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Comparative RNA editing profile of mitochondrial transcripts in cytoplasmic male sterile and fertile pigeonpea reveal significant changes at the protein level

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Abstract

RNA editing is a process which leads to post-transcriptional alteration of the nucleotide sequence of the corresponding mRNA molecule which may or may not lead to changes at the protein level. Apart from its role in providing variability at the transcript and protein levels, sometimes, such changes may lead to abnormal expression of the mitochondrial gene leading to a cytoplasmic male sterile phenotype. Here we report the editing status of 20 major mitochondrial transcripts in both male sterile (AKCMS11) and male fertile (AKPR303) pigeonpea genotypes. The validation of the predicted editing sites was done by mapping RNA-seq reads onto the amplified mitochondrial genes, and 165 and 159 editing sites were observed in bud tissues of the male sterile and fertile plant respectively. Among the resulting amino acid alterations, the most frequent one was the conversion of hydrophilic amino acids to hydrophobic. The alterations thus detected in our study indicates differential editing, but no major change in terms of the abnormal protein structure was detected. However, the above investigation provides an insight into the behaviour of pigeonpea mitochondrial genome in native and alloplasmic state and could hold clues in identification of editing factors and their role in adaptive evolution in pigeonpea.

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  1. http://prep.unl.edu/

  2. https://www.biogem.org/tool/chou-fasman/

  3. https://phobius.sbc.su.se/

  4. https://www.sbg.bio.ic.ac.uk/maxcluster/

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Acknowledgements

We acknowledge the financial support received from ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.

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  1. ICAR-National Research Centre on Plant Biotechnology, New Delhi, 110012, India

    Tanvi Kaila, Swati Saxena, G. Ramakrishna, Anshika Tyagi, Kishor U. Tribhuvan, Harsha Srivastava,  Sandhya, Nagendra Kumar Singh & Kishor Gaikwad

  2. Department of Bio & Nanotechnology, Guru Jambheshwar University of Science & Technology, Hisar, India

    Tanvi Kaila & Ashok Chaudhury

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TK carried out the experiments, prepared the library for sequencing run and wrote the manuscript. SS and AT were involved in sequencing run. TK, SS, AT, KUT and HS were involved in result interpretation, data analysis and finalization of the manuscript. GR maintained the fields of pigeonpea throughout the experiment and contributed to the manuscript. S, AC, and NKS contributed in data analysis and manuscript finalisation. KG conceived the study, designed the experiments, and coordinated the work. All the authors have read and approved the final manuscript.

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Kaila, T., Saxena, S., Ramakrishna, G. et al. Comparative RNA editing profile of mitochondrial transcripts in cytoplasmic male sterile and fertile pigeonpea reveal significant changes at the protein level. Mol Biol Rep 46, 2067–2084 (2019). https://doi.org/10.1007/s11033-019-04657-2

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