Abstract
The regulatory mechanisms of determining which genes specifically expressed in which tissues are still not fully elucidated, especially in plants. Using internal correspondence analysis, I first establish that tissue-specific genes exhibit significantly different synonymous codon usage in rice, although this effect is weak. The variability of synonymous codon usage between tissues accounts for 5.62% of the total codon usage variability, which has mainly arisen from the neutral evolutionary forces, such as GC content variation among tissues. Moreover, tissue-specific genes are under differential selective constraints, inferring that natural selection also contributes to the codon usage divergence between tissues. These findings may add further evidence in understanding the differentiation and regulation of tissue-specific gene products in plants.
Highlights
Within a genome, some synonymous codons are avoided readily, while some are used preferentially
The tissue-specific codon usage in rice was evaluated using a multivariate method, internal correspondence analysis [11]. These analyses reveal a significant difference in synonymous codon usage between genes selectively expressed in different tissues
Variation in Synonymous Codon Usage between Tissues The data set consisting of 675 coding sequences (CDSs) from seven tissues were subjected to CodonW and custom PERL programs to investigate the synonymous codon usage of rice tissues
Summary
Some synonymous codons are avoided readily, while some are used preferentially. The tissue-specific codon usage in rice was evaluated using a multivariate method, internal correspondence analysis [11]. These analyses reveal a significant difference in synonymous codon usage between genes selectively expressed in different tissues.
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