Correspondence analysis

Patterns of synonymous codon usage bias in the model grass Brachypodium distachyon

H. Liu, Huang, Y., Du, X., Chen, Z., Zeng, X., Chen, Y., and Zhang, H., Patterns of synonymous codon usage bias in the model grass Brachypodium distachyon, vol. 11, pp. 4695-4706, 2012.

Brachypodium distachyon has been proposed as a new model for the temperate grass because it is related to the major cereal grain species (such as wheat, barley, oat, maize, rice, and sorghum) and many forage and turf species. In this study, a multivariate statistical analysis was performed to investigate the characteristics of codon bias and the main factors affecting synonymous codon usage in Brachypodium. We found that low- and high-GC content genes with different codon usage occur frequently in the genome.

Synonymous codon usage patterns in different parasitic platyhelminth mitochondrial genomes

L. Chen, Yang, D. Y., Liu, T. F., Nong, X., Huang, X., Xie, Y., Fu, Y., Zheng, W. P., Zhang, R. H., Wu, X. H., Gu, X. B., Wang, S. X., Peng, X. R., and Yang, G. Y., Synonymous codon usage patterns in different parasitic platyhelminth mitochondrial genomes, vol. 12, pp. 587-596, 2013.

We analyzed synonymous codon usage patterns of the mitochondrial genomes of 43 parasitic platyhelminth species. The relative synonymous codon usage, the effective number of codons (NC) and the frequency of G+C at the third synonymously variable coding position were calculated. Correspondence analysis was used to determine the major variation trends shaping the codon usage patterns. Among the mitochondrial genomes of 19 trematode species, the GC content of third codon positions varied from 0.151 to 0.592, with a mean of 0.295 ± 0.116.

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