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Small open reading frames (smORFs, <100 amino acids) are a ubiquitous feature of eukaryotic and prokaryotic genomes. However, only a fraction of these smORFs encode functional proteins, known as microproteinsMicroproteins. Functional microproteinsMicroproteins have been found in all three domains of life, although due to limitations in their prediction and characterization, only a few have been described in plants. Therefore, the catalogization and functional analysis of plant smORF-encoded microproteinsMicroproteins is far from complete. In this chapter, we present a bioinformatic pipeline designed to predict and validate coding smORFs in plant transcriptomes. The workflow comprises several key steps: transcriptome assembly, prediction of potentially coding smORFs, filtration of candidates, and validation of their translation through analysis of mass-spectrometry data.

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Identification of Potentially Coding Small ORFs in Plant Transcriptomes

  • 实验方案

  • 发表日期：

    2026年

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  • Daria Ganaeva,
  • Irina Lyapina,
  • Anna Mamaeva,
  • Igor Fesenko

摘要

Small open reading frames (smORFs, <100 amino acids) are a ubiquitous feature of eukaryotic and prokaryotic genomes. However, only a fraction of these smORFs encode functional proteins, known as microproteinsMicroproteins. Functional microproteinsMicroproteins have been found in all three domains of life, although due to limitations in their prediction and characterization, only a few have been described in plants. Therefore, the catalogization and functional analysis of plant smORF-encoded microproteinsMicroproteins is far from complete. In this chapter, we present a bioinformatic pipeline designed to predict and validate coding smORFs in plant transcriptomes. The workflow comprises several key steps: transcriptome assembly, prediction of potentially coding smORFs, filtration of candidates, and validation of their translation through analysis of mass-spectrometry data.