Comparative chloroplast genome analysis of Camellia oleifera and C. meiocarpa: phylogenetic relationships, sequence variation and polymorphic markers

Tea-oil Camellia, a prominently woody oil crop, serves as a crucial source of edible oil, protein feed, and industrial raw materials. Notably, C. Oleifera and C. meiocarpa yield higher oil production and larger cultivation areas than other Tea-oil Camellia species. However, the taxonomy and phylogenetic relationship between these species remain elusive, complicating their commercial application. Here, we sequenced and analyzed the complete chloroplast genomes of these two species, compared them with related Camellia species, and developed chloroplast DNA markers to distinguish between them. The chloroplast genome of C. Oleifera was 157,009 bp (HZP) and C. meiocarpa was 156,549 bp (CKX) and 156,512 bp (XG) in length. Comparative analysis indicated that distinct differences in the chloroplast genome between HZP and CKX (or XG) than between CKX and XG. The repetitive sequences and interspecific variations among them showed that the differences in number and distribution of CKX and XG were smaller than those in HZP. Phylogenetic analysis showed that C. meiocarpa was not closely related to C. oleifera. A total of 56 pairs of primers were developed to test the polymorphism among them. After PCR and sequencing verification, variations were detected in the target sequences of 17 primers. The data derived from the chloroplast genomes and the newly developed markers are invaluable for understanding the phylogenetic relationships, and assessing the genetic diversity of tea-oil Camellia germplasm resources.