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<p>Identifying hidden coding potential in staple crops like <i>Triticum aestivum</i> is vital for advancing stress resilience. In this study, a multistep in-silico framework was applied to uncover and characterize four previously unannotated small open reading frames (sORFs) within the wheat chloroplast genome (GenBank: AB042240.3). Gene prediction using FGENESH, followed by RNA simulation, physicochemical profiling, and structure–function modelling with PSIPRED, I-TASSER, and ProSA-web, revealed peptides with distinct and stable conformations but no significant similarity to known proteins. Functional annotations suggest roles in metal detoxification, ATP synthesis, nucleotide recycling, and cyclic electron transport—key pathways for abiotic stress tolerance. Comparative genomics demonstrated evolutionary conservation across Poaceae, while RNA-Seq expression profiling with replicate-based statistical validation confirmed stress-specific transcriptional activity. This study expands the functional landscape of the wheat plastome by revealing novel stress-responsive sORFs, offering promising molecular targets for precision biotechnology and new opportunities to enhance wheat resilience under climate change.</p> Graphical Abstract <p></p>

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Genome-wide in-silico identification of putative small chloroplast open reading frames (ORFs) in wheat with potential roles in stress adaptation

  • 期刊论文

  • 发表日期：

    2025年12月15日

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  • A. Foumitha Begum,
  • K. Kiruthika,
  • Kiruba Rajamani

摘要

Identifying hidden coding potential in staple crops like Triticum aestivum is vital for advancing stress resilience. In this study, a multistep in-silico framework was applied to uncover and characterize four previously unannotated small open reading frames (sORFs) within the wheat chloroplast genome (GenBank: AB042240.3). Gene prediction using FGENESH, followed by RNA simulation, physicochemical profiling, and structure–function modelling with PSIPRED, I-TASSER, and ProSA-web, revealed peptides with distinct and stable conformations but no significant similarity to known proteins. Functional annotations suggest roles in metal detoxification, ATP synthesis, nucleotide recycling, and cyclic electron transport—key pathways for abiotic stress tolerance. Comparative genomics demonstrated evolutionary conservation across Poaceae, while RNA-Seq expression profiling with replicate-based statistical validation confirmed stress-specific transcriptional activity. This study expands the functional landscape of the wheat plastome by revealing novel stress-responsive sORFs, offering promising molecular targets for precision biotechnology and new opportunities to enhance wheat resilience under climate change.

Graphical Abstract