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...陆生兰科植物是一类在遗传学上研究相对不足，但兼具文化与经济重要性的植物类群。兰亚族（Orchidinae）包含诸多物种，其块茎可食用，被用于制作统称‘沙勒普（salep）’的传统佳肴。东地中海与西亚地区的野生兰科植物遭过度采挖，已致使诸多物种濒临灭绝，但目前仍缺乏用于监测其贸易的高性价比工具。 # 数据来源：兰亚族-205（Orchidinae-205）：一款用于研究陆生兰科植物演化、分类学与贸易的全基因组定制化诱饵套装 https://doi.org/10.5061/dryad.sj3tx96bn 本研究开发了一款定制化靶向富集诱饵试剂盒，可针对兰亚族广义类群（Orchidinae s.l.）的系统发育基因组学研究需求，对205个全新遗传标记进行靶向富集与测序。其中31个标记的子集可捕获疑似参与葡甘聚糖（glucomannan）合成的基因——葡甘聚糖是一种水溶性多糖，赋予沙勒普独特的品质特性。我们针对该区域原产的73个分类群对该试剂盒进行了测试，结果显示无论物种种类如何，所有位点均能实现高效回收率，且测序总长度优于其他方案（原文截断）。 本数据集包含用于构建兰亚族-205（Orchidinae-205）定制化诱饵套装的相关文件，该套装可靶向捕获兰科（Orchidaceae）兰亚族专属的205个核基因组位点。此外，数据集还包含使用兰亚族-205探针对该族82个参考样本进行测序后得到的外显子与内含子序列。 ## 数据与文件结构说明 本数据集包含以下目录： - 转录组（TRANCRIPTOMES）：通过Trinity软件组装得到的23个兰亚科（Orchidoideae）物种过滤后转录组序列。肽序列（.pep文件）对应TransDecoder鉴定得到的推定开放阅读框的编码序列（.cds文件）。其中14个转录组被用于直系同源基因（orthologue）推断与探针设计。 - 靶标区域（TARGETS）：[原文未完成，tra...]