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

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.

SUBMITTER: Zhang J 

PROVIDER: S-EPMC5862966 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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

Zhang Jinfang J   Wei Lijuan L   Jiang Jun J   Mason Annaliese S AS   Li Haojie H   Cui Cheng C   Chai Liang L   Zheng Benchuan B   Zhu Yongqing Y   Xia Qing Q   Jiang Liangcai L   Fu Donghui D  

Scientific reports 20180321 1

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  ...[more]

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