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,molecularmarkers
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 singlecopy
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 likeDNAmetabolism, cell cycle, and photosynthesis.Aselected 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 theCATþGTRmodel, 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.