Fig 1.
Experimental design: flowchart of analytic phases followed to perform the analysis.
Table 1.
Number of genes observed for each species analysed.
Table 2.
Number of genes observed for each species analysed after the results of systematic review.
Table 3.
Number of genes for conifers and angiosperms trees divided according to their response to a specific abiotic stress. The last column shows the number of genes shared between broadleaves and conifers, subdivided according to their response to a specific abiotic stress.
Fig 2.
Graphical analysis performed using Venn diagrams. The Venn diagram shows the number of genes belonging to the conifer taxonomic group (blue ensemble) and the angiosperms taxonomic group (red ensemble). The insertion between the two sets represents the number of genes found in common between the two taxonomic groups. The analysis is related to the totality of genes observed (a) and grouped by individual stresses (b-e), drought, salt, heat, cold, and frost, respectively. Figure also shows (f) a histogram representing the absolute frequencies of genes divided by taxonomic groups, shared genes and abiotic stresses studied. Species-specific Venn diagram are reported in S1 File.
Fig 3.
Phylogenetic tree obtained from a partitioned supermatrix-based ML methods regarding the analysis of 264 orthogroups and 13 species distributed between two main seed plant lineages (angiosperms species in green and conifers in blue, with Ginkgo biloba L. as outgroup, in black) inferred by various R packages. Double red sign stands for bootstrap supporting of 100%. Otherwise, the percentage of bootstrap supporting is reported. The choice of the substitution model was carried out by using the ModelTest function of the R package Phangorn. Results of the model testing can be found in S4 Table).
Table 4.
Gene and site concordance summary for phylogenetic branches. Branch-specific mean gene concordance factors (mean_gCF) and site concordance factors (mean_sCF) are reported, along with the percentage of genes with gCF > 50% (). Gene discordance factors (gDF1, gDF2, gDFP) indicate the proportion of loci supporting alternative topologies.
Fig 4.
Boxplot showing gene concordance and discordance (a) for the set of orthologous loci used in the phylogenetic inference, and the resulting concatenated phylogenetic tree (b).
Table 5.
Substitution rates in conifer protein-coding genes compared to angiosperms species protein-coding genes. Mean genetic distances at synonymous (Ks) and non-synonymous (Ka) sites are expressed as a number of substitutions per site.
Fig 5.
Distribution of evolutionary estimates for conifer and angiosperms protein-coding genes. (a). Smoothed density plots of Ks estimates. (b). Smoothed density plot of Ka estimates. (c). Histogram plots of Ka/Ks estimates.