Less is more in herbarium-inclusive molecular ecology

This dataset relates to the manuscript entitled "Less is more in herbarium-inclusive molecular ecology: Universal kits capture considerable intraspecific variation", available as a pre-print at BioRXiv: ... The study describes a critical comparison between customised and universal approaches of target capture sequencing in herbarium genomics below the species level. A target capture sequencing tool (Hyb-Seq) was designed for genotyping apomictic clonal lineages of dandelions (Taraxacum officinale), where loci from three approaches were included: A) loci from a previous genotyping-by-sequencing (GBS) study on Taraxacum; B) genes custom selected based on evolutionary adaptive potential; C) loci from universal kits (Angiosperms-353 and Compositae-1061). The genotyping accuracy of these different sets of loci was tested on a set of five apomictic clonal lineages (ACLs) of Taraxacum officinale, including several members with the same multi-locus microsatellite genotype. This dataset comprises important background information to the accessions used in the study, the design of the target capture sequencing tool, scripts and bioinformatic pipelines used in the design of the tool and the analysis of the pilot dataset, and detailed results that were used in the production of the manuscript. Contents: Details of the design of the target capture tool for Taraxacum officinale Pipeline for selecting loci Bioinformatic logbooks detailing the process for the selection and curation of loci to be included in the tool Final design of the tool (an overview of the loci; fasta file with sequences of all the baits) Python scripts to make BED files to split genes into introns and exons Final reference sequences (for sequence read mapping purposes) for all different categories of loci Accession information, for samples used in the generation of the pilot dataset Detailed GPS coordinates for all samples and R script for producing the distribution map in the manuscript Details of the library preparation procedure for the generation of the pilot dataset Details of the bioinformatic analysis of the pilot dataset Results of the MapDamage analysis to check for DNA damage patterns (fragmentation and deamination) in all samples Shell and R scripts detailing the steps performed in the bioinformatic analysis Trimming and filtering of low-quality reads Mapping sequence reads to reference Variant calling & filtering, and counting Analysis of Molecular Variance (AMOVA) Principal Component Analysis (PCA) Genetic distance calculations Results of the sequencing and read mapping Results of the AMOVA, PCA and genetic distance calculations Abstract for the study: Target capture sequencing has enhanced the study of plant evolution and molecular ecology, particularly through the access to degraded DNA from herbarium specimens. Universal “off-the-shelf” kits, such as Angiosperms-353, are cheap and readily available but are considered to expose insufficient variation below the species level. However, this remains to be tested in a direct comparison with customised approaches below the species level. In this study, near-identical genotypes from both herbarium and fresh material of the common dandelion (apomictic lineages in Taraxacum officinale F.H.Wigg.) are characterised with customised and universal approaches of target capture sequencing. An RNA-bait panel was designed to capture (i) highly variable loci normally obtained with a Genotyping-by-Sequencing (GBS) approach customised for dandelions; (ii) custom selected genes with potential for environmental adaptation, likely to harbour intraspecific genetic variation; (iii) conserved exons from universal kits (Angiosperms-353; Compositae-COS). Although exons from universal kits yield considerably less intraspecific genetic variation than both customised approaches, they still provided sufficient genetic variation to discriminate between near-identical genotypes of the same apomictic lineage. Given that universal kits save time, money, and the need for genomic reference data, this approach is recommended to increase the number of samples under budgetary constraints while still capturing considerable levels of intraspecific genetic variation.本数据集关联一篇题为《包含标本馆样本的分子生态学研究中“少即是多”：通用捕获试剂盒可捕获可观的种内变异》的手稿，该手稿以预印本形式发布于BioRXiv平台：…… 本研究针对物种级别以下的标本馆基因组学研究，开展了定制化与通用型靶标捕获测序（target capture sequencing）策略的关键性对比。本研究开发了一款靶标捕获测序工具（Hyb-Seq），用于对蒲公英（Taraxacum officinale）的无融合生殖克隆谱系进行基因分型。该工具涵盖三类来源的基因座：A）既往针对蒲公英开展的测序分型（genotyping-by-sequencing, GBS）研究中使用的基因座；B）基于进化适应潜力定制筛选的基因；C）通用捕获试剂盒（Angiosperms-353与Compositae-1061）对应的基因座。 我们以5个西洋蒲公英无融合生殖克隆谱系（ACLs）为测试对象，验证了不同基因座集的基因分型准确性，其中部分样本拥有完全一致的多位点微卫星基因型。本数据集包含研究中所用种质样本的重要背景信息、靶标捕获测序工具的设计细节、工具开发与试点数据集分析过程中使用的脚本及生物信息学流程，以及手稿撰写所用的详细实验结果。 内容清单： 西洋蒲公英靶标捕获工具的设计细节 基因座筛选流程 记录工具所用基因座筛选与整理全流程的生物信息学日志 工具最终设计方案（含基因座概览、所有捕获探针序列的FASTA文件） 用于生成BED文件以拆分基因内含子与外显子的Python脚本 所有类别基因座的最终参考序列（用于序列读段比对） 试点数据集生成所用样本的种质信息 所有样本的精确GPS坐标，以及手稿中分布地图生成所用的R脚本 试点数据集生成所用的文库制备流程细节 试点数据集的生物信息学分析细节 所有样本的DNA损伤模式（片段化与脱氨基作用）检测结果（MapDamage分析结果） 详述生物信息学分析全流程的Shell与R脚本，涵盖以下分析步骤： 低质量读段的修剪与过滤 序列读段与参考序列的比对 变异检测与过滤及计数 分子方差分析（Analysis of Molecular Variance, AMOVA） 主成分分析（Principal Component Analysis, PCA） 遗传距离计算 测序与读段比对结果 分子方差分析、主成分分析及遗传距离计算结果 本研究的摘要： 靶标捕获测序技术推动了植物进化与分子生态学研究的发展，尤其为获取标本馆样本中的降解DNA提供了可能。通用型“现成”捕获试剂盒（如Angiosperms-353）虽成本低廉且易于获取，但被认为在物种级别以下的变异检测中灵敏度不足。然而，这一观点尚未在物种级别以下与定制化策略的直接对比中得到验证。 本研究采用定制化与通用型靶标捕获测序策略，对普通蒲公英（Taraxacum officinale F.H.Wigg.）的标本馆样本与新鲜样本中的近一致基因型进行了表征。本研究设计了一款RNA诱饵面板，用于捕获三类靶标：(i) 针对蒲公英定制的测序分型（GBS）策略通常获得的高变异基因座；(ii) 基于环境适应潜力筛选的、大概率携带种内遗传变异的定制基因；(iii) 通用试剂盒（Angiosperms-353与Compositae-COS）中的保守外显子。 尽管通用试剂盒的外显子所产生的种内遗传变异远少于两种定制化策略，但仍足以区分同一无融合生殖谱系内的近一致基因型。鉴于通用试剂盒可节省时间与成本，且无需依赖基因组参考数据，本研究推荐在预算有限的情况下采用该策略，以在捕获可观种内遗传变异的同时扩大样本量。