Plant interactions with biotic and abiotic stresses are complex and entail changes at the transcriptional, cellular and physiological level. MicroRNAs (miRNAs) are small (~20–24 nt), non-coding RNAs that play a vital role in wide range of biological processes involved in regulation of gene expression through translation inhibition or degradation of their target mRNAs during stress conditions. Therefore, identification of miRNAs and their targets are of immense value in understanding the regulatory networks triggered during stress. Advancement in computational approaches has opened up ways for the prediction of miRNAs and their possible targets with functional pathways. Our objective was to identify miRNA and their potential targets involved in both biotic and abiotic stresses in maize. A total of 2,019,524 downloaded ESTs from dbEST were processed and trimmed by Seq Clean. The program trashed 264,000 and trimmed 284,979 sequences and the resulting 1,755,534 sequences were submitted for clustering and assembled to RepeatMasker and TGICL. A total of 30 miRNAs were found to hybridize with the potential targets of gene families such as CoA ligase, lipoxygenase 1, Terpenoideyclases, Zn finger, transducing, etc. Ten of the identified miRNAs targeted cytochrome c1 family. Zm_miR23 class targeted 11 different genes. The identified targets are involved in the plant growth and development during biotic and abiotic stresses in maize. These miRNAs may be further used for functional analysis. Furthermore, four and two of the miRNA targets were validated in response to waterlogging tolerance and southern leaf blight resistance, respectively, to understand the miRNA-assisted regulation of target miRNAs. The functional annotation of the predicted targets indicated that these stress-responsive miRNAs regulate cellular function; molecular function and biological process in maize at the post-transcriptional level. The present results have paved way towards better understanding the role of miRNAs in the mechanism of stress tolerance in maize.

中文翻译：

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玉米miRNA及其参与生物和非生物胁迫的基因靶点的计算鉴定

植物与生物和非生物胁迫的相互作用是复杂的，需要在转录、细胞和生理水平上发生变化。MicroRNAs (miRNAs) 是小的 (~20–24 nt) 非编码 RNA，在压力条件下通过翻译抑制或降解靶 mRNA 来调节基因表达的广泛生物过程中发挥着至关重要的作用。因此，miRNA 及其靶标的鉴定对于理解压力期间触发的调节网络具有巨大的价值。计算方法的进步为预测 miRNA 及其功能通路的可能目标开辟了道路。我们的目标是确定 miRNA 及其与玉米生物和非生物胁迫相关的潜在靶标。共有 2,019 个，从 dbEST 下载的 524 个 EST 由 Seq Clean 处理和修剪。该程序删除了 264,000 个序列并修剪了 284,979 个序列，并将产生的 1,755,534 个序列提交用于聚类并组装到 RepeatMasker 和 TGICL。总共发现 30 种 miRNA 与基因家族的潜在靶标杂交，例如 CoA 连接酶、脂氧合酶 1、萜类化合物、锌指、转导等。 鉴定的 miRNA 中有 10 种靶向细胞色素 c1 家族。Zm_miR23 类针对 11 个不同的基因。确定的目标涉及玉米在生物和非生物胁迫期间的植物生长和发育。这些 miRNA 可进一步用于功能分析。此外，四个和两个 miRNA 靶标分别在耐涝和抗南方叶枯病方面得到验证，了解miRNA对靶miRNA的辅助调控。预测靶点的功能注释表明这些应激反应miRNAs调节细胞功能；转录后水平的玉米分子功能和生物学过程。目前的结果为更好地理解 miRNA 在玉米胁迫耐受机制中的作用铺平了道路。