School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.
Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom.
Mol Biol Evol. 2021 Aug 23;38(9):3697-3708. doi: 10.1093/molbev/msab139.
A pangenome is the complete set of genes (core and accessory) present in a phylogenetic clade. We hypothesize that a pangenome's accessory gene content is structured and maintained by selection. To test this hypothesis, we interrogated the genomes of 40 Pseudomonas species for statistically significant coincident (i.e., co-occurring/avoiding) gene patterns. We found that 86.7% of common accessory genes are involved in ≥1 coincident relationship. Further, genes that co-occur and/or avoid each other-but are not vertically inherited-are more likely to share functional categories, are more likely to be simultaneously transcribed, and are more likely to produce interacting proteins, than would be expected by chance. These results are not due to coincident genes being adjacent to one another on the chromosome. Together, these findings suggest that the accessory genome is structured into sets of genes that function together within a given strain. Given the similarity of the Pseudomonas pangenome with open pangenomes of other prokaryotic species, we speculate that these results are generalizable.
泛基因组是指在一个系统发育分支中存在的全部基因（核心基因和附属基因）。我们假设泛基因组的附属基因组成是由选择来构建和维持的。为了验证这一假设，我们对 40 种假单胞菌的基因组进行了统计分析，以研究是否存在显著的共现（即共同出现/回避）基因模式。结果发现，86.7%的常见附属基因参与了至少 1 种共现关系。此外，相互共现和/或回避但不是垂直遗传的基因更有可能具有相同的功能类别，更有可能同时转录，并且更有可能产生相互作用的蛋白质，这超出了随机预期。这些结果并不是由于巧合基因彼此相邻在染色体上。综上所述，这些发现表明附属基因组是由在特定菌株中共同发挥作用的基因集构建而成的。鉴于假单胞菌泛基因组与其他原核生物的开放泛基因组的相似性，我们推测这些结果是普遍适用的。
