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Investigating molecular evolutionary forces and phylogenetic relationships among melatonin precursor-encoding genes of different plant species

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Abstract

A total of 53 plant species accessions from different geographic regions, including four melatonin precursor-coding genes obtained from Arachis hypogaea (ASMT1, 2, 3 and T5H) underwent extensive molecular evolutionary analyses. Evolutionary relationships were inferred and showed that dichotomous bifurcating trees did not reflect the true phylogeny since reticulate events took place due likely to recombination. Thus, a phylogenetic network was reconstructed for each type of enzyme and highlighted the presence of such incompatibilities. GARD algorithm pointed out that ASMT1, 2, and 3-coding gene sequences contained recombination sites with significant topological incongruence on both sides of the breakpoints (for ASMT1, and 2), while only on one side of the breakpoints for ASMT3. In contrast, no statistically recombination signal was recorded in T5H-coding gene. Furthermore, gene duplication was localized in the ancestor of a monophyletic group of Populus accessions. Selection pressure was assessed using several statistical models incorporated in HyPhy package through the datamonkey web server. It was demonstrated that numerous individual sites and tree branches experienced predominantly purifying selection. In contrast, the BUSTED model evidenced a gene-wide episodic diversifying selection in the phylogeny of only three enzyme-coding genes (ASMT, and 2, and T5H). Likewise, it was shown that Mixed Effects Model of Episodic Selection (MEME) model detected only episodic positively selected sites in all four melatonin enzymes-coding genes; whereas, REL model failed to detect neither positive nor negative selection in tested individual sites of ASMT3-coding gene.

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Acknowledgements

The authors thank the Egyptian government for granting a visiting scholarship and the Zagazig University for supporting the research.

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    Authors and Affiliations

    1. Université de Sfax- Institut de L’Olivier- B.P. 14, Ibn Khaldoun, 4061, Sousse, Tunisia

      Moncef Boulila

    2. Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, 44519, Egypt

      Abdelaleim Ismail ElSayed & Ahmad Alsayed Omar

    3. Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa

      Mohammed Suhail Rafudeen

    4. Citrus Research and Education Center, University of Florida, IFAS, Lake Alfred, FL, 33850, USA

      Ahmad Alsayed Omar

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    1. Moncef Boulila
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    Contributions

    MB, AE and AAO conceived and directed this work, designed the experiments, analyzed the data, wrote and revised the manuscript. AIE, and AAO supported PCR and cloning analysis. MSR provided suggestions and revised the manuscript. All authors read and approved the final manuscript.

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    Correspondence to Abdelaleim Ismail ElSayed.

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    Boulila, M., ElSayed, A.I., Rafudeen, M.S. et al. Investigating molecular evolutionary forces and phylogenetic relationships among melatonin precursor-encoding genes of different plant species. Mol Biol Rep 47, 1625–1636 (2020). https://doi.org/10.1007/s11033-020-05249-1

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