Analysis of Codon Usage Bias in the Chloroplast Genome of <i>Tadehagi triquetrum</i>

Wang Fang; Zhou Shengmao; Zhao Xueli

doi:10.11929/j.swfu.202403030

Journal of Southwest Forestry University > 2025 > 45(1): 34-43. > DOI: 10.11929/j.swfu.202403030

Wang F, Zhou S M, Zhao X L. Analysis of Codon Usage Bias in the Chloroplast Genome of Tadehagi triquetrum[J]. Journal of Southwest Forestry University, 2025, 45(1): 34–43. DOI: 10.11929/j.swfu.202403030

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Analysis of Codon Usage Bias in the Chloroplast Genome of Tadehagi triquetrum

College of Forestry, Southwest Forestry University, Kunming Yunnan 650233, China

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Received Date: March 10, 2024
Revised Date: April 25, 2024
Accepted Date: July 13, 2024
Available Online: December 27, 2024

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Abstract

Abstract

To investigate the patterns and causes of the codon usage in the chloroplast genome of Tadehagi triquetrum, the complete chloroplast genome of T. triquetrum was sequenced using the Illumina NovaSeq 6000 platform, assembled and annotated, with the analysis of codon usage of the 52 screened CDS was performed by Codon W, CUSP and OriginPro. The results showed that the average GC content of T. triquetrum chloroplast genome codons was GC₁(45.64%) > GC₂(38.17%) > GC₃(25.56%), and the content of T_3S and A_3S in the synonymous codons encoding amino acids was significantly higher than that of C_3S and G_3S. The ENC values ranged from 38.43 to 55.04 with an average of 45.64, and the CAI values ranged from 0.1 to 0.18 with an average of 0.16, indicating that their codon bias was weak. Analysis of correlation, neutral plotting, ENC‒plot, and PR2‒plot, indicating that mutation and selection jointly affect codon usage bias in the chloroplast genome of T. triquetrum. The optimal 7 codons(CUU, AUU, AUA, GUU, GAU, UCA, GGA) were selected of T. triquetrum by RSCU and ENC values, which were biased to end in A/U.
- Tadehagi triquetrum,
- chloroplast genome,
- codon bias,
- optimal codon

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Analysis of Codon Usage Bias in the Chloroplast Genome of Tadehagi triquetrum

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