The soybean rust pathogen <i>Phakopsora pachyrhizi</i> displays transposable element proliferation that correlates with broad host-range adaptation on legumes

ABSTRACT Asian soybean rust, caused by Phakopsora pachyrhizi , is one of the world’s most economically damaging agricultural diseases. Despite P. pachyrhizi ’s impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. We simultaneously sequenced three P. pachyrhizi genomes uncovering a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. The proliferation of TEs within the genome occurred in several bursts and correlates with the radiation and speciation of the legumes. We present data of clear de-repression of TEs that mirrors expression of virulence-related candidate effectors. We can see a unique expansion in amino acid metabolism for this fungus. Our data shows that TEs play a dominant role in P. pachyrhizi ’s genome and have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity of the genome.