Comparison of the complete genome sequence of two closely related isolates of 'Candidatus Phytoplasma australiense' reveals genome plasticity.
Comparison of the complete genome sequence of two closely related isolates of 'Candidatus Phytoplasma australiense' reveals genome plasticity.
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DOI：
10.1186/1471-2164-14-529
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发表时间：
2013-08-02
期刊：
影响因子：
4.4
通讯作者：
Beever RE
中科院分区：
文献类型：
--
作者：
Andersen MT;Liefting LW;Havukkala I;Beever RE
澳大利亚植原体（Phytoplasma australiense）与澳大利亚和新西兰的至少9种疾病有关。这种植原体的影响在经济和环境上都是相当大的。对一株新西兰分离株的基因组进行了测序，以了解其致病性和生态学。与密切相关的澳大利亚分离物的比较，使我们能够研究基因组重排的机制。测定了一株草莓致死黄化病（SLY）病原菌“澳洲植原体”（Phytoplasma australiense）的全基因组序列。它是959，779个碱基对的环状基因组，具有1126个预测的开放阅读框。尽管比另一个'Ca'大80 kbp。在澳大利亚植原体分离物PAa中，管家基因之间的变异在核苷酸水平上通常小于1%。两个分离株之间的大小差异主要是由于潜在的移动的单位（PMU）的数量和大小，这有助于基因顺序的一些变化。两株分离株基因组的比较显示，一个假定的DNA指导的RNA聚合酶的高度保守的5′ UTR似乎与插入和重排事件有关。两种类型的PMU已被确定的基础上的顺序的三至四个保守的基因，这两个PMU似乎已经存在于最后的共同祖先的'Ca。植原体（Phytoplasma asteris）和Ca.澳大利亚植原体与其他植原体基因组的比较表明，修饰甲基化酶，在一般情况下，种特异性。一种推定的甲基化酶（xorIIM），发现于'Ca。澳大利亚植原体似乎在任何其他厚壁动物中都没有类似物，我们相信它是通过横向基因转移引入的。一个假定的反转录转座子（ltrA）类似于OY-M中发现的存在于两个分离株，虽然所有的例子在PAa似乎是片段。比较分析鉴定了ltrA的高度保守的5′和3′ UTR区域，这可能表明该基因是如何切除和插入的。比较两个组装的Ca。澳大利亚植原体的基因组显示它们具有高度的可塑性。这种比较分析已经提供了关于重排如何发生的线索，以及似乎与这些事件相关的基因组的鉴定。
‘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. 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. 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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影响因子：
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作者：
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