Genome transposon analysis of blackleg pathogen (Leptosphaeria spp.)

Abstract Background To understand presence of genome transposons of blackleg pathogen and to explore potential relationship between transposons and pathogenicity, we performed genome transposon analysis for various blackleg pathogen strains. Results The genome transposon proportion was approximately 30%, 18% and 10% in three blackleg pathogen strains, Lmb V23.1.3, Lbb B3.5 and Lbb CA1, respectively. For the three blackleg pathogen strains, the LTR retrotransposon percentage was obviously more than other types of transposons, and the counts of Ty3/Gypsy superfamily of intact LTR retrotransposons was much greater than that of Ty1/Copia superfamily. The LINE elements were only discovered in the blackleg pathogen strain Lmb V23.1.3. A great many of homologous LTR retrotransposons in Lmb V23.1.3 were younger than those in Lbb B3.5 and Lbb CA1. However, the majority of intact LTR retrotransposons in Lmb V23.1.3 were more ancient than those in Lbb B3.5 and Lbb CA1. Most of Ty1/Copia and Ty3/Gypsy superfamilies of intact LTR retrotransposons from different blackleg pathogen strains clustered into various branches in phylogeny trees. Besides, statistical analysis of gene density and LTR retrotransposon density revealed an inverse relationship between them in three blackleg pathogen strains whose solo-LTR retrotransposons were much more than intact LTR retrotransposons. The blackleg pathogen strain Lmb V23.1.3 contained the highest counts of both solo-LTR and intact LTR retrotransposons, followed by Lbb B3.5 and Lbb CA1, respectively. Pan-genome transposon analysis suggested that there no common families of intact LTR retrotransposons between L. maculans and L. biglobosa species, and fewer common families of intact LTR retrotransposons were identified even between various blackleg pathogen strains of same Leptosphaeria species. Large number of common families of intact LTR retrotransposons in L.biglobosa species were relatively younger than those in L.maculans species. Conclusions The highly virulent L.maculans species has much greater proportion of transposons compared to the weakly virulent L.biglobosa species. There was a considerable evolutionary distance among intact LTR retrotransposons from L.maculans and L.biglobosa species, and there were no common families of intact LTR retrotransposons between the two species. The genome of blackleg pathogen displayed higher proportion of LTR retrotransposons, with a relatively greater abundance of Ty3/Gypsy superfamilies of intact LTR retrotransposons compared to Ty1/Copia superfamilies. The long terminal repeats at both ends of LTR retrotransposons possibly accumulate more mutations over time, and the intermediate domains are relatively conserved. Besides, there were significantly higher number of solo-LTR retrotransposons compared to intact LTR retrotransposons, and an inverse relationship between gene density and LTR retrotransposon density was observed in the blackleg pathogen. LINE elements in Lmb V23.1.3 possibly resulted in its stronger pathogenicity in B.napus crops.