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Genes 2016, 7(3), 11; doi:10.3390/genes7030011

Genome-Wide Identification and Characterization of Long Non-Coding RNAs from Mulberry (Morus notabilis) RNA-seq Data

1,2,†
,
3,†
,
3
,
2
,
3,4
and
2,*
1
College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
2
State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
3
Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
4
Precision Medicine Center, Research Institute of Information Industry for LuoYang (LuoYang Branch of Institute of Computing Technology, Chinese Academy of sciences), Luoyang 471000, China
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editor: Paolo Cinelli
Received: 2 December 2015 / Revised: 19 February 2016 / Accepted: 22 February 2016 / Published: 29 February 2016
(This article belongs to the Section Molecular Genetics)
View Full-Text   |   Download PDF [4056 KB, uploaded 29 February 2016]   |  

Abstract

Numerous sources of evidence suggest that most of the eukaryotic genome is transcribed into protein-coding mRNAs and also into a large number of non-coding RNAs (ncRNAs). Long ncRNAs (lncRNAs), a group consisting of ncRNAs longer than 200 nucleotides, have been found to play critical roles in transcriptional, post-transcriptional, and epigenetic gene regulation across all kingdoms of life. However, lncRNAs and their regulatory roles remain poorly characterized in plants, especially in woody plants. In this paper, we used a computational approach to identify novel lncRNAs from a published RNA-seq data set and analyzed their sequences and expression patterns. In total, 1133 novel lncRNAs were identified in mulberry, and 106 of these lncRNAs displayed a predominant tissue-specific expression in the five major tissues investigated. Additionally, functional predictions revealed that tissue-specific lncRNAs adjacent to protein-coding genes might play important regulatory roles in the development of floral organ and root in mulberry. The pipeline used in this study would be useful for the identification of lncRNAs obtained from other deep sequencing data. Furthermore, the predicted lncRNAs would be beneficial towards an understanding of the variations in gene expression in plants. View Full-Text
Keywords: lncRNAs; Morus notabilis; RNA-seq lncRNAs; Morus notabilis; RNA-seq
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Song, X.; Sun, L.; Luo, H.; Ma, Q.; Zhao, Y.; Pei, D. Genome-Wide Identification and Characterization of Long Non-Coding RNAs from Mulberry (Morus notabilis) RNA-seq Data. Genes 2016, 7, 11.

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