Genome-Wide Identification and Characterization of Small Peptides in Maize.

Small peptides (sPeptides), <100 amino acids (aa) long, are encoded by small open reading frames (sORFs) often found in the 5′ and 3′ untranslated regions (or other parts) of mRNAs, in long non-coding RNAs, or transcripts from introns and intergenic regions; various sPeptides play important roles in multiple biological processes. In this study, we conducted a comprehensive study of maize (Zea mays) sPeptides using mRNA sequencing, ribosome profiling (Ribo-seq), and mass spectrometry (MS) on six tissues (each with at least two replicates). To identify maize sORFs and sPeptides from these data, we set up a robust bioinformatics pipeline and performed a genome-wide scan. This scan uncovered 9,388 sORFs encoding peptides of 2–100 aa. These sORFs showed distinct genomic features, such as different Kozak region sequences, higher specificity of translation, and high translational efficiency, compared with the canonical protein-coding genes. Furthermore, the MS data verified 2,695 sPeptides. These sPeptides perfectly discriminated all the tissues and were highly associated with their parental genes. Interestingly, the parental genes of sPeptides were significantly enriched in multiple functional gene ontology terms related to abiotic stress and development, suggesting the potential roles of sPeptides in the regulation of their parental genes. Overall, this study lays out the guidelines for genome-wide scans of sORFs and sPeptides in plants by integrating Ribo-seq and MS data and provides a more comprehensive resource of functional sPeptides in maize and gives a new perspective on the complex biological systems of plants.

小肽（sPeptides）长度小于100个氨基酸（aa），由小开放阅读框（sORFs）编码，这些小开放阅读框常见于信使核糖核酸（mRNAs）的5′和3′非翻译区（或其他部分）、长链非编码核糖核酸，或来自内含子和基因间区域的转录本；各种小肽在多种生物学过程中发挥重要作用。在本研究中，我们利用信使核糖核酸测序、核糖体图谱分析（Ribo - seq）和质谱分析（MS）对六种组织（每种组织至少有两个重复）的玉米（Zea mays）小肽进行了全面研究。为了从这些数据中识别玉米的小开放阅读框和小肽，我们建立了一个可靠的生物信息学流程，并进行了全基因组扫描。这次扫描发现了9388个编码2 - 100个氨基酸的小肽的小开放阅读框。与典型的蛋白质编码基因相比，这些小开放阅读框显示出独特的基因组特征，例如不同的科扎克区序列、更高的翻译特异性和高翻译效率。此外，质谱数据验证了2695个小肽。这些小肽能够完美地区分所有组织，并且与其亲本基因高度相关。有趣的是，小肽的亲本基因在与非生物胁迫和发育相关的多个功能基因本体术语中显著富集，这表明小肽在其亲本基因调控中具有潜在作用。总体而言，本研究通过整合核糖体图谱分析和质谱数据，为植物中小开放阅读框和小肽的全基因组扫描制定了指南，提供了玉米中功能性小肽更全面的资源，并为植物复杂的生物系统提供了新的视角。