Rampant intraspecific variation of plastid genomes in <i>Gentiana</i> section <i>Chondrophyllae</i>

Exploring the level of intraspecific diversity in taxa experienced radiation is helpful to understanding speciation and biodiversity assembly. <i>Gentiana</i> section <i>Chondrophyllae</i> sensu lato encompasses more than 180 species and occupies more a half of species in the genus. In this study, we collected samples across the range of three species (<i>Gentiana aristata</i>, <i>G. crassuloides</i> and <i>G. haynaldii</i>) in section <i>Chondrophyllae</i> s.l., and recovered the intra-species variation by comparing with closely related taxon. Using 25 newly sequenced plastid genomes together with previously published data, we compared structural differences, quantified the variations in plastome size, and measured nucleotide diversity in various regions. Our results showed that the plastome size variation in the three <i>Chondrophyllae</i> species ranged from 285 to 628 bp, and the size variation in LSC, IR and SSC ranged from 236 to 898 bp, 52 to 393 bp and 135 to 356 bp, respectively. Nucleotide diversity of plastome or any of the four regions was much higher than the control species. The average nucleotide diversity in plastomes of the three species ranged from 0.0010 to 0.0023 in protein coding genes, and from 0.0023 to 0.0061 in intergenic regions. More repeat sequence variations were detected within the three <i>Chondrophyllae</i> species than the control species. Various plastid sequence matrixes resulted in different backbone topology in two target species, showed uncertainty in phylogenetic relationship based inference. In conclusion, our results recovered that species of <i>G.</i> section <i>Chondrophyllae</i> s.l. has high intraspecific plastome variation, and provided insights into the radiation in this speciose lineage.