Data from: Orchidinae-205: A new genome-wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids

Terrestrial orchids are a group of genetically understudied, yet
culturally and economically important plants. The Orchidinae tribe
contains many species that produce edible tubers that are used for the
production of traditional delicacies collectively called ‘salep’.
Overexploitation of wild orchids in the Eastern Mediterranean and Western
Asia threatens to drive many of these species to extinction, but
cost-effective tools for monitoring their trade are currently lacking.
Here we present a custom bait kit for target enrichment and sequencing of
205 novel genetic markers that are tailored to phylogenomic applications
in Orchidinae s.l. A subset of 31 markers capture genes putatively
involved in the production of glucomannan, a water-soluble polysaccharide
that gives salep its distinctive properties. We tested the kit on 73 taxa
native to the area, demonstrating universally high locus recovery
irrespective of species identity, that exceeds the total sequence length
obtained with alternative kits currently available. Phylogenetic inference
with concatenation and coalescent approaches was robust and showed high
levels of support for most clades, including some which were previously
unresolved. Resolution for hybridizing and recently radiated and lineages
remains difficult, but could be further improved by analysing multiple
haplotypes and the non-exonic sequences captured by our kit, with the
promise to shed new light on the evolution of enigmatic taxa with a
complex speciation history. Offering a step-up from traditional barcoding
and universal markers, the genome-wide custom loci targeted by
Orchidinae-205 are a valuable new resource to study the evolution,
systematics and trade of terrestrial orchids.