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

Abstract

Abstract Background: Camellia sinensis var. assamica cv. Duntsa (C. duntsa) is an ancient tea accession in Hunan China. In order to understand the genetic background information of C. duntsa, clarify the relationship between C. duntsa and other tea trees. we sequenced the complete chloroplast genome of C. duntsa using the Illumina NovaSeq platform and compared it to other published chloroplast genomes from tea plants. Results: The C. duntsa chloroplast genome is 157,025 bp in length with a GC content of 37.30%. It consists of a short single copy (SSC) region (18,277 bp), a large single copy (LSC) region (86,586 bp), and two inverted repeat regions (IRs) (26,081 bp). A total of 135 genes were identified, including 87 protein-coding genes (PCGs), 8 ribosomal RNA genes (rRNAs), 37 transfer RNA genes (tRNAs), and 3 pseudogene genes (2 ycf15 and 1 ycf1). In addition, a total of 968 long repetitive sequences were detected by comparative analysis with other tea tree chloroplast genes, of which 409 were forward, 557 were palindromic, and 2 were reverse. Among the 241-249 SSRs loci analyzed for comparison, most of them were single nucleic acid loci composed of A/T. Besides, 6 mutation hotspots (rpoC1, ycf1, petB, ndhD, rpl16, rpoC2) were identified. Conclusion: Phylogenetic analysis showed that C. duntsa shows a relatively close evolutionary relationship with Camellia sinensis var. sinensis cv. Anhua, Camellia sinensis var. sinensis cv. Fudingdabaicha, and Camellia ptilophylla. The results can provide valuable information for better understanding Camellia species chloroplast evolution.