In-silico Sequence Alignment, Phylogeny, Docking, and Domain Analysis of Fatty Acid Desaturase (FAD) Proteins in Pearl Millet (Pennisetum glaucum L.)

Authors

  • Thalari Vasanthrao International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana (502 324), India
  • Mazahar Moin International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana (502 324), India
  • Prabhavathi Kona Dept. of Genetics and Plant Breeding, Professor Jayshankar Telangana Agricultural University (PJTAU), Rajendranagar, Hyderabad, Telangana (500 030), India
  • Wricha Tyagi International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana (502 324), India
  • S. K. Gupta International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana (502 324), India
  • Reddy P. Sudhakar International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana (502 324), India
  • Shashi Bhushan Danam Dept. of Genetics and Plant Breeding, Professor Jayshankar Telangana Agricultural University (PJTAU), Rajendranagar, Hyderabad, Telangana (500 030), India

DOI:

https://doi.org/10.23910/1.2025.6444

Keywords:

FADs, Pennisetum glaucum, lipid metabolism, phylogeny

Abstract

This in-silico analysis was conducted during May and June, 2025 at ICRISAT, Patancheru, Telangana, India to explore the properties of pearl millet FAD (fatty acid desaturase) proteins. The protein sequences were retrieved from the NovoGene Millet database, and analyzed using ExPASy ProtParamto investigate the FAD protein family in pearl millet. Phyre2.1 was used to predict the secondary structures, and protein phylogeny was analyzed using ClustalW to identify evolutionary relationships. Conserved motifs were identified using the MEME online tool. Multiple sequence alignment of PgFAD protein sequences across six genotypes in the pangenome was performed through ClustalW to identify the polymorphism.  A total of 22 PgFAD proteins were identified, and their physiochemical analysis revealed diverse molecular weights, isoelectric points (pI) and hydrophobicity profiles, suggested functional variability. Three-dimensional secondary structure analysis revealed that all PgFADs are rich in alpha helical content (45–66%), suggesting a compact, stable and membrane spanning structure. Low to moderate disordered regions (6 to 22%) in these proteins indicated their enzymatic activities. Protein polymorphism analysis showed that PgFAD-5e and PgFAD-6c are conserved across all six genotypes in the pangenome, whereas PgFAD-5c, PgFAD-5f and PgFAD-1w6 exhibited multiple nonsynonymous mutations particularly in PI526529 genotype. These findings provided insights into the structural and functional diversity of fatty acid desaturases and established a foundation for targeting these genes to enhance lipid stability and improve quality-related traits of pearl millet.

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Published

2025-10-31

How to Cite

1.
Vasanthrao T, Moin M, Kona P, Tyagi W, Gupta SK, Sudhakar RP, et al. In-silico Sequence Alignment, Phylogeny, Docking, and Domain Analysis of Fatty Acid Desaturase (FAD) Proteins in Pearl Millet (Pennisetum glaucum L.). IJBSM [Internet]. 2025 Oct. 31 [cited 2026 Jan. 3];16(Oct, 10):01-13. Available from: https://ojs.pphouse.org/index.php/IJBSM/article/view/6444

Issue

Vol. 16 No. Oct, 10 (2025)

Section

Articles

License

Copyright (c) 2025 Thalari Vasanthrao, Mazahar Moin, Prabhavathi Kona, Wricha Tyagi, S. K. Gupta, Reddy P. Sudhakar, Shashi Bhushan Danam

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