Complete chloroplast genomes of 13 plants of sect. Tuberculata Chang (Camellia L.): Genomic features, comparative analysis, and phylogenetic relationships

Abstract

Abstract Background Sect. Tuberculata belongs to Camellia, and its members are characterized by a wrinkled pericarp and united filaments. All the plants in this group, which are endemic to China, are highly valuable for exploring the evolution of Camellia and have great potential to be used as a source of oil. However, due to the complex and diverse phenotypes of these species and the difficulty of investigating them in the field, their complex evolutionary history and interspecific definition are largely unclear. Results Therefore, we newly sequenced and annotated 12 chloroplast (cp) genomes and retrieved the published cp genome of Camellia anlungensis Chang in sect. Tuberculata. In this study, comparative analysis of the cp genomes of the thirteen sect. Tuberculata species have a typical quadripartite structure characterized by a total sequence length from 156,587 bp to 157,068 bp, including the LSC region (86,212 − 86,732 bp), the SSC region (51,986 − 52,130 bp), and two identical inverted repeat (IR) regions (18,276 − 18,339 bp). A total of 130 to 136 genes specific to the three types were obtained by annotation, including protein-coding genes (coding sequences (CDSs)), tRNA genes, and rRNA genes (87–91, 35–37, and 8, respectively). Simple sequence repeats and interspersed repeats were detected in 69–75 and 27–28, respectively. The total number of codons is 23,045 − 26,557. Comparative analyses revealed six hotspot regions (tRNA-Thr(GGT)-psbD, psbE-petL, ycf15-tRNA-Leu(CAA), ndhF-rpl32, ndhD, and trnL(CAA)-ycf15) in the cp genomes that could serve as potential molecular markers. In addition, the results of the phylogenetic tree constructed on the basis of the cp genomes showed that the thirteen Sect. Tuberculata species formed a monophyletic group and were divided into two evolutionarily independent clades, confirming the independence of the section. Conclusions In summary, we obtained the cp genomes of thirteen plants of sect. Tuberculata and performed the first comparative analysis of this group. These results will help us better identify the plants of this section, deepen our understanding of their genetic characteristics and phylogenetic relationships, and to lay the theoretical foundation for its accurate classification, evolutionary pattern changes, and rational development and utilization in the future.