distinct when the 5′ UTR regions are compared, as the regions of c. 140 bp (GpA) and c. 150 bp (GpB) are highly conserved (Figure 4). Our assessment is that PAa ORFs annotated as fliA are orthologous to rpoD Group B, whereas PA0127 and PA0258 are orthologous to rpoD Group A (see Additional file5).

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