A chromosome-scale assembly of the smallest Dothideomycete genome reveals a unique genome compaction mechanism in filamentous fungi

Abstract

Background: The wide variation in the size of fungal genomes is well known, but the reasons for this size variation are less certain. Here, we present a chromosome-scale assembly of ectophytic Peltaster fructicola, a surface-dwelling extremophile, based on long-read DNA sequencing technology, to assess possible mechanisms associated with genome compaction. Results: At 18.99 million bases (Mb), P. fructicola possesses one of the smallest known genomes sequence among filamentous fungi. The genome is highly compact relative to other fungi, with substantial reductions in repeat content, ribosomal DNA copies, tRNA gene quantity, and intron sizes, as well as intergenic lengths and the size of gene families. Transposons take up just 0.05% of the entire genome, and no full-length transposon was found. We concluded that reduced genome sizes in filamentous fungi such as P. fructicola, Taphrina deformans and Pneumocystis jirovecii occurred through reduction in ribosomal DNA copy number and reduced intron sizes. These dual mechanisms contrast with genome reduction in the yeast fungus Saccharomyces cerevisiae, whose small and compact genome is associated solely with intron loss. Conclusions: Our results reveal a unique genomic compaction architecture of filamentous fungi inhabiting plant surfaces, and broaden the understanding of the mechanisms associated with compaction of fungal genomes.

A devil's bargain with transposable elements in plant pathogens

“…In plant pathogens, closely related Box 2. Genome size expansions in filamentous pathogens Genome size can differ among closely related fungal species [77,78] and even within a single species [49,50,79]. A striking example of genome size expansion comes from rust fungi that have massively expanded genomes.…”

Massive genome reduction occurred prior to the origin of coral algal symbionts

“…In examples of the first scenario, TE-mediated insertions drive intron expansion and are biased toward the 5′ ends of genes to prevent disrupting functional elements (McCoy and Fire 2020), yielding larger intron sizes at 5′ ends; we did not observe this in Ev (Figure 2I). In the second scenario, which has been observed in endosymbiotic/parasitic organisms, the reduction of intron size and density occurs as a result of genome reduction and/or streamlining induced by spatial confinement in the host organism or cell (Wang et al 2020a; Cai et al 2021). Considering the evolutionary history of Symbiodiniaceae, intron contraction in S1/S2 taxa due to their symbiotic lifestyle is more plausible than invoking intron expansion in Ev.…”

The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains

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