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A chromosome-scale assembly of the smallest Dothideomycete genome reveals a unique genome compaction mechanism in filamentous fungi.
Wang B
,
Liang X
,
Gleason ML
,
Hsiang T
,
Zhang R
,
Sun G
.
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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.
31371887 National Natural Science Foundation of China, B07049 the 111 Project from Education Ministry of China, CARS-27 Agriculture Research System of China
Fig. 1. Chromosome level assembly of P. fructicola genome and syntenic blocks of the five chromosomes. a. Dot plot illustrating the comparative analysis of the chromosome level assembly genome and previous draft genome [12]. Scaffolds were grouped into chromosomes. The blue circles highlight major linker regions in chromosome level genome version. b. Circos plot displaying five collinearity blocks among five chromosomes of P. fructicola. From outside to inside, it represents the distribution of chromosome display, GC contents and syntenic regions, respectively
Fig. 2. Phylogeny and genome characteristics of Peltaster fructicola and other 16 studied Dothideomycetes species. a. A maximum likelihood phylogenetic tree constructed from concatenated alignment of 1957 single-copy orthologs conserved across all species. Bootstrap values are indicated on branches. Ustilago maydis with small genome was used as the outgroup. b. Genome size compared among selected species. c. Median length of introns compared among selected species. d. Intergenic length ratio (%) compared among selected species
Fig. 3. Comparison of gene density and genome sizes in selected species
Fig. 4. Length of intergenic region, colinearity, transposable elements (TEs) and gene density analysis between Peltaster fructicola and Zymoseptoria tritici. a. Intergenic length density plot of P. fructicola genome and Z. tritici genome. b. Syntenic blocks between two species are shown in various color lines (BLASTN coverage > 1 kb). P. fructicola (PF) chromosomes are shown as light blue colour, Z. tritici (ZT) 21 chromosomes [22] are shown as colour. Track a-c are the distribution of chromosomes, TEs density and gene density respectively, with densities calculated in 100 kb windows
Fig. 5. Transposons length analysis of P. fructicola (PF) compared with S. cerevisiae (SC) and Z. tritici (ZT). a. Boxplots of proportion of total TE length.
b. Number of full-length transposons are shown (> 90% length over family consensus)
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