DOI: 10.5061/dryad.sj3tx96bn
title: Data from: Orchidinae-205: A new genome-wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids

description: 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.
description: # 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: transcripts of selected orthogroups in the 14 Orchidinae species used for probe design, identified with OrthoFinder. These transcripts were used as a reference file for read assembly to recover target sequences after targeted capture and sequencing. CAPTURE: exon and intron sequences assembled for 82 Orchidinae samples following targeted capture and sequencing, generated with HybPiper. The exons were used to generate alignments and phylogenetic trees. ## Sharing/Access information The raw reads used to assemble the transcriptomes were retrieved from the Sequence Read Archive under the respective project numbers listed in their file names. The raw reads used to assemble the exon sequences are deposited in the Sequence Read Archive under project number PRJNA1053613.