Bibek Saha
M.Sc. Bioinformatics
2 yr 5 mo
Duration
Research Thesis
Title
Identification and Characterization of Lnc RNA in Ricebean (Vigna umbellata)
Objectives
1.To identify novel lncRNAs in Ricebean seed. 2.To identify and annotate targets of predicted lncRNAs. 3.To design and develop a web resource for lncRNA in Ricebean seed.
Abstract
Ricebean, Vigna umbellata is a Kharif-season annual legume. Its seeds are consumed as pulse. It is considered as a minor legume as it is grown in limited areas as an intercrop with maize and sorghum. It is mostly grown in Northern part of India (Mainly Uttarakhand) and North-eastern part of India (Mainly Assam). Its seed contains a good amount of protein and other nutrients. These protein-coding RNA of developing stages of seed largely regulated by non-coding RNA specifically long non-coding RNA. Long non-coding RNAs (lncRNAs) are a large and diverse class of transcribed RNA molecules with a nucleotide length of more than 200 bp and ORF<100 bp that do not encode proteins. It is one of the types of Regulatory non-coding RNA. LncRNAs are important regulators of gene expression by DNA methylation and chromatin remodeling, and in some cases, they act as miRNA (Micro RNA) sponges to enhance the expression of mRNA targeted by miRNA (Tay et al., 2014). LncRNAs are thought to have a wide range of functions in cellular and developmental processes. LncRNA may be positioned beside protein- coding genes or in between genes even it overlaps with coding genes. There has been hardly any work reported for the identification of lncRNA with respect to the Ricebean crop. This study aims to identify lncRNA and annotate its targets for the developing stages of Ricebean seed. A total of 906 novel lncRNAs have been identified. Out of these 906 novel lncRNAs, 82 lncRNAs have targets of 15 miRNAs. It was observed that different lncRNA could have similar miRNA targets. These 15 microRNA had targets of 15 mRNA. Lastly, annotation of 15 mRNA was carried out and it was found that these mRNA regulated different biological, cellular, metabolic processes of the developmental stages of Rice bean seed. ‘RbLncDB’, a web resource has also been developed under the present study to help future researchers in regard to Ricebean seed transcriptome. Keywords: Vigna umbellata; long non-coding RNAs; micro RNA; Reference assembly;lncRNA targeted miRNA.