Investigating molecular evolutionary forces and phylogenetic relationships among melatonin precursor-encoding genes of different plant species
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.
KeywordsMelatonin Molecular evolution Phylogenetic analysis Peanut Recombination Natural selection Bioinformatics Gene duplication
The authors thank the Egyptian government for granting a visiting scholarship and the Zagazig University for supporting the research.
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.
Compliance with ethical standards
Conflicts of interest
The authors declare no conflicts of interest.
- 6.Hoagland DR, Arnon DI (1950) The water-culture method for growing plants without soil. Circular 347:22Google Scholar
- 12.Tamura K (1992) Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+ C-content biases. Mol Biol Evol 9:678–687. https://doi.org/10.1093/oxfordjournals.molbev.a040752 CrossRefPubMedGoogle Scholar
- 29.Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL (2015) Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Mol Biol Evol 32:1342–1353. https://doi.org/10.1093/molbev/msv022 CrossRefPubMedPubMedCentralGoogle Scholar
- 30.Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM, Scheffler K, Kosakovsky Pond SL (2015) Gene-wide identification of episodic selection. Mol Biol Evol 32:1365–1371. https://doi.org/10.1093/molbev/msv035 CrossRefPubMedPubMedCentralGoogle Scholar