Transposable elements contribute to the genome plasticity of species complex.

The extensive genetic diversity of , a serious soil-borne phytopathogen, has led to the concept that encompasses a species complex [ species complex (RSSC)]. Insertion sequences (ISs) are suggested to play an important role in the genome evolution of this pathogen. Here, we identified and analysed transposable elements (TEs), ISs and transposons, in 106 RSSC genomes and 15 spp. We mapped 10 259 IS elements in the complete genome of 62 representative RSSC strains and closely related spp. A unique set of 20 IS families was widespread across the strains, IS and IS being the most abundant. Our results showed six novel transposon sequences belonging to the Tn family carrying passenger genes encoding antibiotic resistance and avirulence proteins. In addition, internal rearrangement events associated with ISs were demonstrated in strains. We also mapped IS elements interrupting avirulence genes, which provided evidence that ISs plays an important role in virulence evolution of RSSC. Additionally, the activity of ISs was demonstrated by transcriptome analysis and DNA hybridization in isolates. Altogether, we have provided collective data of TEs in RSSC genomes, opening a new path for understanding their evolutionary impact on the genome evolution and diversity of this important plant pathogen.