Codon Preference Analysis of Chloroplast Genome in Dendrobium cariniferum
This study aims to clarify the codon usage pattern of chloroplast genome in Dendrobium cariniferum Rchb.f.52 protein coding sequences(CDS)were taken as the object.The guanine-cytosine(GC)contents of each gene and codon were calculated by EMBOSS online program.CodonW software was also utilized to calculate the effective codon number(ENC),relative usage of synonymous codons(RSCU),optimal codon usage frequency(FOP)and the third nucleotide base content of each gene codon.The results are as follows:the average GC content of the ge-nome was 38%,of which was ranked in the descending order of GC1>GC2>GC3.The value of ENC was between 37.04 and 59.52,indicating the weak preference of codon usage.There were 25 codons with RSCu>1 in the ge-nome,11 of which were ended with U,while 11 ones were ended with A,and 3 ones were ended with G.All genes were distributed above the diagonal of the midline in neutral mapping analysis.There was no significant correlation between GC12 and GC3.The codon usage preference was mainly influenced by natural selection factors.Most genes of ENC-plot were distributed below the standard curve.It infers that the natural selection was dominated the codon preference.PR2-plot analysis showed that the codon bases A and G appeared more frequently at codon 3 than T and C.The reason was that the gene mutation was affected codon usage bias,but its preference was mainly affected by natural selection.There were 13 optimal codons in this genome,such as UUU,UUA and AUU,all of which was end in A/U.The finding can provide the theoretical basis for the utilization of excellent genes in chloroplast genome of Dendrobium cariniferum.
万方数据
维普
