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Teichert I, Dahlmann TA, Kück U, Nowrousian M. Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes. Liu H, Wang Q, He Y, Chen L, Hao C, Jiang C, et al. The RNA reads from the same isolates that DNA reads were generated were downloaded from MycoCosm ( ). The original and newly assembled genomes were aligned using NUCmer 4.0.0beta2 ( ) to find corresponding sites. We used SPAdes v3.13.0 ( ) (-careful -cov-cutoff auto) to reassemble D. Subsequently, the reads were quality controlled using TrimGalore ( ) by filtering out the reads with bad base quality (5% variants of mapped reads) were ignored. The genome and transcriptome reads were de-duplicated to remove polymerase chain reaction products using Dedupe in BBTools ( ). We downloaded genomic and transcriptomic read data used in this study from the NCBI database (Table 2).
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lucidum was similar to those we corrected in the haploid genomes of Polyporales in that transitions dominate transversions leading to mostly synonymous amino acid changes. This may be quite challenging, but the editing pattern reported in G. In order to confirm RNA editing in this species, two haplotypes need to be separated and analyzed independently with proper DNA and RNA reads mapped to each of them to identify haplotype-specific polymorphisms indicating possible mis-assemblies that need to be filtered out in analysis of RNA polymorphisms. lucidum is a heterokaryotic species, making the analysis more challenging because of the ploidy combined with segmental duplications. While the reference genome was built by the one of two mating strains (monokaryon), the fruiting-body from which gDNA and RNA were extracted was formed by a dikaryon where two mating strains exist. lucidum using analysis of both gDNA and RNA reads, with 94 sites verified with Sanger sequencing. The report suggested 8906 RNA-editing sites in G. Similar transitions-over-transversions nucleotide patterns of RNA-editing were reported in Ganoderma lucidum. Thus, there is no evidence of RNA editing during the vegetative growth in these five species of Polyporales.
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These polymorphisms were not confirmed in RNA reads used for genome annotation and obtained from the same isolates as DNA. The RNA polymorphism in the remaining four sites can be explained by the differences in isolates used for genome sequencing and for the transcriptomics studies by Wu et al. After this multi-step filtering, all but four sites across four species were eliminated. In addition, when we searched reads pooled rather than aligned reads, we observed distinct groups of gDNA reads matching the polymorphic RNA reads with 100% identify of the entire length and thus corresponding to different parts of the genome (Table 1). That is because the reads having supported the variations were decoupled and mapped to different regions or were not mapped due to the intron length limitation.
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Some of these remaining candidate sites did not show the single-nucleotide variations when the later version of HISAT alignment was used with intron length restriction (2000 bp). lucidum and the five Polyporales fungi were not only different from the typical A-to-I editing but also showed that transitions (A- > G, G- > A, C- > U, U- > C) were preferred over transversions, leading mainly to synonymous changes in contrast to missense changes found in filamentous ascomycetes. It was noted that the editing patterns of both G. reported RNA-editing events in vegetative mycelia of five other species of Polyporales. In Basidiomycota, the first RNA-editing report was from Ganoderma lucidum, a mushroom-forming species of Polyporales, also during fruiting body formation. verticillioides, Neurospora crassa, Sordaria macrospora, and Pyronema confluens (Pezizomycotina), but absent during meiosis in the fission yeast Schizosaccharomyces pombe (Taphrinomycotina). In fungi, adenosine-to-inosine (A-to-I) RNA-editing was shown to occur during sexual development and fruiting body formation in filamentous ascomycetes Fusarium graminearum, F.