Phylotranscriptomic analysis of the origin and early diversification of land plants
Phylotranscriptomic analysis of the origin and early diversification of land plants
复制标题
DOI：
10.1073/pnas.1323926111
复制
发表时间：
2014-11-11
影响因子：
11.1
通讯作者：
Leebens-Mack, James
中科院分区：
文献类型：
--
作者：
Wickett, Norman J.;Mirarab, Siavash;Leebens-Mack, James
重建陆地植物及其藻类亲属的起源和进化是植物遗传学中的一个基本问题，对于理解关键的适应性如何产生至关重要，包括胚胎，维管组织，种子和花。尽管在分子系统学的进展，一些假说的关系仍然弱解决。用快速多样化来推断深层次的遗传可能是有问题的;然而，基因组规模的数据应该会显著增加用于分析的信息特征的数量。最近的植物基因组重建的主要分歧，导致了有前途的，但不一致的结果。一个限制是稀疏的分类单元采样，可能是由于数据生成的困难和成本。为了解决这一限制，转录组数据的92链球菌分类群产生和分析沿着与11个已公布的植物基因组序列。使用多达852个核基因和1，701，170个比对位点进行系统发育重建。进行了69项分析，以测试系统发育推断的数据矩阵或序列遗传学方法的排列的鲁棒性，包括超矩阵，超树和基于聚结的方法，最大似然和贝叶斯方法，分区和未分区的分析，氨基酸与DNA比对。在其他结果中，我们发现强大的支持姐妹集团之间的关系陆地植物和一组链藻绿色藻类，Zygnematophyceae。一个分支，包括苔类和藓类的强有力的支持是不一致的早期陆地植物进化的一个被广泛接受的观点，并建议用于了解基本植物性状的进化系统发育假说应重新评估。
Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances inmolecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the datamatrix or to phylogeneticmethod, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.