Niche-Specificity and the Variable Fraction of the Pectobacterium Pan-Genome
Niche-Specificity and the Variable Fraction of the Pectobacterium Pan-Genome
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DOI：
10.1094/mpmi-21-12-1549
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发表时间：
2008-12-01
影响因子：
3.5
通讯作者：
Charkowski, A. O.
中科院分区：
文献类型：
--
作者：
Glasner, J. D.;Marquez-Villavicencio, M.;Charkowski, A. O.
我们比较了三种密切相关的软腐病原体的基因组序列，这些病原体在宿主范围和地理分布上各不相同，以确定可能导致生活方式差异的遗传差异。所比较的分离株，黑腐果胶杆菌SCRI1043、胡萝卜软腐果胶杆菌WPP14和巴西果胶杆菌1692，代表了该属的不同谱系。通过参考先前公布的黑腐假单胞菌基因组的完整环状染色体和彼此进行的454焦磷酸测序产生的胡萝卜软腐假单胞菌和巴西假单胞菌基因组重叠群占预测基因组大小的96%。由胡萝卜软腐青霉和巴西青霉编码的Orthoprase蛋白彼此大约95%相同，并且与黑腐青霉92%相同。使用Mauve进行多重比对，确定了这些果胶杆菌属物种中保守的3.9 Mb的核心基因组。每个核心基因组在许多点被物种特异性插入或缺失（indels）打断，约占0.9至1.1 Mb。我们表明，存在的一个hrpK样III型分泌系统依赖的效应蛋白在胡萝卜素和巴西青霉和它的缺席从黑腐青霉是不足以解释变异，在他们的响应感染的植物。在这些物种中变化的其他基因包括编码肽毒素产生、酶产生、分泌蛋白和抗生素产生的基因，以及可能与致病性相关的基因调控和代谢的更一般方面的差异。
We compare genome sequences of three closely related soft-rot pathogens that vary in host range and geographical distribution to identify genetic differences that could account for lifestyle differences. The isolates compared, Pectobacterium atrosepticum SCRI1043, P. carotovorum WPP14, and P. brasiliensis 1692, represent diverse lineages of the genus. P. carotovorum and P. brasiliensis genome contigs, generated by 454 pyrosequencing ordered by reference to the previously published complete circular chromosome of P. atrosepticum genome and each other, account for 96% of the predicted genome size. Orthologous proteins encoded by P. carotovorum and P. brasiliensis are approximately 95% identical to each other and 92% identical to P. atrosepticum. Multiple alignment using Mauve identified a core genome of 3.9 Mb conserved among these Pectobacterium spp. Each core genome is interrupted at many points by species-specific insertions or deletions (indels) that account for approximately 0.9 to 1.1 Mb. We demonstrate that the presence of a hrpK-like type III secretion system-dependent effector protein in P. carotovorum and P. brasiliensis and its absence from P. atrosepticum is insufficient to explain variability in their response to infection in a plant. Additional genes that vary among these species include those encoding peptide toxin production, enzyme production, secretion proteins, and antibiotic production, as well as differences in more general aspects of gene regulation and metabolism that may be relevant to pathogenicity.