Plastome Evolution and Comparative Analyses of a Recently Radiated Genus Vanda (Aeridinae, Orchidaceae)

<i>Vanda</i> R.Br. is an epiphytic orchid genus with significant horticultural and ornamental value. Previous molecular studies expanded <i>Vanda</i> including some members from five other genera. However, the interspecific relationships of this recently radiated genus have remained unclear based on several DNA markers until now. In this study, the complete plastome has been used to infer the phylogenetic relationships of <i>Vanda s.l</i>. The five newly obtained plastomes ranged from 146,340 bp to 149,273 bp in length, with a GC content ranging from 36.5% to 36.7%. The five plastomes contained 74 protein-coding genes (CDSs), 38 tRNAs, and 8 rRNAs, and their <i>ndh</i> genes underwent loss or pseudogenization. Comparative plastome analyses of 13 <i>Vanda</i> species revealed high conservation in terms of genome size, structure, and gene order, except for a large inversion from <i>trnG^GCC</i> to <i>ycf3</i> in <i>V. coerulea</i>. Moreover, six CDSs and five non-CDSs were selected as candidate DNA barcodes. Our phylogenetic analyses demonstrated that <i>Vanda s.l.</i> is a monophyletic group with high supporting values based on five different datasets (complete plastome with one IR, 68 CDSs, LSC, five hypervariable non-CDSs, and six hypervariable CDSs), while the phylogenetic relationships among species were fully resolved based on the complete plastome with one IR dataset. Our results confirmed that the complete plastome has a great power in resolving the phylogenetic relationships of recently radiated lineages.