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Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq

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Title Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq
 
Creator Vivek, A.T.
Kumar, Shailesh
 
Subject ncRNAs
RNA-seq
sRNA-seq
miRNA
siRNA
tsRNA
lncRNA
circRNA
 
Description Accepted date: 20 October 2020
Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major
biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse
and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-increasing ncRNAs under study, it
is essential to identify, categorize and annotate these ncRNAs on a genome-wide scale. The use of high-throughput RNA
sequencing (RNA-seq) technologies provides a broader picture of the non-coding component of transcriptome, enabling the
comprehensive identification and annotation of all major ncRNAs across samples. However, the detection of known and
emerging class of ncRNAs from RNA-seq data demands complex computational methods owing to their unique as well as
similar characteristics. Here, we discuss major plant endogenous, regulatory ncRNAs in an RNA sample followed by
computational strategies applied to discover each class of ncRNAs using RNA-seq. We also provide a collection of relevant
software packages and databases to present a comprehensive bioinformatics toolbox for plant ncRNA researchers. We
assume that the discussions in this review will provide a rationale for the discovery of all major categories of plant ncRNAs.
A.T.V. acknowledges the Department of Biotechnology (DBT), Government of India, for providing research fellowship. S.K. acknowledges the core research grant of NIPGR provided by the Department of Biotechnology (DBT), Government of India. Authors gratefully acknowledge all the relevant methods and related work on tools and databases, if not included by any chance in this review. Also, authors are thankful to DBT e-Library Consortium (DeLCON) and Distributed Informatics Sub-Centre (Sub-DIC) facility at the National Institute of Plant Genome Research (NIPGR) for providing access to e-resources.
 
Date 2020-12-22T05:34:11Z
2020-12-22T05:34:11Z
2020
 
Type Article
 
Identifier Briefings in Bioinformatics, (In Press)
1477-4054
https://doi.org/10.1093/bib/bbaa322
https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbaa322/6041165
http://223.31.159.10:8080/jspui/handle/123456789/1135
 
Language en_US
 
Format application/pdf
 
Publisher Oxford University Press