Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Camellia sinensis sp. Baihaozao

Baihaozao (Camellia sinensis sp. Baihaozao) is esteemed in the domain of tea plant cultivation for its early harvest period, profusion of bud trichomes, and exceptional suitability for tea processing. Nevertheless, the intricate phylogenetic relationships among species within this genus remain ambiguous, primarily due to the limited availability of genomic data. This study endeavors to comprehensively investigate the genomic resources of Baihaozao by sequencing, assembling, and annotating its entire chloroplast (cp) genome. The sequencing results indicated that the total length of the Baihaozao cp genome is 157,052 base pairs (bp), with an overall guanine-cytosine (GC) content of 37.30%. The genome exhibits a typical quadripartite structure, consisting of a large single-copy region (LSC) of 86,586 bp, a small single-copy region (SSC) of 18,227 bp, and a pair of inverted repeats (IRs) totaling 52,162 bp. A total of 133 genes were identified within this genome, including 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, 87 protein-coding genes, and 1 pseudogene. Furthermore, the study identified 157 simple sequence repeats (SSRs) and 90 long repeat sequences. Analysis of codon usage bias indicated that codons encoding leucine (Leu) were the most frequently utilized, whereas those encoding cysteine (Cys) were the least utilized. Examination of nucleotide diversity within the Baihaozao cp genome revealed five highly variable regions with elevated Pi values (rps19, rpl32, ndhF, rpl22, matK), suggesting their potential utility as molecular markers. Phylogenetic analysis of 20 cp genomes of the Theaceae family indicated a close evolutionary relationship between Baihaozao and Camellia sinensis OL450428.1. This study not only provides valuable data support for elucidating the maternal origin of cultivated Camellia species but also holds significant scientific implications for further exploring the phylogenetic relationships and germplasm resource utilization of Camellia plants.