Data from: From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

Background: Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have been useful for reconstructing the phylogeny of numerous clades of photosynthetic organisms (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome data. Results: We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa. Conclusions: Analyses of the plastid data recovered a strongly supported framework of relationships for green plants. This includes the placement of Zygnematophyceace as sister to land plants (Embryophyta) and a clade of extant gymnosperms (Acrogymnospermae) with cycads + Ginkgo sister to remaining members and with gnetophytes (Gnetophyta) sister to non-Pinaceae conifers (Gnecup trees); within the monilophyte clade (Monilophyta), relationships are strongly supported with Equisetales + Psilotales sister to Marattiales + leptosporangiate ferns. We also highlight the challenges of using plastid genome sequences in deep-level phylogenomic analyses and provide suggestions for future analyses that will likely incorporate plastid genome data for thousands of species. We particularly emphasize the importance of exploring the effects of different partitioning and character coding protocols for the entire data set as well as subsets of the data.背景：下一代测序技术为日益多样的绿色植物总界（Viridiplantae）类群提供了海量的质体基因组（plastid genome）序列数据。尽管此类数据已被成功用于重建众多光合生物演化支的系统发育关系（例如绿藻、被子植物（angiosperms）与裸子植物（gymnosperms）），但其用于解析整个绿色植物类群演化关系的效用仍不明确。绿色植物总界（Viridiplantae）起源于7亿至15亿年前，物种数量或可达50万种。该演化支是光合碳的主要来源之一，拥有极为丰富的生命形式多样性，涵盖了部分已知体型最小与最大的真核生物。本研究旨在探究利用现有完整或近乎完整的质体基因组数据，推断全面绿色植物系统发育的局限与挑战。 结果：我们从GenBank数据库中获取了360个不同绿色植物类群的完整或近乎完整质体基因组序列，并组装得到其中78个蛋白编码基因的序列数据。对质体基因组数据的系统发育分析不仅得到了支持度优异的主干演化关系，还为以往分析中未被检测到的绿色植物总界内多个主要亚支的演化关系提供了强有力的支持。不过，部分分析结果也存在系统误差的迹象。在若干案例中，基于核苷酸与氨基酸特征的分析得到了支持度较高但拓扑结构相互矛盾的结果；同时，不同类群间以及单个基因组内GC含量的显著差异，影响了部分类群的系统发育定位。 结论：对质体基因组数据的分析构建了支持度极高的绿色植物演化关系框架。其中包括：将双星藻科（Zygnematophyceace）定为陆生植物（Embryophyta）的姊妹群；将现存裸子植物演化支（Acrogymnospermae）划分为苏铁类+银杏类为其余类群的姊妹群，且买麻藤类（Gnetophyta）为非松科针叶树（Gnecup类群）的姊妹群；在蕨类植物演化支（Monilophyta）内，木贼目+松叶蕨目为观音座莲目+薄囊蕨类的姊妹群，该类群的演化关系得到了强有力的支持。本研究同时指出了在深度系统发育组学分析中使用质体基因组序列所面临的挑战，并为未来整合数千物种质体基因组数据的分析工作提供了建议。我们特别强调，需探究不同分区策略与特征编码方案对全数据集及数据子集的影响，这一点至关重要。