RegioDiv: Genetic diversity of herbaceous plants in Germany: Pimpinella saxifraga

Autochthonous seed material of wild species for ecological restoration is produced in accordance with the rules of the German Regiosaatgut system in 22 seed zones (Bucharova et al. 2019, https://doi.org/10.1007/s10592-018-1067-6). The RegioDiv project analysed genetic diversity of more than 30 grassland plant species (grasses, legumes, non-legume herbs) in all seed zones to test how well seed zones represent genetic patterns. Data on spatial patterns of diversity will be used for practical recommendations for species management and seed zone design. We collected appr. 19,000 leaf samples from 28 taxa in 22 seed zones across Germany, which had been subdivided in 72 subregions. Additional samples were available from neighboring countries. In total 14,496 samples underwent ddRAD analysis following Peterson et al. (2012, https://doi.org/10.1371/journal.pone.0037135) using EcoRI and MspI as restriction enzymes and a selected fragment length of 350-450 bp. Each 1152 samples were sequenced per S4 lane of an Illumina Novaseq 6000 (PE150) with a volume of 2,500 Mio. Sequences, resulting in appr. 2 Mio. Sequences per individual sample. A total of 12,389 samples proved to have a sufficient number of DNA sequences for further analysis. In total 11,762 samples remained after excluding references samples and outgroup species for final data analysis. The number of samples originating in Germany in the final data sets ranged between 89 (Tragopogon orientalis) and 891 (Knautia arvensis), with a mean of 339. This project holds all samples used for Pimpinella saxifraga

用于生态修复的野生乡土种子材料，依据德国区域种子（Regiosaatgut）体系的规则，在22个种子区内完成生产（Bucharova等，2019，https://doi.org/10.1007/s10592-018-1067-6）。RegioDiv项目对全部22个种子区内的30余种草原植物类群（禾草、豆科植物、非豆科草本植物）的遗传多样性开展分析，以验证种子区能否有效表征遗传空间格局。相关多样性空间格局数据将为物种管理及种子区设计提供实操指导建议。

研究团队在覆盖全德国的22个种子区（细分为72个子区域）的28个分类群中，采集了约19000份叶片样本，另有邻国提供的额外样本可供使用。按照Peterson等（2012，https://doi.org/10.1371/journal.pone.0037135）的实验方案，使用限制性内切酶EcoRI与MspI，选取350-450 bp的片段长度，对总计14496份样本开展双酶切简化基因组测序（ddRAD）。每1152份样本在Illumina Novaseq 6000的S4测序泳道上进行双端150bp（PE150）测序，单次测序数据量达2500百万条序列，单份样本平均获得约200万条序列。

最终有12389份样本的DNA序列数量满足后续分析的准入标准。在剔除对照样本与外类群物种后，剩余11762份样本用于最终数据分析。最终数据集中源自德国的样本数量介于89份（Tragopogon orientalis）与891份（Knautia arvensis）之间，平均值为339份。本项目包含了用于Pimpinella saxifraga研究的全部样本。