Unravelling the Evolutionary Blueprint of Phytochrome A4 in Legumes: A Molecular Phylogenetic Approach
Vishwa Gohil
Department of Agricultural Statistics, N.M. College of Agriculture, NAU, Navsari, Gujarat 396 450, India.
Alok Shrivastava
Department of Agricultural Statistics, N.M. College of Agriculture, NAU, Navsari, Gujarat 396 450, India.
Kaushal Modha
Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat 396 450, India.
Hemali Pandya *
Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat 396 450, India.
Naresh Chaudhary
Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat 396 450, India.
Nitin Varshney
Department of Agricultural Statistics, N.M. College of Agriculture, NAU, Navsari, Gujarat 396 450, India.
Vipulkumar Patel
Department of Basic Science and Humanities, College of Forestry, Navsari Agricultural University, Navsari, Gujarat 396 450, India.
Yogesh Garde
Department of Agricultural Statistics, N.M. College of Agriculture, NAU, Navsari, Gujarat 396 450, India.
*Author to whom correspondence should be addressed.
Abstract
Background: Phytochromes are the best characterized photoreceptors that perceive Red (R)/Far-Red (FR) signals and mediate key developmental responses in plants. It is well established that photoperiodic control of flowering is regulated by PHY A (phytochrome A) gene. So far, the members of PHY A4 gene family remains unexplored in Glycine max and therefore, their functions are still not deciphered. Phytochrome A4 (PhyA4) has involvement in adaptive responses under low-light and stress conditions. The present study is the first effort to identify any photoreceptor gene (PHYA4) in Glycine max and decipher its phylogeny with related legumes.
Methods: In present study, the nucleotide sequence of Glycine max PhyA4 (GmPhyA4) was used to identify homologous sequences within the Fabaceae family through BLASTn analysis. As well as for protein identify homologous sequences. A total of 17 species Fabaceae PhyA4 homologs, along with Arabidopsis thaliana PHYA as outgroup, were aligned using the CLUSTAL W algorithm in MEGA 11.
Results: The Tamura 3-parameter model with Gamma distribution (T92+G) was identified as the best-fit nucleotide substitution model, based on the lowest BIC and AIC values. For protein JTT (Jones–Taylor–Thornton) substitution model found to best model. Phylogenetic reconstruction was performed using the Maximum Likelihood (ML) method reliability assessment using 1,000 bootstrap replicates.
Conclusion: Phylogenetic analysis confirmed its close evolutionary relationship with other Fabaceae species. This phylogenetic insight underscores the evolutionary conservation and diversification of PhyA4 within legumes, providing a foundation for understanding its functional adaptation in different species and potential applications in crop improvement under varying photoperiodic conditions.
Keywords: Phytochrome A4, BLASTn, BLASTp ClustalW, substitution model, phylogenetic analysis