Comprehensive temporal reprogramming ensures dynamicity of transcriptomic profile for adaptive response in Taxus contort
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ORIGINAL ARTICLE
Comprehensive temporal reprogramming ensures dynamicity of transcriptomic profile for adaptive response in Taxus contorta Aasim Majeed1 · Amandeep Singh1 · Ram Kumar Sharma2 · Vikas Jaitak3 · Pankaj Bhardwaj1 Received: 15 November 2019 / Accepted: 3 July 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Plants respond to the environmental perturbations by triggering the dynamic changes within the transcriptome. The assessment of these oscillations within the transcriptome would offer insights into the ecological adaptation of the plants. We evaluated how the transcriptome of Taxus contorta swings under natural conditions to elucidate its adaptive response. Thus, our study provides new insights into the performance of T. contorta under a changing environment during different seasons. The abundance estimation using the RNAseq approach revealed 6727 differentially expressed genes. Comprehensive reprogramming was observed in Taxol biosynthesis, maintenance of redox homeostasis, and generation of effective shield to UV-B, high light intensity, and temperature. Besides differential expression, the alternative splicing (AS) and single nucleotide variations (SNVs) also confer flexibility to the transcriptome of T. contorta. 1936 differentially expressing transcripts were also found to exhibit Differential Exon Usage (DEU) as well as differential SNVs. LC–MS-based untargeted metabolic analysis revealed 7774 ion features, among which around 334 putatively identified metabolites were differentially regulated. Our results showed that the swing and the oscillations of the transcriptome and metabolome of T. contorta ensure adaptability and better survival under changing environment. In addition, varying patterns of AS and SNVs compliment the adaptation provided by differential expression. Keywords RNAseq · Differential gene expression · Taxus contorta · Taxol biosynthesis alternative splicing · Single nucleotide variations
Introduction Plants respond to environmental perturbation and adapt to it by changing their gene expression profiles (Blödner et al. 2007). The assessment of such dynamics of transcriptomic variations would not only provide insights into the ecological adaptation of plants but also performance. Most of the Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00438-020-01709-2) contains supplementary material, which is available to authorized users. * Pankaj Bhardwaj [email protected]; [email protected] 1
Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
2
Biotechnology Department, CSIR - Institute of Himalayan Bioresource Technology, Pālampur, Himachal Pradesh, India
3
Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, India
studies on the identification of genomic constituents and genetic mechanisms responsible for adaptation to the environmental changes are confin
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