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Novel structures and evolution of tRNA genes: insight into the chloroplast tRNAs of family Sapindaceae

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Abstract

Transfer ribonucleic acids (tRNAs) are small non-coding ribonucleic acids that decode messenger RNA sequences and are directly involved in protein synthesis by carrying amino acids to the ribosome. However, the chloroplast genome needs to better understand tRNAs' phylogeny and evolutionary mechanisms. The present study aimed to delineate the novel structural variations and evolutionary characteristics in the chloroplast genome tRNAs of thirty-six Sapindaceae species. Several novel tRNA structures were identified in the Sapindaceae chloroplast genome. The length of tRNAs ranged from 64 to 93 nucleotides, containing 27–29 anticodons. Pair-wise sequence results showed the conserved nucleotide consensus sequence U-U-C-x-A–x-U in Sapindaceae. The structural analysis revealed that, except for a few tRNAs (tRNAHis, tRNAGly, tRNAThr, tRNAPhe, tRNATry, tRNAMet, and tRNAPro), all contained a G nucleotide at the 1st position in the acceptor's arm of tRNAs secondary structure. The rate of transition and transversion of tRNAs are Iso-acceptor-specific. Evolutionary analysis revealed that Sapindaceae chloroplast tRNAs might have evolved polyphyletically with a high percentage of gene loss. Phylogenetic analysis revealed that the chloroplast genome's tRNAs evolved from several common ancestors. At the same time, tRNAVal and tRNAMet appear to be the ancestral tRNAs that underwent duplication diversification to give rise to other tRNAs. Our findings will help us understand the evolution of the tRNA and suggest a key role in chloroplast tRNA biology.

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Acknowledgements

The authors thank researchers who helped and supported the data collection and bioinformatics analysis.

Funding

Researchers Supporting Project number (RSPD2023R741), King Saud University. This work was supported by the National Key R & D Program of China (No. 2018YFA0606102), the Strategic Priority Research Program of the Chinese Academy of Sciences (No. XDA19020303, No. XDA26010202), and the Natural Science Foundation of China (No. 41771056).

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Authors and Affiliations

  1. Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Chaoyang District, Beijing, People’s Republic of China

    Khurram Shahzad & Junhu Dai

  2. Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China

    Khurram Shahzad, Zhong-Hu Li & Hanif Khan

  3. Department of Biology, The University of Haripur, Haripur, Khyber Pakhtunkhwa, Pakistan

    Azizullah Aziullah, Umar Zeb & Saleha Ashfaq

  4. School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People’s Republic of China

    Umar Zeb & Fengjie Cui

  5. Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan

    Sajid Fiaz

  6. Department of Food Industries, Faculty of Agriculture, Damietta University, Damietta, Egypt

    Eman A. Mahmoud

  7. Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia

    Ihab Mohamed Moussa

  8. Department of Plant Production, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia

    Hosam O. Elansary

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  1. Khurram Shahzad
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Contributions

It is stated that each Author contributes substantially to the article. KS was a significant contributor to writing and organizing the research plan in the manuscript. HK, AA, UZ, FC, JD and SA guided the interpretation and discussion. SF, EAM, IMM, HOE provided technical expertise, editing, and funding acquisition. JD and KS helped in writing the manuscript. All authors have seen and approved the final manuscript and have taken due care to ensure the work's integrity.

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Shahzad, K., Li, ZH., Khan, H. et al. Novel structures and evolution of tRNA genes: insight into the chloroplast tRNAs of family Sapindaceae. Genet Resour Crop Evol 71, 893–914 (2024). https://doi.org/10.1007/s10722-023-01671-z

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