Landscape of novel smORFs predicted from crop genomes with evolutionary and functional analysis

IF 3.4 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics Pub Date : 2025-06-11 DOI:10.1016/j.ygeno.2025.111070

Zhao Peng, Cuihong Wan

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引用次数: 0

Abstract

Numerous small open reading frames (smORFs) and related smORF-encoded peptides (SEPs) have been identified in model plants. However, a genome-wide overview of smORFs has yet to be established in plants, especially in crops. Here, we predicted millions of novel smORFs in Arabidopsis and 14 commonly cultivated crops by bioinformatic approaches. We found that the smORFs may reflect recurrent polyploidy events and genome rearrangements during evolution, and some smORFs are under strong purifying selection. About 70 % of orthogroups contain SEPs from one species, while 0.1 % of orthogroups contain SEPs from all species. Orthogroup size variation suggests that species-specific features are shaped by factors, including evolutionary relationship, genome size, and genome duplication. DNA repair and translation are major functions of conserved SEPs. Species-specific functions were also observed, such as salt stress responses in Brassica. Our work provides a valuable resource of smORFs and SEPs, offering insights into the understanding of their characteristics.

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基于进化和功能分析的作物基因组预测新型smorf景观

在模式植物中已经发现了许多小的开放阅读框（smorf）和相关的smorf编码肽（sep）。然而，smorf的全基因组概况尚未在植物中建立，特别是在作物中。在这里，我们用生物信息学方法预测了拟南芥和14种常用栽培作物中数百万个新的smorf。我们发现smorf可能反映了进化过程中反复发生的多倍体事件和基因组重排，并且一些smorf处于强烈的净化选择之下。大约70%的正形群含有来自一个物种的sep，而0.1%的正形群含有来自所有物种的sep。正群大小的变化表明，物种特有的特征是由进化关系、基因组大小和基因组复制等因素形成的。DNA修复和翻译是保守sep的主要功能。此外，还观察到了物种特有的功能，如芸苔属植物对盐胁迫的反应。我们的工作为smorf和sep提供了宝贵的资源，为理解它们的特征提供了见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genomics 生物-生物工程与应用微生物

CiteScore

9.60

自引率

2.30%

发文量

260

审稿时长

60 days

期刊介绍： Genomics is a forum for describing the development of genome-scale technologies and their application to all areas of biological investigation. As a journal that has evolved with the field that carries its name, Genomics focuses on the development and application of cutting-edge methods, addressing fundamental questions with potential interest to a wide audience. Our aim is to publish the highest quality research and to provide authors with rapid, fair and accurate review and publication of manuscripts falling within our scope.