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Research article - Peer-reviewed, 2017

Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants

Li, Zhen; De La Torre, Amanda R.; Sterck, Lieven; Canovas, Francisco M.; Avila, Concepcion; Merino, Irene; Antonio Cabezas, Jose; Teresa Cervera, Maria; Ingvarsson, Par K.; Van de Peer, Yves


Phylogenetic relationships among seed plant taxa, especially within the gymnosperms, remain contested. In contrast to angio-sperms, 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.


single-copy genes; gymnosperms; angiosperms; seed plants; phylogenomics

Published in

Genome Biology and Evolution
2017, volume: 9, number: 5, pages: 1130-1147

Authors' information

Li, Zhen
Flanders Institute for Biotechnology (VIB)
De La Torre, Amanda R.
University of California Davis (UC Davis)
Sterck, Lieven
Ghent University
Canovas, Francisco
University of Málaga
Avila, Concepción
University of Málaga
Swedish University of Agricultural Sciences, Department of Plant Biology
Cabezas, José Antonio
Cervera, María Teresa
Umeå University
Swedish University of Agricultural Sciences, Department of Plant Biology
Van de Peer, Yves
University of Pretoria

UKÄ Subject classification

Bioinformatics and Systems Biology

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