Codon usage bias

Effects of nucleotide usage on the synonymous codon usage patterns of biofilm-associated genes in Haemophilus parasuis

L. Y. Wang, Ma, L. N., Liu, Y. S., Wang, L. Y., Ma, L. N., and Liu, Y. S., “Effects of nucleotide usage on the synonymous codon usage patterns of biofilm-associated genes in Haemophilus parasuis”, vol. 15, p. -, 2016.

To provide a new perspective on the evolutionary characteristics shaping the genetic diversity of Haemophilus parasuis biofilms, the relative synonymous codon usage values, codon usage bias values, effective number of codons (ENC) values, codon adaptation index (CAI) values, and the base components were calculated. Our objective was to implement a comparative analysis to evaluate the dynamic evolution of biofilm-associated genes in H. parasuis. The analysis of genetic diversity provides evidence that some biofilm-associated genes have similar genetic features.

Genome-wide identification and evolutionary analysis of nucleotide-binding site-encoding resistance genes in Lotus japonicus (Fabaceae)

H. Song, Wang, P. F., Li, T. T., Xia, H., Zhao, S. Z., Hou, L., and Zhao, C. Z., “Genome-wide identification and evolutionary analysis of nucleotide-binding site-encoding resistance genes in Lotus japonicus (Fabaceae)”, vol. 14, pp. 16024-16040, 2015.

Nucleotide-binding site (NBS) disease resistance genes play a crucial role in plant defense responses against pathogens and insect pests. Many NBS-encoding genes have been detected in Lotus japonicus, an important forage crop in many parts of the world. However, most NBS genes identified so far in L. japonicus were only partial sequences. We identified 45 full-length NBS-encoding genes in the L. japonicus genome, and analyzed gene duplications, motifs, and the molecular phylogeny to further understand the NBS gene family.

Codon usage bias analysis for the spermidine synthase gene from Camellia sinensis (L.) O. Kuntze

E. You, Wang, Y., Ding, Z. T., Zhang, X. F., Pan, L. L., and Zheng, C., “Codon usage bias analysis for the spermidine synthase gene from Camellia sinensis (L.) O. Kuntze”, vol. 14, pp. 7368-7376, 2015.

The spermidine synthase (SPDS) gene exists widely in all types of plants. In this paper, the codon usage of the SPDS gene from Camellia sinensis (CsSPDS) was analyzed. The results showed that the codon usage of the CsSPDS gene is biased towards the T-ended or A-ended codons, which is similar to that observed in 73 genes selected from the C. sinensis genome. An ENC-plot for 15 SPDS genes from various plant species suggested that mutational bias was the major factor in shaping codon usage in these genes.

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