Abstract
The genome sequence of
Ustilago hordei
revealed that transposable elements were involved in restructuring of the genome, which affected fungal reproductive biology and evolution of genes encoding effector proteins. Comparison to other smuts indicated loss of genome defense components in
Ustilago maydis
and control of repetitive sequences by repeat-induced point mutation in
U. hordei
.
Ustilago hordei
is a biotrophic parasite of barley (
Hordeum vulgare
). After seedling infection, the fungus persists in the plant until head emergence when fungal spores develop and are released from sori formed at kernel positions. The 26.1-Mb
U. hordei
genome contains 7113 protein encoding genes with high synteny to the smaller genomes of the related, maize-infecting smut fungi
Ustilago maydis
and
Sporisorium reilianum
but has a larger repeat content that affected genome evolution at important loci, including mating-type and effector loci. The
U. hordei
genome encodes components involved in RNA interference and heterochromatin formation, normally involved in genome defense, that are lacking in the
U. maydis
genome due to clean excision events. These excision events were possibly a result of former presence of repetitive DNA and of an efficient homologous recombination system in
U. maydis
. We found evidence of repeat-induced point mutations in the genome of
U. hordei
, indicating that smut fungi use different strategies to counteract the deleterious effects of repetitive DNA. The complement of
U. hordei
effector genes is comparable to the other two smuts but reveals differences in family expansion and clustering. The availability of the genome sequence will facilitate the identification of genes responsible for virulence and evolution of smut fungi on their respective hosts.