Xu Ruirui, Liu Caiyun, Li Ning, Zhang Shizhong
Key Laboratory of Biology and Molecular Biology in University of Shandong, Weifang University, Weifang, Shandong, 261061, China.
State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Technology, Shandong Agricultural University, 61# Daizong Street, Tai'an, Shandong, 271018, China.
Mol Genet Genomics. 2016 Dec;291(6):2015-2030. doi: 10.1007/s00438-016-1236-6. Epub 2016 Jul 30.
Argonaute (AGO) proteins, which are found in yeast, animals, and plants, are the core molecules of the RNA-induced silencing complex. These proteins play important roles in plant growth, development, and responses to biotic stresses. The complete analysis and classification of the AGO gene family have been recently reported in different plants. Nevertheless, systematic analysis and expression profiling of these genes have not been performed in apple (Malus domestica). Approximately 15 AGO genes were identified in the apple genome. The phylogenetic tree, chromosome location, conserved protein motifs, gene structure, and expression of the AGO gene family in apple were analyzed for gene prediction. All AGO genes were phylogenetically clustered into four groups (i.e., AGO1, AGO4, MEL1/AGO5, and ZIPPY/AGO7) with the AGO genes of Arabidopsis. These groups of the AGO gene family were statistically analyzed and compared among 31 plant species. The predicted apple AGO genes are distributed across nine chromosomes at different densities and include three segment duplications. Expression studies indicated that 15 AGO genes exhibit different expression patterns in at least one of the tissues tested. Additionally, analysis of gene expression levels indicated that the genes are mostly involved in responses to NaCl, PEG, heat, and low-temperature stresses. Hence, several candidate AGO genes are involved in different aspects of physiological and developmental processes and may play an important role in abiotic stress responses in apple. To the best of our knowledge, this study is the first to report a comprehensive analysis of the apple AGO gene family. Our results provide useful information to understand the classification and putative functions of these proteins, especially for gene members that may play important roles in abiotic stress responses in M. hupehensis.
在酵母、动物和植物中发现的AGO（Argonaute）蛋白是RNA诱导沉默复合体的核心分子。这些蛋白在植物生长、发育以及对生物胁迫的响应中发挥着重要作用。最近在不同植物中报道了AGO基因家族的完整分析和分类。然而，尚未在苹果（Malus domestica）中对这些基因进行系统分析和表达谱分析。在苹果基因组中鉴定出了约15个AGO基因。为了进行基因预测，分析了苹果AGO基因家族的系统发育树、染色体定位、保守蛋白基序、基因结构和表达情况。所有AGO基因在系统发育上都与拟南芥的AGO基因聚类为四组（即AGO1、AGO4、MEL1/AGO5和ZIPPY/AGO7）。对AGO基因家族的这些组在31种植物物种中进行了统计分析和比较。预测的苹果AGO基因以不同密度分布在九条染色体上，包括三个片段重复。表达研究表明，15个AGO基因在至少一种测试组织中表现出不同的表达模式。此外，基因表达水平分析表明，这些基因大多参与对NaCl、PEG、热和低温胁迫的响应。因此，几个候选AGO基因参与了生理和发育过程的不同方面，可能在苹果的非生物胁迫响应中发挥重要作用。据我们所知，本研究是首次报道对苹果AGO基因家族的全面分析。我们的结果为理解这些蛋白的分类和推定功能提供了有用信息，特别是对于可能在湖北海棠非生物胁迫响应中发挥重要作用的基因成员。
