Complete Chloroplast Genomes and Comparative Analyses of Three Paraphalaenopsis (Aeridinae, Orchidaceae) Species

Abstract

<i>Paraphalaenopsis</i>, a genus of perennial herbs from the family Orchidaceae, contains a number of ornamental species. However, there is no information on the chloroplast genomes of <i>Paraphalaenopsis</i>, which limits our studies of this genus. In this study, we reported the chloroplast genomes of three species of <i>Paraphalaenopsis</i> (<i>P. labukensis</i>, <i>P. denevel</i>, and <i>P. laycockii</i> 'Semi-alba') and performed comprehensive comparative analysis. These three chloroplast genomes showed a typical quadripartile structure. Their lengths ranged from 147,311 bp to 149,240 bp. Each genome contained 120 unique genes, including 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Comparative analysis revealed major differences in sequence divergence in the three chloroplast genomes. In addition, six hypervariable regions were identified (<i>psbM-trnD^GUC</i>, <i>psbB</i>, <i>ccsA</i>, <i>trnK^UUU</i>, <i>trnS^GCU-trnG^UCC</i>, <i>rps16-trnQ^UUG</i>) that can be used as DNA molecular markers. Phylogenetic relationships were determined using the chloroplast genomes of 28 species from 12 genera of Aeridinae. Results suggested that <i>Paraphalaenopsis</i> was a clade of Aeridinae that was sister to the <i>Holcoglossum-Vanda</i> clade, with 100% bootstrap support within Aeridinae. The findings of this study provided the foundation for future studies on the phylogenetic analysis of Aeridinae.