State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China.
J Integr Plant Biol. 2014 Dec;56(12):1164-78. doi: 10.1111/jipb.12233. Epub 2014 Sep 8.
To date, only a limited number of solanaceous miRNAs have been deposited in the miRNA database. Here, genome-wide bioinformatic identification of miRNAs was performed in six solanaceous plants (potato, tomato, tobacco, eggplant, pepper, and petunia). A total of 2,239 miRNAs were identified following a range of criteria, of which 982 were from potato, 496 from tomato, 655 from tobacco, 46 from eggplant, 45 were from pepper, and 15 from petunia. The sizes of miRNA families and miRNA precursor length differ in all the species. Accordingly, 620 targets were predicted, which could be functionally classified as transcription factors, metabolic enzymes, RNA and protein processing proteins, and other proteins for plant growth and development. We also showed evidence for miRNA clusters and sense and antisense miRNAs. Additionally, five Pi starvation- and one arbuscular mycorrhiza (AM)-related cis-elements were found widely distributed in the putative promoter regions of the miRNA genes. Selected miRNAs were classified into three groups based on the presence or absence of P1BS and MYCS cis-elements, and their expression in response to Pi starvation and AM symbiosis was validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). These results show that conserved miRNAs exist in solanaceous species and they might play pivotal roles in plant growth, development, and stress responses.
迄今为止，仅有少数茄科 miRNA 被存入 miRNA 数据库。本研究在 6 种茄科植物（马铃薯、番茄、烟草、茄子、辣椒和矮牵牛）中利用基因组范围的生物信息学方法对 miRNA 进行了鉴定。通过一系列标准共鉴定出 2239 个 miRNA，其中 982 个来自马铃薯，496 个来自番茄，655 个来自烟草，46 个来自茄子，45 个来自辣椒，15 个来自矮牵牛。在所有物种中，miRNA 家族的大小和 miRNA 前体的长度均存在差异。相应地，预测到了 620 个靶标，这些靶标可被功能分类为转录因子、代谢酶、RNA 和蛋白质加工蛋白以及与植物生长和发育相关的其他蛋白。我们还证明了 miRNA 簇和 sense 和 antisense miRNAs 的存在。此外，在 miRNA 基因的假定启动子区域广泛分布着 5 个 Pi 饥饿和 1 个丛枝菌根（AM）相关的顺式元件。根据是否存在 P1BS 和 MYCS 顺式元件，选择的 miRNA 被分为 3 组，其对 Pi 饥饿和 AM 共生的响应通过定量反转录-聚合酶链反应（qRT-PCR）进行了验证。这些结果表明保守的 miRNA 存在于茄科物种中，它们可能在植物生长、发育和应激反应中发挥关键作用。
