Analysis of the Structural Characteristics and Codon Usage Biase of the Mitochondrial Genome in Tea Cultivar &#x02018;Damianbai&#x02019;

YIN Minghua; ZHANG Mutong; XU Zilin; OUYANG Qian; WANG Meixuan; LI Wenting

doi:10.13305/j.cnki.jts.2025.01.006

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Journal of Tea Science ›› 2025, Vol. 45 ›› Issue (1) : 61-78. DOI: 10.13305/j.cnki.jts.2025.01.006

Analysis of the Structural Characteristics and Codon Usage Biase of the Mitochondrial Genome in Tea Cultivar ‘Damianbai’

YIN Minghua^1,2, ZHANG Mutong¹, XU Zilin¹, OUYANG Qian¹, WANG Meixuan¹, LI Wenting¹

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Abstract

Camellia sinensis cv. ‘Damianbai’ is a national cultivar in Guangxin District, Shangrao. Its mitochondrial genome structure and codon preference are still unclear. Using ‘Damianbai’ as the experimental material, high-throughput sequencing technology was used to sequence, assemble, and annotate the entire mitochondrial genome of ‘Damianbai’. Bioinformatics software was used to analyze the structural characteristics and codon preferences of its mitochondrial genome. The results show that the mitochondrial genome of ‘Damianbai’ was 886 354 bp in length, with a complete single circular molecule structure and a GC content of 45.76%. A total of 78 functional genes were annotated in the mitochondrial genome of ‘Damianbai’, including 41 protein-coding genes, 33 tRNA genes and 4 rRNA genes. A total of 59 SSRs (mainly A/T single nucleotide repeats) and 100 Long repeats (mainly positive and palindromic repeats) were detected in the mitochondrial genome of ‘Damianbai’. The codon bias of the mitochondrial genome in ‘Damianbai’ is relatively weak, with a preference for codons ending in A or U. The codon usage bias of the mitochondrial genome of ‘Damianbai’ is mainly influenced by natural selection, and is less affected by internal mutation pressure. The optimal codons for the mitochondrial genome of ‘Damianbai’ are 14 (AAU, GAU, CAU, UUU, AUU, GCU, GGA, ACU, GUU, CGA, UUA, UUG, UCA, UCU). The mitochondrial genomes of 11 closely related species exhibit high homology with the mitochondrial genome of ‘Damianbai’ in the gene region. The mitochondrial genomes of ‘Damianbai’ and ‘Lingyunbaihao’ (ON782577) have the highest collinearity, and their gene arrangement orders are basically the same. There are 62 highly homologous gene fragments between the mitochondrial genome and chloroplast genome of ‘Damianbai’. ‘Damianbai’ and ‘Lingyunbaihao’ belong to a small branch separately, indicating they are closely related. This study analyzed the mitochondrial genome sequence characteristics and phylogenetic relationships of ‘Damianbai’, providing a reference for strengthening the identification of ‘Damianbai’ germplasm and the development and utilization of its resource diversity.

Key words

Camellia sinensis cv. ‘Damianbai’ / codon usage biase / mitochondrial genome / structural features

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YIN Minghua, ZHANG Mutong, XU Zilin, OUYANG Qian, WANG Meixuan, LI Wenting. Analysis of the Structural Characteristics and Codon Usage Biase of the Mitochondrial Genome in Tea Cultivar ‘Damianbai’[J]. Journal of Tea Science. 2025, 45(1): 61-78 https://doi.org/10.13305/j.cnki.jts.2025.01.006

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