Hussain Khalid, Mungikar Kanak, Kulkarni Abhijeet, Kamble Avinash
Department of Botany, Savitribai Phule Pune University, Pune, 411007, Maharashtra, India.
Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, Maharashtra, India.
Gene. 2018 May 5;653:57-64. doi: 10.1016/j.gene.2018.02.017. Epub 2018 Feb 8.
Upon confrontation with unfavourable conditions, plants invoke a very complex set of biochemical and physiological reactions and alter gene expression patterns to combat the situations. MicroRNAs (miRNAs), a class of small non-coding RNA, contribute extensively in regulation of gene expression through translation inhibition or degradation of their target mRNAs during such conditions. Therefore, identification of miRNAs and their targets holds importance in understanding the regulatory networks triggered during stress. Structure and sequence similarity based in silico prediction of miRNAs in Cajanus cajan L. (Pigeonpea) draft genome sequence has been carried out earlier. These annotations also appear in related GenBank genome sequence entries. However, there are no reports available on context dependent miRNA expression and their targets in pigeonpea. Therefore, in the present study we addressed these questions computationally, using pigeonpea EST sequence information. We identified five novel pigeonpea miRNA precursors, their mature forms and targets. Interestingly, only one of these miRNAs (miR169i-3p) was identified earlier in draft genome sequence. We then validated expression of these miRNAs, experimentally. It was also observed that these miRNAs show differential expression patterns in response to Fusarium inoculation indicating their biotic stress responsive nature. Overall these results will help towards better understanding the regulatory network of defense during pigeonpea -pathogen interactions and role of miRNAs in the process.
面对不利条件时，植物会引发一系列非常复杂的生化和生理反应，并改变基因表达模式以应对这些情况。微小RNA（miRNA）是一类小的非编码RNA，在这种情况下，它们通过抑制翻译或降解其靶标mRNA，在基因表达调控中发挥着广泛作用。因此，鉴定miRNA及其靶标对于理解应激过程中触发的调控网络具有重要意义。此前已基于结构和序列相似性，对木豆（Cajanus cajan L.）基因组草图序列中的miRNA进行了计算机预测。这些注释也出现在相关的GenBank基因组序列条目中。然而，关于木豆中依赖上下文的miRNA表达及其靶标的报道尚无。因此，在本研究中，我们利用木豆EST序列信息，通过计算机方法解决了这些问题。我们鉴定出了5个新的木豆miRNA前体、它们的成熟形式及其靶标。有趣的是，这些miRNA中只有一个（miR169i-3p）在基因组草图序列中较早被鉴定出来。然后，我们通过实验验证了这些miRNA的表达。还观察到这些miRNA在响应镰刀菌接种时表现出差异表达模式，表明它们具有生物胁迫响应特性。总体而言，这些结果将有助于更好地理解木豆与病原体相互作用过程中的防御调控网络以及miRNA在该过程中的作用。
