Li Zhen, De La Torre Amanda R, Sterck Lieven, Cánovas Francisco M, Avila Concepción, Merino Irene, Cabezas José Antonio, Cervera María Teresa, Ingvarsson Pär K, Van de Peer Yves
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
Center for Plant Systems Biology, VIB, Ghent, Belgium.
Genome Biol Evol. 2017 May 1;9(5):1130-1147. doi: 10.1093/gbe/evx070.
Phylogenetic relationships among seed plant taxa, especially within the gymnosperms, remain contested. In contrast to angiosperms, for which several genomic, transcriptomic and phylogenetic resources are available, there are few, if any, molecular markers that allow broad comparisons among gymnosperm species. With few gymnosperm genomes available, recently obtained transcriptomes in gymnosperms are a great addition to identifying single-copy gene families as molecular markers for phylogenomic analysis in seed plants. Taking advantage of an increasing number of available genomes and transcriptomes, we identified single-copy genes in a broad collection of seed plants and used these to infer phylogenetic relationships between major seed plant taxa. This study aims at extending the current phylogenetic toolkit for seed plants, assessing its ability for resolving seed plant phylogeny, and discussing potential factors affecting phylogenetic reconstruction. In total, we identified 3,072 single-copy genes in 31 gymnosperms and 2,156 single-copy genes in 34 angiosperms. All studied seed plants shared 1,469 single-copy genes, which are generally involved in functions like DNA metabolism, cell cycle, and photosynthesis. A selected set of 106 single-copy genes provided good resolution for the seed plant phylogeny except for gnetophytes. Although some of our analyses support a sister relationship between gnetophytes and other gymnosperms, phylogenetic trees from concatenated alignments without 3rd codon positions and amino acid alignments under the CAT + GTR model, support gnetophytes as a sister group to Pinaceae. Our phylogenomic analyses demonstrate that, in general, single-copy genes can uncover both recent and deep divergences of seed plant phylogeny.
种子植物类群之间的系统发育关系，尤其是裸子植物内部的关系，仍存在争议。与有多种基因组、转录组和系统发育资源的被子植物不同，几乎没有能用于裸子植物物种间广泛比较的分子标记。由于可用的裸子植物基因组很少，最近获得的裸子植物转录组对于识别单拷贝基因家族作为种子植物系统发育分析的分子标记是一个很大的补充。利用越来越多可用的基因组和转录组，我们在广泛的种子植物集合中鉴定出单拷贝基因，并利用这些基因推断主要种子植物类群之间的系统发育关系。本研究旨在扩展当前种子植物的系统发育工具包，评估其解决种子植物系统发育的能力，并讨论影响系统发育重建的潜在因素。我们总共在31种裸子植物中鉴定出3072个单拷贝基因，在34种被子植物中鉴定出2156个单拷贝基因。所有研究的种子植物共有1469个单拷贝基因，这些基因通常参与DNA代谢、细胞周期和光合作用等功能。一组选定的106个单拷贝基因为种子植物系统发育提供了良好的分辨率，但不包括买麻藤类植物。尽管我们的一些分析支持买麻藤类植物与其他裸子植物之间的姐妹关系，但在没有第三密码子位置的串联比对和CAT + GTR模型下的氨基酸比对构建的系统发育树支持买麻藤类植物作为松科的姐妹群。我们的系统发育基因组分析表明，一般来说，单拷贝基因可以揭示种子植物系统发育中近期和深层的分歧。
