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. 2018 Mar 21;8(1):4960.
doi: 10.1038/s41598-018-23334-1.

Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species

Jinfang Zhang  1 , Lijuan Wei  2 , Jun Jiang  1 , Annaliese S Mason  3 , Haojie Li  1 , Cheng Cui  1 , Liang Chai  1 , Benchuan Zheng  1 , Yongqing Zhu  4 , Qing Xia  1 , Liangcai Jiang  5 , Donghui Fu  6
Affiliations

Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species

Jinfang Zhang et al. Sci Rep. .

Abstract

Non-coding RNA (ncRNA) is abundant in plant genomes, but is poorly described with unknown functionality in most species. Using whole genome RNA sequencing, we identified 1885, 1910 and 1299 lncRNAs and 186, 157 and 161 miRNAs at the whole genome level in the three Brassica species B. napus, B. oleracea and B. rapa, respectively. The lncRNA sequences were divergent between the three Brassica species. One quarter of lncRNAs were located in tandem repeat (TR) region. The expression of both lncRNAs and miRNAs was strongly biased towards the A rather than the C subgenome in B. napus, unlike mRNA expression. miRNAs in genic regions had higher average expression than miRNAs in non-genic regions in B. napus and B. oleracea. We provide a comprehensive reference for the distribution, functionality and interactions of lncRNAs and miRNAs in Brassica.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Pipeline for lncRNAs identification from RNA-seq data.
Figure 2
Figure 2
Characteristics of lncRNAs in B. napus, B. oleracea and B. rapa. (A) Distribution of mRNAs, lncRNAs and miRNAs on each chromosome. (B) Proportion of antisense lncRNAs, intronic lncRNAs and lincRNA identified in Brassica. (C) Length of lncRNAs in Brassica species.
Figure 3
Figure 3
Distribution of conserved miRNA families in B. napus, B. oleracea and B. rapa.
Figure 4
Figure 4
qRT-PCR validation of miRNAs and lncRNAs in Brassica.
Figure 5
Figure 5
Expression of conserved miRNA families in Brassica. The expression levels are given in log10(TPM). TPM, transcripts per million clean tags.
See this image and copyright information in PMC

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