Analysis of codon usage bias in the chloroplast genome of Liparis kumokiri
To understand the condon usage bias in the chloroplast genome of Liparis kumokiri and the main factors affecting the codon usage bias,the complete chloroplast sequence was downloaded from GenBank database,and 51 protein coding sequences were obtained after screening.CodonW software and EMBOSS online program were used to analyze its codon usage patterns.The results showed that the third codon positions of the chloroplast genome sequence of L.kumokiri are mostly A and T,and GC3 is only 29％,much lower than GCi(46％)and GC2(39％).The ENC value ranged from 42 to 60,which indicated that the codon usage bias was relatively low.There was an extremely significant positive correlation between ENC and GC3.Combining neutral plot,ENC-plot and PR2-plot analysis,the results showed that natural selection pressure was the dominant factor affecting the codon usage bias in the chloroplast genome of L.kumokiri,while the role of base mutation was extremely limited.The RSCU data analysis of synonymous codons identified a total of seven optimal codons,including UUG,CUU,UCA,ACA,AAU,AGA and GGA.The results of correspondence analysis showed that the codon usage patterns of different types of genes were different,in which photosynthetic system genes had similar codon usage bias,and other types of genes showed significant differences in bias.
万方数据
维普
