Tissue specific long non-coding RNAs are involved in aroma formation of black tea

•Analysis of RNAseq data predicted 33319 novel and 81 conserved long non-coding RNAs of tea from young tissues.•Around 1654 tissue specific long non-coding RNAs were identified.•Some long non-coding RNAs were predicted to be endogenous target mimics of microRNAs.•A total of 3556 long non-coding RNAs...

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Bibliographic Details
Published in:Industrial crops and products 2019-07, Vol.133, p.79-89
Main Authors: Varshney, Deepti, Rawal, Hukam C., Dubey, Himanshu, Bandyopadhyay, Tanoy, Bera, Biswajit, Kumar, P. Mohan, Singh, Nagendra Kumar, Mondal, Tapan Kumar
Format: Article
Language:English
Subjects:
Aroma formation
Epigenetics
Gene expression
Long non-coding RNA
mRNAs-lncRNA interaction
Tea
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Summary:•Analysis of RNAseq data predicted 33319 novel and 81 conserved long non-coding RNAs of tea from young tissues.•Around 1654 tissue specific long non-coding RNAs were identified.•Some long non-coding RNAs were predicted to be endogenous target mimics of microRNAs.•A total of 3556 long non-coding RNAs were found associated with aroma formation pathways of tea leaf. With the progress of sequencing technology coupled with in silico approaches, disclosure of long non-coding RNA (lncRNAs) from RNAseq data has become easy and reliable. Till today, no methodical investigation of lncRNAs and their regulatory roles in tea have been studied. In this study, using 170 RNAseq data (˜7157 million reads) of 11 harvestable tissues, 33,400 putative high certainty lncRNAs were discovered, among which 99.76% were found to be putative novel lncRNAs. The expression analysis of lncRNAs from 53 RNAseq data of 7 tissues (axillary bud, a bud and a leaf, a bud and 2 leaves, apical bud and 2 leaves, 2nd leaf, 4th leaf, and 6th leaf) demonstrated their tissue-specific expression. Further, around 1,654 lncRNAs were found to be endogenous target mimics of miRNAs that interacted with 698 mRNAs of tea genome. Based on their target i.e. coding-gene partners by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway showed that 378 lncRNAs are involved in major aroma formation pathway of tea. Present study also provides valuable information to uncover the various molecular functions of lncRNAs that regulate aroma formation of tea.
ISSN:0926-6690
1872-633X
DOI:10.1016/j.indcrop.2019.03.020