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The chloroplast (cp) genome is useful in the study of phylogenomics, molecular dating, and molecular evolution.  Gentiana  sect.  Kudoa  is a predominantly alpine flowering plant that is valued for its contributions to medicine, ecology, and horticulture. Previous evolutionary studies showed that the plastid gene loss pattern and intra-sectional phylogenetics in sect.  Kudoa  are still unclear. In this study, we compared 11  Gentiana  plastomes, including 7 newly sequenced plastomes from sect.  Kudoa , to represent its three serious: ser.  Ornatae , ser.  Verticillatae , and ser.  Monanthae . The cp genome sizes of the seven species ranged from 137,278 to 147,156 bp. The plastome size variation mainly occurred in the small single-copy and long single-copy regions rather than the inverted repeat regions. Compared with sect.  Cruciata , the plastomes in ser.  Ornatae  and ser.  Verticillatae  had lost approximately 11 kb of sequences containing 11  ndh  genes. Conversely, far fewer losses were observed in ser.  Monanthae.  The phylogenetic tree revealed that sect.  Kudoa  was not monophyletic and that ser.  Monanthae  was more closely related to other sections rather than sect.  Kudoa.  The molecular dating analysis indicated that ser.  Monanthae  and sect.  Kudoa  diverged around 8.23 Ma. In ser.  Ornatae  and ser.  Verticillatae , the divergence occurred at around 0.07–1.78 Ma. The nucleotide diversity analysis indicated that the intergenic regions  trnH-psbA ,  trnK-trnQ ,  ycf3-trnS  and  rpl32-trnL  constituted divergence hotspots in both sect.  Kudoa  and  Gentiana , and would be useful for future phylogenetic and population genetic studies.

The Complete Plastome Sequences of Seven Species in Gentiana sect. Kudoa (Gentianaceae): Insights Into Plastid Gene Loss and Molecular Evolution