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

Abstract

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.

Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms

“…After decades of efforts in phylogenetic reconstruction, evolutionary relationships of the main lineages of seed plants are still controversial. In particular, several alternative hypotheses regarding the phylogenetic placement of Gnetales have not been completely resolved (electronic supplementary material, figure S1) [1], although some phylogenomic analyses based on plastid genomes or multiple nuclear genes have been conducted [3,[9][10][11]16,18,41]. For instance, Lee et al [41] analysed 22 838 sets of orthogroups (ESTs) for 101 genera across land plants and placed Gnetales as sister to the rest of gymnosperms (bootstrap support greater than 95%), whereas the Gnepine hypothesis was supported by a coalescent analysis of 305 nuclear genes in Xi et al [16] and a supermatrix analysis of the first-and second-codon positions of 674 genes in Wickett et al [18], although the support values were not high or other hypotheses were not completely rejected.…”

Genomics of clinal local adaptation inPinus sylvestrisunder continuous environmental and spatial genetic setting

“…Bait design was based on a set of P. sylvestris transcripts described previously (Z. Li et al, 2017).…”

“…Bait design was based on a set of P. sylvestris transcripts described previously (Z. Li et al, 2017). Briefly transcriptomes of P. sylvestris were assembled from 454 read data derived from different developmental stages using the Newbler software (v2.8.1).…”

Utilization of tissue ploidy level variation inde novotranscriptome assembly ofPinus sylvestris

“…These were identified by self-blasting the SuperTranscripts. All SuperTranscripts that had blast hits within itself (other than the obvious 100% self-match) were identified as potential mosaics Additionally, in order to inspect the effect on commonly applied clustering procedures that are used to decrease the allelic redundancy of assembled transcriptomes, the Trinity assembly selected (TRINITY guided ) was clustered using CD-HIT-EST version 4.7 ((L. Fu et al, 2012;Weizhong Li & Godzik, 2006) with sequence identity cut-off (-c) 0.95, a commonly used threshold (Hodgins, Yeaman, Nurkowski, Rieseberg, & Aitken, 2016;Li et al, 2017;Wachowiak et al, 2015). The assemblies of P. sylvestris obtained using these two additional secondary clustering strategies are deposited in the NCBI TSA repository, under BioProject XXX.…”