**Role of Next-Generation RNA-Seq Data in Discovery and Characterization of Long Non-Coding RNA in Plants Role of Next-Generation RNA-Seq Data in Discovery and Characterization of Long Non-Coding RNA in Plants**

DOI: 10.5772/intechopen.72773

Shivi Tyagi, Alok Sharma and Santosh Kumar Upadhyay Shivi Tyagi, Alok Sharma and Santosh Kumar Upadhyay Additional information is available at the end of the chapter

Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/intechopen.72773

## **Abstract**

The next-generation sequencing (NGS) technologies embrace advance sequencing technologies that can generate high-throughput RNA-seq data to delve into all the possible aspects of the transcriptome. It involves short-read sequencing approaches like 454, illumina, SOLiD and Ion Torrent, and more advance single-molecule long-read sequencing approaches including PacBio and nano-pore sequencing. Together with the help of computational approaches, these technologies are revealing the necessity of complex non-coding part of the genome, once dubbed as "junk DNA." The ease in availability of high-throughput RNA-seq data has allowed the genome-wide identification of long noncoding RNA (lncRNA). The high-confidence lncRNAs can be filtered from the set of whole RNA-seq data using the computational pipeline. These can be categorized into intergenic, intronic, sense, antisense, and bidirectional lncRNAs with respect to their genomic localization. The transcription of lncRNAs in plants is carried out by plant-specific RNA polymerase IV and V in addition to RNA polymerase II and target the epigenetic regulation through RNA-directed DNA methylation (RdDM). lncRNAs regulate the gene expression through a variety of mechanism including target mimicry, histone modification, chromosome looping, etc. The differential expression pattern of lncRNA during developmental processes and different stress responses indicated their diverse role in plants.

**Keywords:** next-generation sequencing (NGS), high-throughput RNA-seq, long non-coding RNA (lncRNA), expression, development, stress
