The chloroplast genome of Camellia sinensis var. assamica cv. Duntsa (Theaceae) and comparative genome analysis: mutational hotspots and phylogenetic relationships

Camellia sinensis (L.) O. Kuntze var. assamica cv. Duntsa (herein C. duntsa) has been used since ancient times in Hunan, China. To understand the genetic background information of C. duntsa and clarify the relationship between C. duntsa and other tea cultivars and varieties (taxa), the complete chloroplast genome of C. duntsa was sequenced using the Illumina NovaSeq platform, which was then compared with other published chloroplast genomes from tea plants. The C. duntsa chloroplast genome is 157,025 bp in length with a guanine–cytosine content of 37.30%. It consists of a short single-copy region (18,277 bp), a large single-copy region (86,586 bp), and two inverted repeat regions (26,081 bp). A total of 135 genes were identified, comprising 87 protein-coding genes, eight ribosomal RNA genes, 37 transfer RNA genes, and three pseudogene genes (two ycf15 and one ycf1). In addition, 968 long repetitive sequences were detected by comparative analysis with other tea plant chloroplast genes, of which 409 were forward, 557 were palindromic, and two were reverse. A total of 241–249 simple sequence-repeat loci were analyzed for comparison; most of these were single nucleic acid loci composed of A/T. In addition, six mutation hotspots (rpoC1, ycf1, petB, ndhD, rpl16, and rpoC2) were identified. Phylogenetic analysis showed that C. duntsa has a relatively close evolutionary relationship with C. sinensis var. sinensis cultivars anhua and fudingdabaicha and with Camellia ptilophylla Hung T. Chang. These results can provide valuable information for a better understanding of chloroplast evolution in Camellia species.