Spring-Pearson Senanu M, Stone Joshua K, Doyle Adina, Allender Christopher J, Okinaka Richard T, Mayo Mark, Broomall Stacey M, Hill Jessica M, Karavis Mark A, Hubbard Kyle S, Insalaco Joseph M, McNew Lauren A, Rosenzweig C Nicole, Gibbons Henry S, Currie Bart J, Wagner David M, Keim Paul, Tuanyok Apichai
Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America.
Menzies School of Health Research and Infectious Disease Department, Royal Darwin Hospital. Darwin, Northern Territory, Australia.
PLoS One. 2015 Oct 20;10(10):e0140274. doi: 10.1371/journal.pone.0140274. eCollection 2015.
The pangenomic diversity in Burkholderia pseudomallei is high, with approximately 5.8% of the genome consisting of genomic islands. Genomic islands are known hotspots for recombination driven primarily by site-specific recombination associated with tRNAs. However, recombination rates in other portions of the genome are also high, a feature we expected to disrupt gene order. We analyzed the pangenome of 37 isolates of B. pseudomallei and demonstrate that the pangenome is 'open', with approximately 136 new genes identified with each new genome sequenced, and that the global core genome consists of 4568±16 homologs. Genes associated with metabolism were statistically overrepresented in the core genome, and genes associated with mobile elements, disease, and motility were primarily associated with accessory portions of the pangenome. The frequency distribution of genes present in between 1 and 37 of the genomes analyzed matches well with a model of genome evolution in which 96% of the genome has very low recombination rates but 4% of the genome recombines readily. Using homologous genes among pairs of genomes, we found that gene order was highly conserved among strains, despite the high recombination rates previously observed. High rates of gene transfer and recombination are incompatible with retaining gene order unless these processes are either highly localized to specific sites within the genome, or are characterized by symmetrical gene gain and loss. Our results demonstrate that both processes occur: localized recombination introduces many new genes at relatively few sites, and recombination throughout the genome generates the novel multi-locus sequence types previously observed while preserving gene order.
类鼻疽伯克霍尔德菌的泛基因组多样性很高，约5.8%的基因组由基因组岛组成。基因组岛是已知的重组热点，主要由与tRNA相关的位点特异性重组驱动。然而，基因组其他部分的重组率也很高，我们预计这一特征会破坏基因顺序。我们分析了37株类鼻疽伯克霍尔德菌的泛基因组，证明该泛基因组是“开放的”，每测序一个新基因组大约能鉴定出136个新基因，并且全球核心基因组由4568±16个同源物组成。核心基因组中与代谢相关的基因在统计学上显著富集，与移动元件、疾病和运动性相关的基因主要与泛基因组的辅助部分相关。在所分析的1至37个基因组中出现的基因频率分布与一种基因组进化模型非常匹配，在该模型中，96%的基因组重组率非常低，但4%的基因组很容易发生重组。利用成对基因组中的同源基因，我们发现尽管之前观察到重组率很高，但菌株间的基因顺序高度保守。除非基因转移和重组过程高度局限于基因组内的特定位点，或者具有对称的基因得失特征，否则高频率的基因转移和重组与保持基因顺序是不相容的。我们的结果表明这两个过程都存在：局部重组在相对较少的位点引入许多新基因，而全基因组的重组在保持基因顺序的同时产生了之前观察到的新型多位点序列类型。
