Abstract
Helopeltis theivora or the tea mosquito bug (TMB) is reportedly one of the most devastating pests of tea plant (Camellia sinensis) causing threat to the beverage crop. Long non-coding RNAs (lncRNAs) constitute a group of endogenous RNAs that play gene regulatory roles in eukaryotes. In the present study, 9502 lncRNAs were identified from healthy and TMB-infested C. sinensis tissues using high-throughput strand-specific RNA sequencing, out of which 80 lncRNAs got differentially expressed in response to TMB infestation. Determination of genes that could act as potential targets of lncRNAs revealed that the identified lncRNAs could possibly target as many as 5804 genes. Differential gene expression (DGE) analysis led to the identification of 3665 differentially expressed genes (DEGs), of which, the expression of 1767 genes got upregulated and 1898 genes got downregulated during tea plant’s response to TMB. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs and lncRNA-target genes have shown that TMB infestation might have triggered transcriptomic reprogramming leading to altered primary and secondary metabolism in C. sinensis. LncRNAs can act as competing endogenous RNAs (ceRNAs) to bind with common microRNA (miRNA) response elements (MREs) involving a competition between mRNAs and lncRNAs. We report 11 lncRNAs competing with 14 mRNAs to bind with 28 miRNAs forming the ceRNA network. The expression of 6 DEGs and 5 differentially expressed lncRNAs (DELs) has been validated by qRT-PCR.
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Data Availability
The data sets generated and analyzed in this article are available in the NCBI SRA (Sequence read archive, http://www.ncbi.nlm.nih.gov/sra/) repository under the bioproject accession number PRJNA815732.
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Acknowledgements
The authors would like to thank the authorities of DTRDC, Kurseong and Sungma-Turzum Tea Estate, Darjeeling for their help to conduct the research work. The authors would like to acknowledge Mrinmoy Purkayastha for valuable discussions regarding the TMB infestation experiment. We thankfully acknowledge Preetom Regon and Mehzabin Rehman for their help in setting up of qPCRs. KSB thankfully acknowledges fellowship support received from Council of Scientific and Industrial Research, India (Award No. 09/059(0064)/2018-EMR-I). The authors are thankful to DST, Govt. of India, for providing DST-FIST Support to Department of Botany, Gauhati University, where this research work was carried out.
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This work was supported by financial assistance from Science and Engineering Research Board, Govt. of India under the grant Number: ECR/2017/000710.
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KSB contributed to data curation, investigation, methodology, software, writing—original draft, visualization, and writing—review and editing. PMB contributed to data curation and software. BT contributed to resources and supervision. SSG contributed to supervision. NA contributed to conceptualization, funding acquisition, methodology, writing- review and editing, and supervision.
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Bordoloi, K.S., Baruah, P.M., Tanti, B. et al. Helopeltis theivora Responsive Transcriptomic Reprogramming Uncovers Long Non-coding RNAs as Possible Regulators of Primary and Secondary Metabolism in Tea Plant. J Plant Growth Regul 42, 6523–6548 (2023). https://doi.org/10.1007/s00344-022-10893-x
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DOI: https://doi.org/10.1007/s00344-022-10893-x