Comparative analysis of six new chloroplast genomes in Platanthera (Orchidaceae) enhances understanding of its diversification

Platanthera is among the most diverse genera of orchids in north temperate regions, with high species diversity in Asia and North America. Despite many ecological studies in this group, little is known about its genomic diversity. Here, we report the newly annotated chloroplast genomes from six species in subgenus Limnorchis from North America and compare them with plastomes published for Platanthera species from Asia and Europe. We found that the plastomes of species in subg. Limnorchis are among the smallest reported for Platanthera thus far. While major structural differences were not detected in the newly sequenced species, ndh genes were frequently absent or contained internal stop codons, suggesting their lack of functionality in subg. Limnorchis but not in other species of Platanthera. Numerous SSRs, primarily A/T repeats, were detected across the six species, and patterns of codon usage varied little among species. Phylogenetic analysis indicated strong support for monophyly of recognized subgenera, as well as consistency with patterns suggested from nuclear loci in subg. Limnorchis. The new plastome sequences contribute to greater understanding of genome variation in relation to diversification of Platanthera and will be useful for phylogenetic analysis.