A comparative study of the evolution and codon usage bias in WOX gene family of three Camellia sinensis cultivars

WANG Zhanjun, WU Ziqi, WANG Zhaoxia, OU Zulan, LI Jie, CAI Qianwen, XU Zhongdong, ZHANG Zhaoliang

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2022, Vol. 46 ›› Issue (2) : 71-80.

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南京林业大学学报（自然科学版）
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JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2022, Vol. 46 ›› Issue (2) : 71-80. DOI: 10.12302/j.issn.1000-2006.202108049

A comparative study of the evolution and codon usage bias in WOX gene family of three Camellia sinensis cultivars

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Abstract

【Objective】The WOX gene family plays an important molecular regulatory role in model plant tissue culture. Phylogeny studies and research on the codon usage bias in the WOX gene family in non-model plants are helpful for exploring genetic evolution and gene expression characteristics, which serve as a guideline for establishing a transgenic system.【Method】In this study, bioinformatics were used to identify the WOX genes among all coding sequences of three Camellia sinensis cultivars. The evolutionary patterns were analyzed using ClustalX 2.1 and MEGA X software. The codon usage index of the coding sequence of the WOX gene was analyzed, and the codon usage pattern and the source of codon variation were explored using Perl language, Codon W1.4.2, and SPSS 23.0. The main factors affecting codon usage bias were analyzed based on the results of ENc-GC3s, a PR2-plot analysis, and a neutral analysis.【Result】A total of 42 WOX members were identified in this study, of which 11 were CSA, 18 were CSS and 13 were DASZ. The phylogenetic analysis revealed that the evolution of WOX genes of the three Camellia sinensis cultivars is highly conserved. The codon bias analysis revealed that the codons of WOX genes preferred to use A/T and end with A/T in the three Camellia sinensis cultivars; the codon usage patterns of WOX genes in CSA and DASZ are similar, indicating that they are closely related. When CSA and CSS are used as transgenic receptors, individual codons in WOX genes of three Camellia sinensis cultivars need to be optimized. Nicotiana tabacum is the best heterologous expression receptor for WOX genes of three Camellia sinensis cultivars. ENc-GC3s mapping the PR2 analysis, and the neutrality analysis indicate that the natural selection is the main reason for the codon usage bias of WOX genes in the three Camellia sinensis cultivars.【Conclusion】This study showed that WOX genes of three Camellia sinensis cultivars are evolutionarily conserved, codons prefer to use A/T and end with A/T, and the codon usage bias is mainly due to the natural selection. The results reveal the optimization information of codons when transforming tea plants, and tobacco is the best heterologous expression receptor.

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Camellia sinensis / WOX gene family / evolutionary analysis / codon usage bias / transgene expression

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WANG Zhanjun , WU Ziqi , WANG Zhaoxia , et al . A comparative study of the evolution and codon usage bias in WOX gene family of three Camellia sinensis cultivars[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2022, 46(2): 71-80 https://doi.org/10.12302/j.issn.1000-2006.202108049

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