Analysis of codon usage bias in potato transcriptionally specific expressed genes under red and blue light treatments
In this study,1206 and 691 specifically expressed genes were screened based on the transcriptome data of po-tato under red light treatment and blue light treatment,with white light as control,respectively.The coding sequences(CDS)of the selected genes were analyzed by CodonW and CUSP for codon usage bias.The results showed that the codon usage bias of po-tato genes under both red and blue light treatments was weak,with both preferring codons ending in A or T(U).The total num-ber of sequence codons GC under two light treatments was highly significantly correlated with GC3s.Codons with relative synony-mous codon usage(RSCU)greater than 1.00 were high-frequency codons.The number of high-frequency codons under two light treatments was 30,and the types of high-frequency codons were identical.Based on the results of ENc-plot,PR2-plot and neutral plots,it was found that the specifically expressed genes under two light treatments were mainly affected by natural selection.In this study,the 26 and 28 best codons were also screened from genes specifically expressed under blue and red light treatments,respectively.The ratio of codon usage frequency of specifically expressed genes under different light treatments in potato to that in other organisms and the clustering analysis showed that both tomato and tobacco could be used as recep-tors for heterologous expression of potato specifically ex-pressed genes under red and blue light treatments.
red and blue lightpotatotranscriptomespecifically expressed genescodonpreference
万方数据
维普
