Limits...
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.

Show MeSH

Related in: MedlinePlus

Conserved core genes of PMUs. Gene order (5′-3′) of three and four highly conserved genes found in the Potential Mobile Units (PMUs) of ‘Ca. Phytoplasma australiense’ and ‘Ca. Phytoplasma asteris’. The “AY-WB PMU” arrangement is the only one found in AY-WB, the “SLY PMU” arrangement is the only type found in SLY, whereas OY-M and PAa have examples of both types.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3750655&req=5

Figure 3: Conserved core genes of PMUs. Gene order (5′-3′) of three and four highly conserved genes found in the Potential Mobile Units (PMUs) of ‘Ca. Phytoplasma australiense’ and ‘Ca. Phytoplasma asteris’. The “AY-WB PMU” arrangement is the only one found in AY-WB, the “SLY PMU” arrangement is the only type found in SLY, whereas OY-M and PAa have examples of both types.

Mentions: There appear to be two distinct types of PMU based on the arrangement of three to four key ORFs. These ORFs are annotated as tmk-a, dnaC or B, dnaG, and a conserved hypothetical protein (CHPtap) that appears to be associated with tmk-a. The arrangement of these ORFs in AY-WB PMUs is in the order (5′-3′) tmk-a, CHPtap, dnaB, and dnaG. In SLY these ORFs are (5′-3′) dnaC, CHPtap, and tmk-a, with no dnaG (Figure 3). In PAa, the majority of PMUs have the arrangement as found solely in SLY; however, two of the AY-WB arrangements are also present. In OY-M, only one example of the SLY arrangement can be detected, and that is in the PMU containing ORFs 428–430. Although the DNA helicase (PAM428) is of comparable size to the DNA helicases from PMUs of SLY, PAM429 and PAM430 are truncations of the respective ORFs found in the SLY PMUs. Consequently we conclude that this OY-M PMU seems to be accumulating errors and is possibly in the process of being eliminated.


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)

Conserved core genes of PMUs. Gene order (5′-3′) of three and four highly conserved genes found in the Potential Mobile Units (PMUs) of ‘Ca. Phytoplasma australiense’ and ‘Ca. Phytoplasma asteris’. The “AY-WB PMU” arrangement is the only one found in AY-WB, the “SLY PMU” arrangement is the only type found in SLY, whereas OY-M and PAa have examples of both types.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Conserved core genes of PMUs. Gene order (5′-3′) of three and four highly conserved genes found in the Potential Mobile Units (PMUs) of ‘Ca. Phytoplasma australiense’ and ‘Ca. Phytoplasma asteris’. The “AY-WB PMU” arrangement is the only one found in AY-WB, the “SLY PMU” arrangement is the only type found in SLY, whereas OY-M and PAa have examples of both types.
Mentions: There appear to be two distinct types of PMU based on the arrangement of three to four key ORFs. These ORFs are annotated as tmk-a, dnaC or B, dnaG, and a conserved hypothetical protein (CHPtap) that appears to be associated with tmk-a. The arrangement of these ORFs in AY-WB PMUs is in the order (5′-3′) tmk-a, CHPtap, dnaB, and dnaG. In SLY these ORFs are (5′-3′) dnaC, CHPtap, and tmk-a, with no dnaG (Figure 3). In PAa, the majority of PMUs have the arrangement as found solely in SLY; however, two of the AY-WB arrangements are also present. In OY-M, only one example of the SLY arrangement can be detected, and that is in the PMU containing ORFs 428–430. Although the DNA helicase (PAM428) is of comparable size to the DNA helicases from PMUs of SLY, PAM429 and PAM430 are truncations of the respective ORFs found in the SLY PMUs. Consequently we conclude that this OY-M PMU seems to be accumulating errors and is possibly in the process of being eliminated.

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