Data from: Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events

• Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications.
• We assembled a dataset of transcriptomes and genomes from 169 species in Caryophyllales, of which 43 were newly generated for this study, representing one of the densest sampled genomic-scale datasets available. We carried out phylogenomic analyses using a modified phylome strategy to reconstruct the species tree. We mapped phylogenetic distribution of polyploidy events by both tree-based and distance-based methods, and explicitly tested scenarios for allopolyploidy.
• We identified twenty-six ancient and more recent polyploidy events distributed throughout Caryophyllales. Two of these events were inferred to be allopolyploidy.
• Through dense phylogenomic sampling, we show the propensity of polyploidy throughout the evolutionary history of Caryophyllales. We also provide a framework for utilizing transcriptome data to detect allopolyploidy, which is important as it may have different macro-evolutionary implications compared to autopolyploidy.

• 多倍化（polyploidy）的宏演化遗留效应研究受限于生命之树各分支中这类多倍化事件采样的不完整性。为更好地定位并解析这些事件，我们亟需兼具全面的分类群采样与可精准重构基因复制（gene duplications）事件频率与发生位置的同源性推断（homology inference）方法。
• 本研究组装了涵盖石竹目（Caryophyllales）169个物种的转录组（transcriptome）与基因组（genome）数据集，其中43套数据为本研究全新组装生成，是当前已公开的采样密度最高的基因组级数据集之一。我们采用改良后的phylome策略开展系统发育基因组学分析以重构物种树；同时通过基于树与基于距离的两种方法绘制多倍化事件的系统发育分布特征，并明确检验了异源多倍化（allopolyploidy）的各类演化场景。
• 本研究共鉴定出遍布石竹目各演化支的26处古老及新近发生的多倍化事件，其中2处被推断为异源多倍化事件。
• 依托高密度的系统发育基因组学采样，本研究揭示了多倍化在石竹目整个演化历史中的广泛发生倾向；同时我们还搭建了一套利用转录组数据检测异源多倍化的分析框架——鉴于异源多倍化与同源多倍化（autopolyploidy）可能存在迥异的宏演化效应，该框架具备重要的研究价值。