“…Similarly, monocotyledonous and dicotyledonous plants have their own independent and intersecting branches (Figure S6), which is consistent with previous research [3]. Interestingly, among widely expressed VQ genes, we found that four genes (GbVQ3, GbVQ12, GbVQ33, and GbVQ34) in Ginkgo biloba, one gene (TcVQ2) in Taxus chinensis, and three genes (PtVQ29, PtVQ30, and PtVQ58) in Pinus tabulaeformis were clustered with AtVQ14, AtVQ9, and AtVQ5 (Figure S6), which were reported as influencing seed development, mediating salinity stress responses, and regulating plant defense, respectively [5,22,26]; three genes (GbVQ26, GbVQ27, and GbVQ29) found in Ginkgo biloba, three genes (TcVQ13, TcVQ14, and TcVQ15) in Taxus chinensis, and three genes (PtVQ37, PtVQ38, and PtVQ39) in Pinus tabulaeformis were clustered with AtVQ22, AtVQ27, and AtVQ28 (Figure S6), which are related to plant defense and growth [18,48,49]. Among them, GbVQ29, TcVQ13, and PtVQ38 are the only VQ genes in the collinear block shared by these gymnosperms, which indicates that these genes have a very conservative, important role and status in seed plants.…”