Exploring the potential of Angiosperms353 markers for species identification of Eastern Mediterranean orchids

Tuberous orchids are ecologically vulnerable species, threatened by a range of environmental pressures such as overharvesting, grazing and land use change. Conservation efforts require accurate species identification, but are impeded by limited phylogenetic resolution of traditional genetic markers, which is exacerbated by widespread taxonomic conflict regarding the classification of orchids. Target enrichment holds promise to resolve both these challenges by offering a large set of nuclear loci with which to increase phylogenetic resolution and evaluate competing species models. Here, we evaluate the effectiveness of the Angiosperms353 markers for distinguishing over 50 tuberous orchid species native to Greece and we explore the possibility of narrowing these markers to a smaller set that could function as a minimal probe set. Our methodology consists of a three-tiered approach: 1) generating a species-level phylogeny using all Angiosperms353 loci with sufficient target recovery, ..., We collected 165 orchid samples representing 56 unique taxa in Greece, and sequenced these following targeted capture and enrichment with the Angiosperms353 baits. The recovered exon sequences were aligned and trimmed to generate gene trees for 335 out of 353 target genes. , , # Data from: Exploring the potential of Angiosperms353 markers for species identification of Eastern Mediterranean orchids

[https://doi.org/10.5061/dryad.qrfj6q5sb](https://doi.org/10.5061/dryad.qrfj6q5sb)

## Description of the data and file structure

This datasets contains the exons sequences, gene alignments and gene trees generated for 165 orchid samples through hybridisation capture and sequencing with the Angiosperms353 baits. The samples were collected in Greece and represent 56 taxa of the Greek native orchid flora. Target sequences were assembled bioinformatically with HybPiper (Johnson et al., 2016) by mapping sequencing reads against a custom reference file including CDS sequences of the 353 target loci from 7 different orchid transcriptomes (McLay et al., 2021) and building contigs with the mapped reads. The exons were used to create gene alignments for 148 out of 165 individuals with MAFFT (Katoh & Standley, 2013) and trimmed with TrimAL (Capella-Gutiérrez et al., 2009) p...,