Data from: Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid

PREMISE OF THE STUDY: We explored the phylogenetic utility of entire plastid DNA sequences in Daucus and compared the results with prior phylogenetic results using plastid and nuclear DNA sequences. METHODS: We used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20 Daucus taxa and outgroups, analyzed the data with phylogenetic methods, and examined evidence for mitochondrial DNA transfer to the plastid (DcMP). KEY RESULTS: Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. Subsets of the data, including regions traditionally used as phylogenetically informative regions, provide various degrees of soft congruence with the entire data set. There are areas of hard incongruence, however, with phylogenies using nuclear data. We extended knowledge of a mitochondrial to plastid DNA insertion sequence previously named DcMP and identified the first instance in flowering plants of a sequence of potential nuclear genome origin inserted into the plastid genome. There is a relationship of inverted repeat junction classes and repeat DNA to phylogeny, but no such relationship with nonsynonymous mutations. CONCLUSIONS: Our data have allowed us to (1) produce a well-resolved plastid phylogeny of Daucus, (2) evaluate subsets of the entire plastid data for phylogeny, (3) examine evidence for plastid and nuclear DNA phylogenetic incongruence, and (4) examine mitochondrial and nuclear DNA insertion into the plastid.研究背景：本研究探讨了完整质体DNA（plastid DNA）序列在胡萝卜属（Daucus）中的系统发育应用价值，并将本研究结果与此前基于质体DNA及核DNA（nuclear DNA）序列获得的系统发育研究结果进行了对比。 研究方法：本研究采用Illumina测序技术，获取了20个胡萝卜属类群的37份种质样品及外类群（outgroups）的完整质体基因组序列；使用系统发育分析方法对数据进行解析，并检测了线粒体DNA（mitochondrial DNA）向质体转移的序列（DcMP）的相关证据。 主要研究结果：本研究基于全数据集构建的系统发育树分辨率极高，绝大多数外部演化支（external clades）及多数内部演化支（internal clades）的自举支持率（bootstrap support）均为100%，仅胡萝卜（D. carota）及其近缘物种D. syrticus所构成的演化支除外。本研究数据的子集（包含传统上被用作系统发育信息区域的序列区段）与全数据集呈现出不同程度的软一致性（soft congruence），但与基于核DNA数据构建的系统发育树存在显著的硬不一致性（hard incongruence）。本研究拓展了此前命名为DcMP的线粒体-质体DNA插入序列的认知范围，并首次在被子植物（flowering plants）中发现了一段潜在源自核基因组（nuclear genome）的序列插入至质体基因组（plastid genome）的案例。此外，反向重复边界（inverted repeat junction）类型与重复序列与系统发育树拓扑结构存在相关性，但非同义突变（nonsynonymous mutations）与系统发育树之间并无此类关联。 结论：本研究的数据助力我们完成了以下四项工作：（1）构建了分辨率良好的胡萝卜属质体系统发育树；（2）评估了全质体数据子集的系统发育应用潜力；（3）检测了质体与核DNA系统发育不一致性的相关证据；（4）探究了线粒体及核DNA向质体基因组插入的相关现象。