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Codon Usage Bias for Fatty Acid Genes FAE1 and FAD2 in Oilseed Brassica Species

Author

Listed:
  • Rajat Chaudhary

    (ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
    These authors contributed equally to this work.)

  • Subhash Chand

    (ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
    These authors contributed equally to this work.)

  • Bharath Kumar Alam

    (ICAR-National Research Centre for Orchids, Pakyong 737106, India)

  • Prashant Yadav

    (ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur 321303, India)

  • Vijay Kamal Meena

    (ICAR-Indian Agricultural Research Institute, New Delhi 110012, India)

  • Manoj Kumar Patel

    (ICAR-Indian Agricultural Research Institute, New Delhi 110012, India)

  • Priya Pardeshi

    (ICAR-Indian Agricultural Research Institute, New Delhi 110012, India)

  • Sanjay Singh Rathore

    (ICAR-Indian Agricultural Research Institute, New Delhi 110012, India)

  • Yashpal Taak

    (ICAR-Indian Agricultural Research Institute, New Delhi 110012, India)

  • Navinder Saini

    (ICAR-Indian Agricultural Research Institute, New Delhi 110012, India)

  • Devendra Kumar Yadava

    (ICAR-Indian Agricultural Research Institute, New Delhi 110012, India)

  • Sujata Vasudev

    (ICAR-Indian Agricultural Research Institute, New Delhi 110012, India)

Abstract

Codon usage bias (CUB) phenomenon varies with the species and even within the genes of the same species, where few codons are preferred more frequently than their other synonymous codons. It also categorizes the differences between species. Nucleotide compositional analysis reveals the molecular mechanisms of genes and the evolutionary relationship of a gene in dissimilar plant species. In the present study, three orthologous sequences of each FAE1 ( FAE1.1 , FAE1.2 , and FAE1.3 ) and FAD2 ( FAD2.1 , FAD2.2 , and FAD2.3 ) genes, from six Brassica species were accessed using the GenBank database. Further, CUB-related parameters such as nucleotide composition (AT and GC content), relative synonymous codon usage (RSCU), the effective number of codons (ENC), frequency of optimal codons ( Fop ), relative codon usage bias (RCBS), neutrality plot (GC12 vs. GC3), parity rule-2 [(A3/(A3 + T3) vs. (G3/(G3 + C3)], and correspondence analysis (COA) were analyzed to compare codon bias in U’s triangle Brassica species. The FAE1 genes were AT-biased and FAD2 genes were GC-biased across the studied Brassica species. RSCU values indicated that both the genes had moderate codon usage frequency for selected amino acids. The evolutionary study confirmed that codon usage preference is similar within the species grouped into the same cluster for FAE1 ; however, B. nigra performed differently for FAD2.2 orthologue. The high ENC value, low Fop , and RSCU value highlighted that FAE1 and FAD2 genes had a low level of gene expression and moderate preference for codon usage across the Brassicas . In addition, neutrality plot, parity rule, and correspondence analysis revealed that natural selection pressure had significantly contributed to CUB for FAE1 genes, whereas mutation and selection pressure occurred for FAD2 genes. This study would help to decode codon optimization, improve the level of expression of exogenous genes, and transgenic engineering to increase fatty acid profiling for the betterment of seed oil in Brassica species.

Suggested Citation

  • Rajat Chaudhary & Subhash Chand & Bharath Kumar Alam & Prashant Yadav & Vijay Kamal Meena & Manoj Kumar Patel & Priya Pardeshi & Sanjay Singh Rathore & Yashpal Taak & Navinder Saini & Devendra Kumar Y, 2022. "Codon Usage Bias for Fatty Acid Genes FAE1 and FAD2 in Oilseed Brassica Species," Sustainability, MDPI, vol. 14(17), pages 1-21, September.
    • Handle: RePEc:gam:jsusta:v:14:y:2022:i:17:p:11035-:d:906326
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    References listed on IDEAS

    as
    1. Sanjay Singh Rathore & Subhash Babu & Kapila Shekhawat & Vinod K. Singh & Pravin Kumar Upadhyay & Rajiv Kumar Singh & Rishi Raj & Harveer Singh & Fida Mohammad Zaki, 2022. "Oilseed Brassica Species Diversification and Crop Geometry Influence the Productivity, Economics, and Environmental Footprints under Semi-Arid Regions," Sustainability, MDPI, vol. 14(4), pages 1-18, February.
    2. Shivendra Kumar & Ramdeo Seepaul & Ian M. Small & Sheeja George & George Kelly O’Brien & James J. Marois & David L. Wright, 2021. "Interactive Effects of Nitrogen and Sulfur Nutrition on Growth, Development, and Physiology of Brassica carinata A. Braun and Brassica napus L," Sustainability, MDPI, vol. 13(13), pages 1-19, June.
    3. Mian Zhou & Jinhu Guo & Joonseok Cha & Michael Chae & She Chen & Jose M. Barral & Matthew S. Sachs & Yi Liu, 2013. "Non-optimal codon usage affects expression, structure and function of clock protein FRQ," Nature, Nature, vol. 495(7439), pages 111-115, March.
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