India has a rich diversity of flora with a vast collection of medicinal plants. About 7000 flowering plants of India are reported with medicinal properties. However, research on medicinal plants is lacking in their molecular aspect. In order to generate and investigate the molecular resources of an ethno-medicinally important Allium species i.e., Allium hookeri, commonly known as hooker chives, we perform transcriptomic profiling of the herb. The involvement of miRNAs in metabolites regulation in A. hookeri is also anticipated. In the present study, we have de novo assembled and characterized the transcriptome of hooker chives roots using Illumina paired-end sequencing technology and searched for genes from the assembled transcripts. Furthermore, we have identified miRNAs from the plant and tried to co-relate with the transcripts. The discovery of these miRNA:target pairs will provide a basis for further understanding of their function in its growth and development.
Hooker chives Allium hookeri belonging to Allium species are one of the traditional medicinal herbs widely used in the state of Manipur Northeast India. However the availability of genetic resources is limited in this species. In order to understand the molecular basis of its medicinal properties the availability of genetic resources is a must. Herein the transcriptome and small RNA libraries of root tissue are prepared and analyzed by next generation sequencing on Illumina platform. From the transcriptome approximately 102.9 million clean sequence reads were obtained and used for de novo assembly which generated 117189 non-redundant transcripts. Of these transcripts, 39472 were annotated for their function. Whereas in case of small RNA library, out of 33.58 million raw reads generated, 33.54 million clean reads were obtained which were checked for microRNA prediction. We identify a total of 108 conserved miRNAs and 14novel miRNAs in A. hookeri.