Codon usage bias of chloroplast genome in Catalpa bungei C. A. Mey.

【Objective】Analyzed the codon usage bias of Catalpa bungei C. A. Mey. chloroplast genome to provide theoretical basis for the research of C. bungei and even Catalpa chloroplast genomics, species evolution characteristics and genetic diversity analysis.【Method】Codon correlation parameters, neutral plots, ENC-plot and PR2-plot were analyzed for 51 chloroplast gene coding regions(CDS) sequences of C. bungei by Codon W 1.4.2 and cusp and chips of EMBOSS expiorer. And through the constitutive high and low expression-biased gene library, ENC value and RSCU value were used as reference criteria to screen the optimal codon.【Result】The average GC_all content of 51 gene codons was 38.48%, and GC content at different positions of codons was as follows:GC₁(47.03%) >GC₂(39.93%) >GC₃(28.09%), indicating that GC at the third position was not evenly distributed. ENC ranged from 34.93 to 56.50, with an average of 46.87. GC₂ was extremely significantly positively correlated with GC₁(P<0.01), while GC₃ was not significantly positively correlated with GC₁ and GC₂(P>0.05). ENC was significantly positively correlated with GC_all, GC₁, GC₃ and N(P<0.05, the same below). The codon number(N) was positively correlated with GC₃ and ENC. There were 30 codons with RSCU>1, among which 29 codons ended in A or U. Neutral plot analysis results showed that the correlation coefficient between GC₃ and GC₁₂ was 0.0188, and there was no significant correlation between them, and the regression coefficient was 0.143. ENC-plot analysis showed that most of the genes deviated from the ENC expected standard curve, and a few were distri-buted near the expected curve. There were 7 codons distributed in the range of GC₃ content from -0.05 to 0.15, and there were 44 codons in the other regions, which were far from the ENC standard curve. PR2-plot analysis results showed that fewer genes fell on the middle line, and more genes were distributed in the lower right part of the graph, indicating that there was a bias in the use frequency of each base, namely T>A, G>C.There was bias(T>A, G>C) in the use frequency of each base, indicating that the bias of the genome codon was more influenced by the selection effect. Finally, 7 optimal codons were selected as UUU, CUU, CCU, AAA, GAU, CGA and GGU.【Conclusion】The chloroplast genomes of C. bungei show weak codon bias, preferring to use codons ending in A or U, which is mainly affected by selection pressure and less affected by mutation and other factors.