Analysis of Repeat Sequence and Codon Bias of Chloroplast Genome in Scutellaria baicalensis
In this study, repeat sequences and codon bias analysis of the whole chloroplast genome in Scutellaria baicalensis was performed by REPuter, MISA and Codon W softwares. The number and distribution of repeat sequences were calculated and RSCU, ENC, GC3s, amino acid frequency and the total content of GC were counted to determine the optimal codon. The results showed that the repeats were mostly forward repeats (F) and the palindromic repeats (P) and were mainly distributed in the LSC region. 43 simple repeat sequences (SSR) were detected, which mostly distributed in the IGS region, and the distribution of cpSSR accounted for 65.12％. According to RSCU value and GC content, 31 codons, such as UCU, UCA, AGU and so on, were selected as the optimal codons, which all ended with A/T. The most frequently used amino acid was leucine, and the lowest was cysteine, and the ENC value of 50.52 indicated that the codons were weak in preference. The results of this study could provide the basic information for the screening of molecular markers of Scutellaria baicalensis, and it might have important guiding significance in its molecular transformation and genetic transformation.
NETL
NSTL
万方数据
维普
