Composition and Diversity of LTR Retrotransposons in the Coffee Leaf Rust Genome (Hemileia vastatrix)

Coffee leaf rust is the most damaging disease for coffee cultivation around the world. It is caused by a fungal pathogen, Hemileia vastatrix (Hva), belonging to the phylum Basidiomycota. Coffee leaf rust causes significant yield losses and increases costs related to its control, with evaluated losses of USD 1–2 billion annually. It attacks both the cultivated coffee species Coffea canephora (Robusta coffee) and Coffea arabica (Arabica coffee). New races, or pathotypes, are constantly emerging with increased virulence, suggesting a rapid evolution of the pathogen. Previous genetic and genomic studies have indicated a limited nucleotide diversity of Hva despite a high genetic diversity and large genome size estimated to be ~800 Mb, with a high content of repeated sequences (>74%). Despite several genomic resources and the release of a recent partial genome sequence, the diversity of these repeated sequences and how they may impact the evolution of the leaf rust genome have not been investigated in detail. In an attempt to characterize the transposable elements within the Hva genomes, we report here new lineages of long terminal repeat (LTR) retrotransposons, called CO-HUI, Soroa, and Baco, which are classified into Gypsy, and and Labe and Mapi, which are classified as Copia. The CO-HUI and Soroa elements represent the main part of all Hva transposable elements, as well as approximately 37% of the available genome assemblies. Mapi and CO-HUI are the main expressed families in RNA-seq data. Although Soroa is the lineage showing more insertions into exons and genes, Mapi seems to be more frequently involved in co-expression with genes. All these new families are also present in the Pucciniales, suggesting that they dynamically participate in their genome evolution.