Construction of anti-codon table of the plant kingdom and evolution of tRNA selenocysteine (tRNA(Sec))

BACKGROUND: The tRNAs act as a bridge between the coding mRNA and incoming amino acids during protein translation. The anti-codon of tRNA recognizes the codon of the mRNA and deliver the amino acid into the protein translation chain. However, we did not know about the exact abundance of anti-codons in the genome and whether the frequency of abundance remains same across the plant lineage or not. RESULTS: Therefore, we analysed the tRNAnome of 128 plant species and reported an anti-codon table of the plant kingdom. We found that CAU anti-codon of tRNA(Met) has highest (5.039%) whereas GCG anti-codon of tRNA(Arg) has lowest (0.004%) abundance. However, when we compared the anti-codon frequencies according to the tRNA isotypes, we found tRNA(Leu) (7.808%) has highest abundance followed by tRNA(Ser) (7.668%) and tRNA(Gly) (7.523%). Similarly, suppressor tRNA (0.036%) has lowest abundance followed by tRNA(Sec) (0.066%) and tRNA(His) (2.109). The genome of Ipomoea nil, Papaver somniferum, and Zea mays encoded the highest number of anti-codons (isoacceptor) at 59 each whereas the genome of Ostreococcus tauri was found to encode only 18 isoacceptors. The tRNA(Sec) genes undergone losses more frequently than duplication and we found that tRNA(Sec) showed anti-codon switch during the course of evolution. CONCLUSION: The anti-codon table of the plant tRNA will enable us to understand the synonymous codon usage of the plant kingdom and can be very helpful to understand which codon is preferred over other during the translation. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-020-07216-3.