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

[https://doi.org/10.5061/dryad.sj3tx96bn](https://doi.org/10.5061/dryad.sj3tx96bn)

This dataset contains the files used to generate the Orchdidinae-205 custom bait set for targeted capture of 205 nuclear genomic loci tailored to the Orchidinae subtribe of the Orchidaceae family. It also contains the exon and intron sequences that were recovered for 82 reference samples in the tribe using the Orchidinae-205 probes.

## Description of the data and file structure

The dataset consists of the following directories:

TRANCRIPTOMES: Filtered transcriptome assemblies for 23 Orchidoideae species, generated with Trinity. Peptide sequences (.pep files) correspond to the coding sequences (.cds files) of the putative open reading frames identified by TransDecoder.  14 of these transcriptomes were selected for orthologue inference and probe design.

TARGETS: tra...