Analysis Of Codon Usage Patterns Of The Chloroplast Genomes In The Poaceae Family And Rna Editing Sites In The Chloroplast Transcripts Of Ageratina Adenophorum

Codon usage patterns of23Poaceae chloroplast genomes were analysed in this study. Neutrality analysis indicated that the codon usage patterns have significant correlations withGC12andGC3and also showed strong bias towards a high representation of NNA and NNT codons. The Nc-plot showed that although a large proportion of points follow the parabolic line of trajectory, several genes with low ENc values lie below the expected curve, suggesting that mutational bias played a major role in the codon biology of the Poaceae chloroplast genome. Parity Rule2plot analysis showed that T was used more frequently than A in all the genomes. Correspondence analysis of relative synonymous codon usage indicated that the first axis explained only a partial amount of variation of codon usage. Furthermore, the gene length and expression level were also found to drive codon usage variation. These findings revealed that besides natural selection, other factors might also exert some influences in shaping the codon usage bias in Poaceae chloroplast genomes. The optimal codons of these23genomes were also identified in this study. The cluster analysis of the RSCU from chloroplast genes could be used as a complementary method for phylogenetic relationships analysis.RNA editing is an important approach which land plants apply to regulate the gene expression at post-transcriptional levels in chloroplast transcript. We predicted the RNA editing sites in the cp genome of c A. adenophorum using the Prep-Cp and CURE tools. Forty two editing sites were identified and distributed in19protein-coding genes, of which all were C to U conversion. Among them,8RNA editing sites occurred in the first position of codon, and the rest34sites occurred in the second position of codon. We didn’t find RNA editing sites occurred in the third position of codon. To ascertain the accuracy of the prediction, we compared the DNA sequences and cDNA sequences of four genes using PCR and RT-PCR combined with sequencing. Ten editing sites were found to be actual existence. Finally, the second structures and the transmenbrane domains of these proteins were also analyzed using bioinformatics methods to identify the effect of the editing. Results indicated that ndhB-467 editing can cause an increase in transmenbrane protein domains while editing in ndhB-149will change the secondary structure.