Whole-Genome-Based Phylogeny and Divergence of the Genus Brucella
Whole-Genome-Based Phylogeny and Divergence of the Genus Brucella
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DOI：
10.1128/jb.01581-08
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发表时间：
2009-04-15
影响因子：
3.2
通讯作者：
Keim, Paul
中科院分区：
文献类型：
--
作者：
Foster, Jeffrey T.;Beckstrom-Sternberg, Stephen M.;Keim, Paul
布鲁氏菌是家畜和野生动物的世界性细菌病原体，但由于遗传多样性有限，系统发育重建一直具有挑战性。我们利用全基因组比较评估了5种布鲁氏菌的分类和进化关系——流产布鲁氏菌、melitensis布鲁氏菌、猪布鲁氏菌、犬布鲁氏菌和卵布鲁氏菌。我们利用来自13个基因组的单核苷酸多态性（snp）建立了系统发育，并利用与土壤细菌和机会性人类病原体Ochrobactrum anthropi密切相关的土壤细菌来扎根。全基因组测序和基于snp的方法为解决高度保守的布鲁氏菌物种提供了必要的遗传细节水平。布鲁氏菌基因组之间的比较显示，所有基因组中共有20,154个同源snp。与人类赭杆菌的根显示，B. ovis谱系是基础的其余布鲁氏菌谱系。我们发现猪芽孢杆菌是一个高度分化的分支，具有广泛的种内遗传多样性。此外，在我们的分析中，猪B.被确定为副球菌，只有当犬B.基因组被包括在内时才形成单系进化支。根据这些数据使用分子钟表明，大多数布鲁氏菌在过去8.6万至29.6万年间从它们共同的羊分枝杆菌祖先中分化出来，这是在它们的家畜宿主被驯化之前。对布鲁氏菌系统发育的详细了解将有助于更好地了解该属的生态学、进化史和宿主关系，并可用于确定适当的基因分型方法，用于分子流行病学和临床研究的快速检测和诊断分析。
Brucellae are worldwide bacterial pathogens of livestock and wildlife, but phylogenetic reconstructions have been challenging due to limited genetic diversity. We assessed the taxonomic and evolutionary relationships of five Brucella species-Brucella abortus, B. melitensis, B. suis, B. canis, and B. ovis-using whole-genome comparisons. We developed a phylogeny using single nucleotide polymorphisms (SNPs) from 13 genomes and rooted the tree using the closely related soil bacterium and opportunistic human pathogen, Ochrobactrum anthropi. Whole-genome sequencing and a SNP-based approach provided the requisite level of genetic detail to resolve species in the highly conserved brucellae. Comparisons among the Brucella genomes revealed 20,154 orthologous SNPs that were shared in all genomes. Rooting with Ochrobactrum anthropi reveals that the B. ovis lineage is basal to the rest of the Brucella lineage. We found that B. suis is a highly divergent clade with extensive intraspecific genetic diversity. Furthermore, B. suis was determined to be paraphyletic in our analyses, only forming a monophyletic clade when the B. canis genome was included. Using a molecular clock with these data suggests that most Brucella species diverged from their common B. ovis ancestor in the past 86,000 to 296,000 years, which precedes the domestication of their livestock hosts. Detailed knowledge of the Brucella phylogeny will lead to an improved understanding of the ecology, evolutionary history, and host relationships for this genus and can be used for determining appropriate genotyping approaches for rapid detection and diagnostic assays for molecular epidemiological and clinical studies.