The complete chloroplast genome sequences of four Liparis species (Orchidaceae) and phylogenetic implications

Liparis Richard (Malaxideae, Epidendroideae) is a large and diverse genus of the family Orchidaceae, the taxonomy of which is complicated and controversial. In this study, we sequenced, assembled and analyzed four complete chloroplast genomes of Liparis species including L. kumokiri, L. makinoana, L. pauliana, and L. viridiflora, and evaluated their phylogenetic relationships with related species for the first time. These four chloroplast genomes (size range 153,095 to 158,239 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 83,533-86,752 bp), a small single copy (SSC, 17,938-18,156 bp) and a pair of inverted repeats (IRs, 26,421-26,933 bp). The genomes contain 133 genes, including 87 protein coding genes, 38 tRNAs and 8 rRNA genes. The genome arrangements, gene contents, gene order, long repeats and simple sequence repeats were similar with small differences observed among these four chloroplast genomes. Five highly variable regions including ycf1, ndhA, ndhF, trnQ and trnK were identified from the comparative analysis with other nine related Liparis species, which had the potential to be used as DNA markers for species identification and phylogenetic studies of Liparis species. Phylogenetic analysis based on the complete chloroplast genome sequences strongly supported the polyphyly of Liparis and its further division into three branches. These results provided valuable information to illustrate the complicated taxonomy, phylogeny and evolution process of the Liparis genus.