Genomic Characteristics, Codon Preference, and Phylogenetic Analysis of Chloroplasts of Camellia sinensis cv. &#x02018;Damianbai&#x02019;

YIN Minghua; ZHANG Jiaxin; LE Yun; HE Fanfan; HUANG Tianhui; ZHANG Mutong

doi:10.13305/j.cnki.jts.2024.03.009

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Journal of Tea Science ›› 2024, Vol. 44 ›› Issue (3) : 411-430. DOI: 10.13305/j.cnki.jts.2024.03.009

Genomic Characteristics, Codon Preference, and Phylogenetic Analysis of Chloroplasts of Camellia sinensis cv. ‘Damianbai’

YIN Minghua^1,2,3,4, ZHANG Jiaxin¹, LE Yun¹, HE Fanfan¹, HUANG Tianhui¹, ZHANG Mutong¹

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Abstract

‘Damianbai’ was approved as a national tea cultivar by the National Crop Variety Approval Committee in 1985, but its origin and evolutionary relationship with other tea resources are still unclear. Using ‘Damianbai’ as the experimental material, high-throughput sequencing technology was used to sequence, assemble and annotate the entire chloroplast genome of ‘Damianbai’. In order to provide a basis for studying its phylogenetic evolutionary relationship, bioinformatics software was used to analyze the characteristics, phylogeny, and codon preference of its chloroplast genome. The results show that the chloroplast genome of the tea cultivar ‘Damianbai’ had a total length of 157 129 bp and was a typical tetrad structure, including 1 LSC region (86 687 bp), 1 SSC region (18 282 bp), and 2 IR regions (including IRa and IRb, both of which were 26 080 bp). A total of 135 functional genes were annotated in the chloroplast genome of ‘Damianbai’, including 90 CDS genes, 8 rRNA genes, and 37 tRNA genes. A total of 52 SSRs and 50 Longrepeat sequences were detected in the chloroplast genome of ‘Damianbai’. The SSRs had only A/T single nucleotide repeat sequences, while Longrepeat sequences had only two types: forward repeat and palindrome repeat. The codon usage bias in the chloroplast genome of tea cultivar ‘Damianbai’ was mainly influenced by natural selection, and was less affected by internal mutation pressure. The chloroplast gene of tea cultivar ‘Damianbai’ had 14 optimal codons (AAU, GAU, UGU, AAA, UAA, GCA, GCU, GGU, CCU, GUA, CGU, CUU, AGU, UCU). The Camellia sinensis cv. ‘Damianbai’ had a close genetic relationship with Camellia sinensis isolate Baiyin cultivar Phoenix Dancong Tea (OL690374). This study analyzed the chloroplast genome sequence characteristics and phylogenetic relationships of ‘Damianbai’, which provided a reference basis for strengthening the identification of tea cultivar ‘Damianbai’ and the development and utilization of its resource diversity.

Key words

Camellia sinensis cv. ‘Damianbai’ / chloroplast genome / codon usage bias / optimal codons / phylogenetic analysis / sequence characteristics

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YIN Minghua, ZHANG Jiaxin, LE Yun, HE Fanfan, HUANG Tianhui, ZHANG Mutong. Genomic Characteristics, Codon Preference, and Phylogenetic Analysis of Chloroplasts of Camellia sinensis cv. ‘Damianbai’[J]. Journal of Tea Science. 2024, 44(3): 411-430 https://doi.org/10.13305/j.cnki.jts.2024.03.009

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