Abstract

Plant transcriptomes are very complex in nature and includes overlapping transcripts, transcribed intergenic regions, and abundant non-coding ribonucleic acids (RNAs). With RNA-Seq approach using next generation sequencing technology, complementary deoxyribonucleic acid (cDNA) library constructed either from Messenger ribonucleic acid (mRNA) or from ribosomal ribonucleic acid (rRNA) minus total RNA can be directly sequenced for transcriptome studies. The transcriptome analysis is mainly hampered by presence of unwanted abundant rRNA transcripts in cDNA library, which may represent majority species in RNA-Seq if not removed carefully from the total RNA. Though many commercial kits are available in the market for isolation of high quality mRNA from total RNA and their efficiency to remove rRNA contaminants from mRNA may vary. In the present study an effort has been made to isolate high quality mRNA with minimal rRNA contamination through designing an experiment with the use of two commercially available kits. 

Key word: RNA-Seq, transcriptome, next generation sequencing, ribosomal RNA, bioanalyzer.

Abbreviation

Abbreviations: RNAs, ribonucleic acids; rRNA, ribosomal ribonucleic acid; mRNA, messenger ribonucleic acid; cDNA, complementary deoxyribonucleic acid; tRNA, transfer ribonucleic acid; miRNA, micro ribonucleic acid; siRNA, short interfering ribonucleic acid; ncRNA, non coding ribonucleic acid.