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Background    Shigella flexneri  is the primary cause of bacillary dysentery in the developing countries.  S. flexneri  serotype 1c is a novel serotype, which is found to be endemic in many developing countries, but little is known about its genomic architecture and virulence signatures. We have sequenced for the first time, the complete genome of  S. flexneri  serotype 1c strain Y394, to provide insights into its diversity and evolution.    Results  We generated a high-quality reference genome of  S. flexneri  serotype 1c using the hybrid methods of long-read single-molecule real-time (SMRT) sequencing technology and short-read MiSeq (Illumina) sequencing technology. The Y394 chromosome is 4.58 Mb in size and shares the basic genomic features with other  S. flexneri  complete genomes. However, it possesses unique and highly modified O-antigen structure comprising of three distinct O-antigen modifying gene clusters that potentially came from three different bacteriophages. It also possesses a large number of hypothetical unique genes compared to other  S. flexneri  genomes.    Conclusions  Despite a high level of structural and functional similarities of Y394 genome with other  S. flexneri  genomes, there are marked differences in the pathogenic islands. The diversity in the pathogenic islands suggests that these bacterial pathogens are well adapted to respond to the selection pressures during their evolution, which might contribute to the differences in their virulence potential.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4109-4) contains supplementary material, which is available to authorized users.

Bacteriophages are the major drivers of Shigella flexneri serotype 1c genome plasticity: a complete genome analysis