Abstract
Epichloe fungi are endophytes of cool season grasses, both wild species and commercial cultivars, where they may exhibit mutualistic or pathogenic lifestyles. The Epichloe-grass symbiosis is of great interest to agricultural research for the fungal bioprotective properties conferred to host grasses but also serves as an ideal system to study the evolution of fungal plant-pathogens in natural environments. Here, we assembled and annotated gapless chromosome-level genomes of two pathogenic Epichloe sibling species. Both genomes have a bipartite genome organization, with blocks of highly syntenic gene-rich regions separated by blocks of AT-rich DNA. The AT-rich regions show an extensive signature of RIP (repeat-induced point mutation) and the expansion of this compartment accounts for the large difference in genome size between the two species. This study reveals how the rapid evolution of repeat structure can drive divergence between closely related taxa and highlights the evolutionary role of dynamic compartments in fungal genomes.
Highlights
Despite their small size, fungal genomes can provide big insights into eukaryote genome organization and evolution
The AT-rich regions show an extensive signature of repeat-induced point mutation (RIP) and the expansion of this compartment accounts for the large difference in genome size between the two species
Consistent with this, we found that of 6923 orthologs shared by both species, most were located in gene-rich regions, whereas only one gene in E. typhina (Ety_007361) and two in E. clarkii (Ecl_003362 and Ecl_005753) were located in ATrich regions (Fig. 3, yellow lines)
Summary
Fungal genomes can provide big insights into eukaryote genome organization and evolution. Plant-colonizing fungi and oomycetes, in particular, frequently have genomes with a bipartite organization: a conserved “core genome” containing the majority of genes and a highly variable compartment characterized by a high repeat-content and few genes [1]. In some cases these repeat-rich re gions are targeted by repeat-induced point mutation (RIP), a defense mechanism against transposable element proliferation, which leads to locally high mutation rates, C-to-T mutations, reduced G/C content and increased genetic diversity [2,3]. We still lack an understanding of how widespread this bipartite genome organization is, how it varies across taxa and how it relates to evolutionary processes [8]
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