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Background   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.    Results  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.    Conclusions  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.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5366-6) contains supplementary material, which is available to authorized users.

Comparative analysis reveals the Genomic Islands in Pasteurella multocida population genetics: on Symbiosis and adaptability