Abstract
BackgroundThe 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.ResultsAt 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.ConclusionsOur 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.
Highlights
The wide variation in the size of fungal genomes is well known, but the reasons for this size variation are less certain
We found that the P. fructicola genome was overall gene-dense with shorter intron (Fig. 2c) and intergenic lengths (Fig. 4a) but longer exon lengths compared to Z. tritici genome which shows overall gene-sparse (Fig. 4b)
When compared to Transposable elements (TEs) families in Z. tritici, we found that P. fructicola had a reduced battery of Class I and Class II transposable elements (Table 1)
Summary
The wide variation in the size of fungal genomes is well known, but the reasons for this size variation are less certain. 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. By the early twenty-first century, sequencing of the human genome was complete [1]. Because the DNA which encoded proteins accounted for only 1.0% ~ 1.5% of the total DNA, the human genome was characterized as a C-value paradox; that is, not compact [3]. The habitats of compact-genome species are usually extreme environments. It is reasonable to hypothesize that streamlining of genome size and function is driven by restrictions imposed by their lifestyles [3]. Fungi in the sooty blotch and flyspeck (SBFS) complex exclusively colonize plant surfaces, which are extreme environments characterized by prolonged desiccation, nutrient limitation, and exposure to solar radiation [10]. Recent research has presented compelling evidence that SBFS fungi underwent profound reductive evolution during the transition from plantpenetrating parasites to plant-surface colonists [11,12,13,14]
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