Analysis of Codon Usage Bias and Phylogenesis in the Chloroplast Genome of Ancient Tea Tree Camellia taliensis in Forest-tea Garden

TONG Yan; HUANG Hui; WANG Yuhua

doi:10.13305/j.cnki.jts.2023.03.010

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Journal of Tea Science ›› 2023, Vol. 43 ›› Issue (3) : 297-309. DOI: 10.13305/j.cnki.jts.2023.03.010

Analysis of Codon Usage Bias and Phylogenesis in the Chloroplast Genome of Ancient Tea Tree Camellia taliensis in Forest-tea Garden

TONG Yan¹, HUANG Hui^1,2, WANG Yuhua^1,*

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Abstract

Camellia taliensis is one of the important tea plants which is often grown in forest-tea gardens, which participated in the origin and domestication of C. sinensis var. assamica. To determine the codon usage bias pattern and its main influencing factors in the chloroplast genome of C. taliensis, neutral plotting, ENC-plot, PR2-plot analyses were performed and the optimal codons were found. The results show that the GC content of 54 CDS sequences was 37.68%, while GC₁ and GC₂ content were 46.44% and 39.77%, higher than GC₃(27.67%), indicating that the third base of the codon preferred to end in A/U. The effective codon number (ENC) ranged from 35.64 to 56.67 , with an average value of 46.1, demonstrating weak codon usage bias in chloroplast genome of C. taliensis. Neutral plotting, ENC-plot, PR2-plot analyses show that the main factor affecting the codon usage bias of the C. taliensis chloroplast genome was natural selection. In total, 11 optimal codons were identified in the chloroplast genome of C. taliensis. Although phylogenetic trees constructed by matK gene and CDS sequence display different topological structures, all trees show that C. taliensis and C. gymnogyna are clustered into one branch and are closely related to cultivated tea plant. This study provided the basis for analyses of genetic evolution, phylogeny and improved agronomic traits of C. taliensis.

Key words

Camellia taliensis / chloroplast genome / codon usage bias / forest-tea garden / phylogenetic analysis

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TONG Yan, HUANG Hui, WANG Yuhua. Analysis of Codon Usage Bias and Phylogenesis in the Chloroplast Genome of Ancient Tea Tree Camellia taliensis in Forest-tea Garden[J]. Journal of Tea Science. 2023, 43(3): 297-309 https://doi.org/10.13305/j.cnki.jts.2023.03.010

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