Karasov Talia L, Barrett Luke, Hershberg Ruth, Bergelson Joy
Committee On Genetics Genomics & Systems Biology, University of Chicago, Chicago, Illinois, United States of America.
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America.
PLoS One. 2017 Sep 7;12(9):e0184195. doi: 10.1371/journal.pone.0184195. eCollection 2017.
Bacterial strains of the same species collected from different hosts frequently exhibit differences in gene content. In the ubiquitous plant pathogen Pseudomonas syringae, more than 30% of genes encoded by each strain are not conserved among strains colonizing other host species. Although they are often implicated in host specificity, the role of this large fraction of the genome in host-specific adaptation is largely unexplored. Here, we sought to relate variation in gene content between strains infecting different species to variation that persists between strains on the same host. We fully sequenced a collection of P. syringae strains collected from wild Arabidopsis thaliana populations in the Midwestern United States. We then compared patterns of variation observed in gene content within these A. thaliana-isolated strains to previously published P. syringae sequence from strains collected on a diversity of crop species. We find that strains collected from the same host, A. thaliana, differ in gene content by 21%, 2/3 the level of gene content variation observed across strains collected from different hosts. Furthermore, the frequency with which specific genes are present among strains collected within the same host and among strains collected from different hosts is highly correlated. This implies that most gene content variation is maintained irrespective of host association. At the same time, we identify specific genes whose presence is important for P. syringae's ability to flourish within A. thaliana. Specifically, the A. thaliana strains uniquely share a genomic island encoding toxins active against plants and surrounding microbes, suggesting a role for microbe-microbe interactions in dictating the abundance within this host. Overall, our results demonstrate that while variation in the presence of specific genes can affect the success of a pathogen within its host, the majority of gene content variation is not strongly associated with patterns of host use.
从不同宿主收集的同一物种的细菌菌株常常在基因含量上表现出差异。在无处不在的植物病原菌丁香假单胞菌中，每个菌株编码的基因中有超过30%在定殖于其他宿主物种的菌株中并不保守。尽管它们常常与宿主特异性有关，但基因组中这一大部分在宿主特异性适应中的作用在很大程度上尚未得到探索。在这里，我们试图将感染不同物种的菌株之间的基因含量差异与同一宿主上的菌株之间持续存在的差异联系起来。我们对从美国中西部野生拟南芥种群收集的一组丁香假单胞菌菌株进行了全基因组测序。然后，我们将这些从拟南芥分离的菌株中观察到的基因含量变异模式与先前发表的从多种作物物种收集的丁香假单胞菌序列进行了比较。我们发现，从同一宿主拟南芥收集的菌株在基因含量上相差21%，这是从不同宿主收集的菌株中观察到的基因含量变异水平的2/3。此外，特定基因在同一宿主内收集的菌株以及从不同宿主收集的菌株中出现的频率高度相关。这意味着大多数基因含量变异与宿主关联无关而得以维持。同时，我们鉴定出了对于丁香假单胞菌在拟南芥中茁壮成长至关重要的特定基因。具体而言，拟南芥菌株独特地共享一个编码对植物和周围微生物有活性的毒素的基因组岛，这表明微生物-微生物相互作用在决定该宿主内的丰度方面发挥了作用。总体而言，我们的结果表明，虽然特定基因存在的变异会影响病原体在其宿主内的成功，但大多数基因含量变异与宿主利用模式并没有强烈关联。
