Analysis of codon usage patterns of the chloroplast genomes in the Poaceae family
Yuerong Zhang A B E , Xiaojun Nie B E , Xiaoou Jia B , Cunzhen Zhao D , Siddanagouda S. Biradar B , Le Wang B , Xianghong Du C and Song Weining A B C F
+ Author Affiliations
- Author Affiliations
A State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling 712100, Shaanxi, China.
B College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
C Yangling Branch of China Wheat Improvement Centre, Northwest A&F University, Yangling 712100, Shaanxi, China.
D College of Animal Science, Northwest A&F University, Yangling 712100, Shaanxi, China.
E These authors contributed equally to this work.
F Corresponding author. Email: sweining2002@yahoo.com
Australian Journal of Botany 60(5) 461-470 https://doi.org/10.1071/BT12073
Submitted: 27 March 2012 Accepted: 26 May 2012 Published: 13 August 2012
Abstract
Codon usage patterns of 23 Poaceae chloroplast genomes were analysed in this study. Neutrality analysis indicated that the codon usage patterns have significant correlations with GC12 and GC3 and 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 Rule 2 plot 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 these 23 genomes were also identified in this study.
Additional keywords: mutational bias, optimal codon.
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