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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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Circular representation of the chromosome of SLY isolate of ‘Candidatus Phytoplasma australiense’. The genome sequence was annotated by BASys (Bacterial Annotation System). The protein coding genes on the forward (red arrows) and reverse (blue arrows) strands are shown. The Clusters of Orthologous Groups (COG) functional categories of the protein coding genes in the forward (outermost circle) and reverse (innermost circle) directions are colour-coded as designated in the inset. Allocation to a particular COG functional group was determined by BLAST searches against protein databases as described in van Domselaar et al.[44].
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Figure 1: Circular representation of the chromosome of SLY isolate of ‘Candidatus Phytoplasma australiense’. The genome sequence was annotated by BASys (Bacterial Annotation System). The protein coding genes on the forward (red arrows) and reverse (blue arrows) strands are shown. The Clusters of Orthologous Groups (COG) functional categories of the protein coding genes in the forward (outermost circle) and reverse (innermost circle) directions are colour-coded as designated in the inset. Allocation to a particular COG functional group was determined by BLAST searches against protein databases as described in van Domselaar et al.[44].

Mentions: The genome of ‘Ca. Phytoplasma australiense’ NZSb11 (hereafter referred to as SLY) consists of a single circular chromosome of 959,779 bp (Figure 1) and a single plasmid of 3,635 bp (pPASb11). Sequence analysis of pPASb11 was reported previously[10]. In accordance with the precedent established with OY-M, the initiation codon for the dnaA gene was chosen as the start point for numbering the genome. There are 1126 ORFs in SLY genome that are predicted to be protein-coding genes (see Additional file1), two rRNA operons, and 35 tRNAs (one of which is a pseudo tRNA). The majority of translation initiation codons for the predicted protein-coding genes are ATG (777), while GTG (73) and TTG (276) are also proposed. A putative function has been assigned to 528 ORFs, while 598 ORFs have no assigned function, and are described as hypothetical proteins. In accordance with previous phytoplasma genome sequencing projects, TGA was interpreted as a stop codon. The general features and comparison with other phytoplasma genomes is summarised in Table 1.


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)

Circular representation of the chromosome of SLY isolate of ‘Candidatus Phytoplasma australiense’. The genome sequence was annotated by BASys (Bacterial Annotation System). The protein coding genes on the forward (red arrows) and reverse (blue arrows) strands are shown. The Clusters of Orthologous Groups (COG) functional categories of the protein coding genes in the forward (outermost circle) and reverse (innermost circle) directions are colour-coded as designated in the inset. Allocation to a particular COG functional group was determined by BLAST searches against protein databases as described in van Domselaar et al.[44].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Circular representation of the chromosome of SLY isolate of ‘Candidatus Phytoplasma australiense’. The genome sequence was annotated by BASys (Bacterial Annotation System). The protein coding genes on the forward (red arrows) and reverse (blue arrows) strands are shown. The Clusters of Orthologous Groups (COG) functional categories of the protein coding genes in the forward (outermost circle) and reverse (innermost circle) directions are colour-coded as designated in the inset. Allocation to a particular COG functional group was determined by BLAST searches against protein databases as described in van Domselaar et al.[44].
Mentions: The genome of ‘Ca. Phytoplasma australiense’ NZSb11 (hereafter referred to as SLY) consists of a single circular chromosome of 959,779 bp (Figure 1) and a single plasmid of 3,635 bp (pPASb11). Sequence analysis of pPASb11 was reported previously[10]. In accordance with the precedent established with OY-M, the initiation codon for the dnaA gene was chosen as the start point for numbering the genome. There are 1126 ORFs in SLY genome that are predicted to be protein-coding genes (see Additional file1), two rRNA operons, and 35 tRNAs (one of which is a pseudo tRNA). The majority of translation initiation codons for the predicted protein-coding genes are ATG (777), while GTG (73) and TTG (276) are also proposed. A putative function has been assigned to 528 ORFs, while 598 ORFs have no assigned function, and are described as hypothetical proteins. In accordance with previous phytoplasma genome sequencing projects, TGA was interpreted as a stop codon. The general features and comparison with other phytoplasma genomes is summarised in Table 1.

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