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 GC
1(45.64%) > GC
2(38.17%) > GC
3(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.