甜龙竹叶绿体基因组密码子偏好性分析OA

To explore the codon usage preference and influencing factors of chloroplast genome in Dendrocalamus brandisii,50 protein-coding sequences of chloroplast genome of D.brandisii were as materials,the GC content at different codon positions(GC1,GC2,GC3),effective codon number(ENC),codon adaptation index(CAI),codon bias index(CBI),frequency of optimal codon usage(Fop)and relative synonymous codon usage(RSCU)were analyzed using software such as Codon W 1.4.2,CUSP and Excel.The results showed that the GC content followed the trend of GC1(47.70%)>GC2(39.39%)>GC3(30.99%)with average GC content 39.36%,which indicated there was an uneven distribution of GC content in chloroplast genome of D.brandisii.Codon preference was found to favor A/U endings,with the third base(GC3)showing a greater preference for A/U compared to the first(GC1)and second(GC2)bases.The means of ENC,CAI,CBI and Fop were 50.41,0.17,-0.09 and 0.36,respectively,indicating a weak codon usage preference in chloroplast genome of D.brandisii.Neutral plot,ENC-plot and PR2-plot analyses further demonstrated that codon usage preference in chloroplast genome of D.brandisii was primarily influenced by natural selection factor.And 11 optimal codons were identified,including GCU,UGU and GGU et al.Above results provided reference for the genomic research of D.brandisii and laid the foundation for subsequent studies in related fields.