1. Proteogenomic Analysis of Trichophyton rubrumAided by RNA Sequencing
- Author
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Xu, Xingye, Liu, Tao, Ren, Xianwen, Liu, Bo, Yang, Jian, Chen, Lihong, Wei, Candong, Zheng, Jianhua, Dong, Jie, Sun, Lilian, Zhu, Yafang, and Jin, Qi
- Abstract
Infections caused by dermatophytes, Trichophyton rubrumin particular, are among the most common diseases in humans. In this study, we present a proteogenomic analysis of T. rubrumbased on whole-genome proteomics and RNA-Seq studies. We confirmed 4291 expressed proteins in T. rubrumand 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. rubrumannotations. 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. rubrumand represents the first survey of T. rubrumgenome 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).
- Published
- 2015
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