School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China.
Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China.
Genomics. 2022 Sep;114(5):110444. doi: 10.1016/j.ygeno.2022.110444. Epub 2022 Aug 3.
Small open reading frames (smORFs) have been acknowledged as an important partner in organism functions ranging from bacteria to higher eukaryotes. However, there is a lack of investigation of smORFs in green algae, despite their importance in ecology and evolution. We applied bioinformatic analysis, ribosome profiling, and small peptide proteomics to provide a genome-wide and high-confident smORF database in the model green alga Chlamydomonas reinhardtii. The whole genome was screened first to mine potential coding smORFs. Then conservative analysis, ribosome profiling, and proteomics data were processed to identify conserved smORFs and generate translation evidence. The combination of procedures resulted in 2014 smORFs that might exist in the C. reinhardtii genome. The expression of smORFs in Cd treatment suggested that two smORFs might participate in redox reaction, three in inorganic phosphate transport, and one in DNA repair under stress. Our study built a genome-widely database in C. reinhardtii, providing target smORFs for further research.
小开放阅读框 (smORFs) 已被公认为从细菌到高等真核生物的生物体功能的重要伙伴。然而，尽管绿藻在生态学和进化中很重要，但对其 smORFs 的研究却很少。我们应用生物信息学分析、核糖体分析和小肽蛋白质组学，在模式绿藻莱茵衣藻中提供了一个全基因组和高置信度的 smORF 数据库。首先对整个基因组进行筛选，以挖掘潜在的编码 smORFs。然后对保守分析、核糖体分析和蛋白质组学数据进行处理，以识别保守的 smORFs 并生成翻译证据。这些程序的结合产生了 2014 个可能存在于莱茵衣藻基因组中的 smORFs。Cd 处理中 smORFs 的表达表明，两个 smORFs 可能参与氧化还原反应，三个参与无机磷运输，一个参与应激下的 DNA 修复。我们的研究在莱茵衣藻中建立了一个全基因组范围的数据库，为进一步的研究提供了目标 smORFs。
