Proteogenomic
Analysis of <i>Trichophyton rubrum</i> Aided by RNA Sequencing
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Abstract
Infections caused by dermatophytes, Trichophyton
rubrum in particular, are among the most common diseases
in humans. In this study, we present a proteogenomic analysis of T. rubrum based on whole-genome proteomics and RNA-Seq
studies. We confirmed 4291 expressed proteins in T.
rubrum and validated their annotated gene structures
based on 35 874 supporting peptides. In addition, we identified
323 novel peptides (not present in the current annotated protein database
of T. rubrum) that can be used to enhance
current T. rubrum annotations. A total
of 104 predicted genes supported by novel peptides were identified,
and 127 gene models suggested by the novel peptides that conflicted
with existing annotations were manually assigned based on transcriptomic
evidence. RNA-Seq confirmed the validity of 95% of the total peptides.
Our study provides evidence that confirms and improves the genome
annotation of T. rubrum and represents
the first survey of T. rubrum genome
annotations based on experimental evidence. Additionally, our integrated
proteomics and multisourced transcriptomics approach provides stronger
evidence for annotation refinement than proteomic data alone, which
helps to address the dilemma of one-hit wonders (uncertainties supported
by only one peptide)