Genome transposon analysis of blackleg causal pathogen

Abstract Background To understand genome transposon presence of blackleg pathogen and the relationship between its pathogenicity and transposons, we performed transposon analysis of blackleg pathogen through bioinformatics. Results For three pathogen strains, their genome transposon proportion was distantly beyond 4%, the pathogen strain Lmb V23.1.3 indicated the most genome transposons, followed by Lbb B3.5 and Lbb CA1, the LTR retrotransposons proportion was obviously more than other types of transposons and the Ty3/Gypsy retrotransposon proportion was greater than Ty1/Copia retrotransposons. there were no Ty1/Copia retrotransposons in Lbb CA1. Most Ty1/Copia and Ty3/Gypsy retrotransposons presented distinct evolutionary distance among different pathogen strains. Besides, the higher LTR retrotransposon density, the lower gene density, the Solo-LTR retrotransposons were much greater than intact LTR retrotransposons. Both Solo-LTR and intact LTR retrotransposon counts were the highest in Lmb V23.1.3, followed by Lbb B3.5 and Lbb CA1 respectively. Many intact LTR retrotransposons in Lmb V23.1.3 were more ancient than those in Lbb B3.5 and Lbb CA1. However, lots of homologous LTR retrotransposons in Lmb V23.1.3 were younger than those in Lbb B3.5 and Lbb CA1. No common intact LTR retrotransposons were identified between L. maculans species and L. biglobosa species, and significantly few even between two strains of the same pathogen species. Large number of special intact LTR retrotransposons in L. biglobosa were relatively younger than those in L. maculans. In addition, the LINE elements only occurred in Lmb V23.1.3, which was possibly responsible for its stronger pathogenicity. Conclusions Some pathogen strains of L. biglobosa species also contained genome transposon of distantly beyond 4%. For both L. biglobosa and L. biglobosa species, the LTR retrotransposon proportion was obviously more than other types of transposons. There was distinct evolutionary distance of LTR retrotransposons and no common intact LTR retrotransposons between two pathogen species. The Ty3/Gypsy retrotransposon proportion was greater than Ty1/Copia retrotransposons. Large number of special intact LTR retrotransposons in L. biglobosa were relatively younger than those in L. maculans. The LINE elements only occurred in Lmb V23.1.3 of L. maculans species, which was possibly responsible for its stronger pathogenicity.