A chromosome-scale assembly of the smallest Dothideomycete genome reveals a unique genome compaction mechanism in filamentous fungi
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ABSTRACT:
PROVIDER: PRJNA498715 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8115200_1.fastq.gz | Fastqsanger.gz | |||
| SRR8115200_2.fastq.gz | Fastqsanger.gz | |||
| SRR8115198_1.fastq.gz | Fastqsanger.gz | |||
| SRR8115198_2.fastq.gz | Fastqsanger.gz | |||
| SRR8115199_1.fastq.gz | Fastqsanger.gz |
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Project description: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.
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Project description:The meiotic cohesin Rec8 is required for the stepwise segregation of chromosomes during the two rounds of meiotic division. By directly measuring chromosome compaction in living cells of the fission yeast Schizosaccharomyces pombe, we found an additional role for the meiotic cohesin in the compaction of chromosomes during meiotic prophase. In the absence of Rec8, chromosomes were decompacted relative to those of wild-type cells. Conversely, loss of the cohesin-associated protein Pds5 resulted in hyper-compaction. While this hyper-compaction requires Rec8, binding of Rec8 to chromatin was reduced in the absence of Pds5, indicating that Pds5 promotes chromosome association of Rec8. To explain these observations, we propose that meiotic prophase chromosomes are organized as chromatin loops emanating from a Rec8-containing axis; the absence of Rec8 disrupts the axis, resulting in disorganized chromosomes, whereas reduced Rec8 loading results in a longitudinally compacted axis with fewer attachment points and longer chromatin loops. Keywords: ChIP-chip analysis ChIP analysis of Rec8: In all cases, hybridization data for ChIP fraction was compared with that of SUP (supernatant) fraction. Pombe chromosome II, III array was used.
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Project description:Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance, and are significant opportunistic parasites of humans. They are characterized by having a specialized infection apparatus, an obligate intracellular lifestyle, rudimentary mitochondria and the smallest eukaryotic genomes. Extreme genome compaction has led to minimal gene sizes affecting even conserved ancient complexes such as the ribosome. Here we present the high-resolution cryo-EM structure of the microsporidian ribosome which illustrates how genome compaction has resulted in the smallest eukaryotic cytoplasmic ribosome. Selection pressure has led to the loss of two ribosomal proteins and removal of essentially all eukaryote-specific rRNA expansion segments reducing the ribosomal RNA to a functionally conserved core. The structure also highlights how one microsporidia-specific and several repurposed existing ribosomal proteins compensate for the extensive reduction of the rRNA. The microsporidian ribosome is kept in an inactive state by two previously uncharacterized dormancy factors that specifically target the functionally important E-site, P-site and polypeptide exit tunnel. This study visualizes the distinct effects of evolutionary pressure on RNA and protein coding genes, provides a new mechanism for ribosome inhibition and can serve as a structural basis for the development of small molecule inhibitors against microsporidian parasites.
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Project description:The meiotic cohesin Rec8 is required for the stepwise segregation of chromosomes during the two rounds of meiotic division. By directly measuring chromosome compaction in living cells of the fission yeast Schizosaccharomyces pombe, we found an additional role for the meiotic cohesin in the compaction of chromosomes during meiotic prophase. In the absence of Rec8, chromosomes were decompacted relative to those of wild-type cells. Conversely, loss of the cohesin-associated protein Pds5 resulted in hyper-compaction. While this hyper-compaction requires Rec8, binding of Rec8 to chromatin was reduced in the absence of Pds5, indicating that Pds5 promotes chromosome association of Rec8. To explain these observations, we propose that meiotic prophase chromosomes are organized as chromatin loops emanating from a Rec8-containing axis; the absence of Rec8 disrupts the axis, resulting in disorganized chromosomes, whereas reduced Rec8 loading results in a longitudinally compacted axis with fewer attachment points and longer chromatin loops. Keywords: ChIP-chip analysis
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