Genetic relationship of Pleione based on the chloroplast genome

Pleione (Orchidaceae) is a very famous horticultural plant with a high international reputation for its unique flower shape and abundant color. The small difference in morphological characteristics among Pleione species caused by weak reproductive isolation and easy hybridization makes the taxonomic status of individual species very confusing. Chloroplast (cp) genome information is of great significance for the study of plant phylogeny and taxonomy. In this study, the cp genomes of Pleione were sequenced and the complete cp structure and sequence characteristics of 19 species were compared and analyzed. The cp genome of Pleione species exhibited a conserved tetrad structure and each species encoded 135 protein-coding genes, 38 tRNA and 8 RNA genes. The cp genome sizes of 19 Pleione were 157964–159269 bp and the length of LSC, SSC and IR were 85953–87172 bp, 18499–18712 bp, 26459–26756 bp, respectively. Palindromic and forward repeats accounted for a high proportion and the SSRs were mainly mononucleotide repeats in Pleione. Analysis of chloroplast sequence differences indicated that the differences in coding regions were smaller than those in non-coding regions, and the variation in LSC and SSC regions was greater than that in IR regions. Phylogenetic analysis showed that all Pleione species inferred from the cp genome were clustered together and received high support. However, the genetic relationship of Pleione plants is different from the current update system of this genus. Therefore, the demarcation of Pleione interspecific relationships still needs further investigation due to the lack of sufficient evidence. The cp genome serves as valuable information for the identification of Pleione species and the study of phylogenetic relationships.