Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.
Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China.
BMC Genomics. 2019 Jan 18;20(1):63. doi: 10.1186/s12864-018-5366-6.
Pasteurella multocida (P. multocida) is a widespread opportunistic pathogen that infects human and various animals. Genomic Islands (GIs) are one of the most important mobile components that quickly help bacteria acquire large fragments of foreign genes. However, the effects of GIs on P. multocida are unknown in the evolution of bacterial populations.
Ten avian-sourced P. multocida obtained through high-throughput sequencing together with 104 publicly available P. multocida genomes were used to analyse their population genetics, thus constructed a pan-genome containing 3948 protein-coding genes. Through the pan-genome, the open evolutionary pattern of P. multocida was revealed, and the functional components of 944 core genes, 2439 accessory genes and 565 unique genes were analysed. In addition, a total of 280 GIs were predicted in all strains. Combined with the pan-genome of P. multocida, the GIs accounted for 5.8% of the core genes in the pan-genome, mainly related to functional metabolic activities; the accessory genes accounted for 42.3%, mainly for the enrichment of adaptive genes; and the unique genes accounted for 35.4%, containing some defence mechanism-related genes.
The effects of GIs on the population genetics of P. multocida evolution and adaptation to the environment are reflected by the proportion and function of the pan-genome acquired from GIs, and the large quantities of GI data will aid in additional population genetics studies.
多杀巴斯德氏菌（Pasteurella multocida，P. multocida）是一种广泛存在的机会致病菌，可感染人类和各种动物。基因组岛（Genomic Islands，GIs）是细菌快速获得大量外源基因的最重要的移动元件之一。然而，GIs 对细菌种群进化过程中多杀巴斯德氏菌的影响尚不清楚。
通过高通量测序获得的 10 株禽源多杀巴斯德氏菌与 104 株公开的多杀巴斯德氏菌基因组一起用于分析其群体遗传学，从而构建了一个包含 3948 个蛋白编码基因的泛基因组。通过泛基因组揭示了多杀巴斯德氏菌的开放进化模式，并分析了 944 个核心基因、2439 个辅助基因和 565 个独特基因的功能成分。此外，在所有菌株中总共预测了 280 个 GIs。结合多杀巴斯德氏菌的泛基因组，GIs 占泛基因组核心基因的 5.8%，主要与功能代谢活动有关；辅助基因占 42.3%，主要用于适应性基因的富集；独特基因占 35.4%，包含一些防御机制相关基因。
通过从 GIs 获得的泛基因组的比例和功能反映了 GIs 对多杀巴斯德氏菌进化和适应环境的群体遗传学的影响，大量的 GI 数据将有助于进一步的群体遗传学研究。
