Data from: Mining from transcriptomes: 315 single-copy orthologous genes concatenated for the phylogenetic analyses of Orchidaceae

Phylogenetic relationships are hotspots for orchid studies with
controversial standpoints. Traditionally, the phylogenies of orchids are
based on morphology and subjective factors. Although more reliable than
classic phylogenic analyses, the current methods are based on a few gene
markers and PCR amplification, which are labor intensive and cannot
identify the placement of some species with degenerated plastid genomes.
Therefore, a more efficient, labor-saving and reliable method is needed
for phylogenic analysis. Here, we present a method of orchid phylogeny
construction using transcriptomes. Ten representative species covering
five subfamilies of Orchidaceae were selected, and 315 single-copy
orthologous genes extracted from the transcriptomes of these organisms
were applied to reconstruct a more robust phylogeny of orchids. This
approach provided a rapid and reliable method of phylogeny construction
for Orchidaceae, one of the most diversified family of angiosperms. We
also showed the rigorous systematic position of holomycotrophic species,
which has previously been difficult to determine because of the
degenerated plastid genome. We concluded that the method presented in this
study is more efficient and reliable than methods based on a few gene
markers for phylogenic analyses, especially for the holomycotrophic
species or those whose DNA sequences have been difficult to amplify.
Meanwhile, a total of 315 single-copy orthologous genes of orchids are
offered and more informative loci could be used in the future orchid
phylogenetic studies.