Resistance genes are groups of genes encoding proteins required for tolerance or immunity during plant adaptation to adverse external stress. Multiple environmental stresses have driven the molecular selection of these genes. Resistance gene clusters such as the NBS-LRR family are large and exhibit a high degree of functional differentiation (Shao et al., 2019). HSP and sHSP encode important heat-responsive proteins and molecular chaperones, and the copy number of sHSPs is significantly increased in polyploid plants with multiple branches. Genes from different subclasses may have diversified in function (Bondino et al., 2012). In contrast, the molecular chaperone gene PFDN, which displays only marginal differences between different groups, is expanded in polyploid plants such as soybean (Cao et al., 2016). Furthermore, the number of chilling injury-related gene (CRG) family members in Cruciferae is affected by polyploidy (Song et al., 2020). On the other hand, evolution of the AOX gene family is primarily mediated by intron/exon loss or gain, and fragment deletion, although gene loss and duplication, as well as tandem blocking, also play essential roles in the origin and maintenance of the family (Pu et al., 2015; Tables 1, 2; Figure 3).

Natural selection often drives the evolution of disease resistance-related genes to establish functional differentiation between these genes, with various external hazards leading to the vast expansion of the genes. For example, there are many structural variations in the leucine-rich repeat receptor-like kinase (LRR-RLK) gene family (Man et al., 2020). The resistance I genes from the NBS-LRR superfamily originated from Chlorophyta (green algae) and were classified into five categories according to their structural characteristics [Chlorophyta: RNL; Charophyta: CNL; Embryophyta (land plants): TNL, HNL, and PNL] (Shao et al., 2019). NLR genes (CNL, TNL) are clearly classified as being found in Solanaceae species; however, their prevalence varies markedly, with few reported within the genome of tomato plants and many more in those of potatoes and peppers (Borrelli et al., 2018). Another example is offered by the evolution of the AGO gene family, which encodes proteins associated with antiviral activity. This family may have experienced 133–143 repeat events and 272–299 loss events, including five major repeats. Specifically, the differentiation of green algae may have formed four major branches (I: 1/10, II: 5, III: 4/6/8/9, IV: 2/3/7) of the AGO gene family (Singh et al., 2015). Similarly, the DRB gene family is divided into two branches based on differences in the number of double-stranded RNA binding motifs (dsRBM); the number of DRB proteins also varies among different species (Clavel et al., 2016). The plant RDR (RNA-dependent RNA enzyme) family originated from copies of three monophyletic genes, RDRα, RDRβ, and RDRγ, and was dependent on species divergence (Zong et al., 2009). Plant DCL (Dicer-like), however, followed the evolutionary traces of early plant evolution through independent replication, remodeling its RNA binding pocket in response to virus resistance (Mukherjee et al., 2013). Finally, expansion of the TLP gene family in green algae (1), mosses (6), and angiosperms (>20), may be based on tandem and segmental duplication events (Cao et al., 2016; Tables 1, 2; Figure 3).

Transcription factors function as regulatory elements of various plant processes, including growth, the stress response, and reproduction (Yang et al., 2008; Lian et al., 2014; Zhao et al., 2014; Finet et al., 2016; Vasco et al., 2016; Feng et al., 2017; Wu et al., 2017; Naramoto et al., 2020). Due to the rich evolutionary history of plants, TF gene families tend to have more members and a higher degree of functional differentiation compared with structural protein-related coding genes (Finet et al., 2016). In particular, the AHL gene family, which is related to plant growth and development, may have evolved from the fusion of algal PPC structural proteins and AT-hook motifs, and is thought to have originated in bryophytes. This family can be divided into three groups (A: I; B: II, III), with a high degree of gene loss and numerous duplication events throughout evolution (Zhao et al., 2014). The WOX gene family, which is involved in cell division, originated in green algae and is primarily divided into nine classes (WOX1/2, WOX5/7, WOX3, WOX4, WOX6, WOX11/12, WOX13, and WUS) with WOX13 being recognized as the oldest branch. Indeed, WOX genes exhibit significant variation in their motifs and number of members throughout their evolutionary process (Lian et al., 2014). CPP-like genes, which are associated with plant development, are divided into four branches: Gene deletion and species-specific amplification have been important in expanding this gene family, while positive selection has served as the primary evolutionary driving force (Yang et al., 2008).

The SPL/SBP family mainly includes nine subbranches, among which there are obvious evolutionary differences; their formation may be completed before the differentiation of the angiosperms (Preston and Hileman, 2013). The nine evolutionary branches, namely, SPL evolutionary branch-I, evolutionary branch-II, evolutionary branch-IV, evolutionary branch-V, evolutionary branch-VI, evolutionary branch-VII, evolutionary branch-VIII, and evolutionary branch-IX, are characterized by differences in function and altered mi RNA regulatory differences (Preston and Hileman, 2013). The TCP gene family consists of two main classes (classes I and II, i.e.: the CIN and CYC/TB1 evolutionary branches) (Liu et al., 2019). Among them, all land plants have CIN evolutionary branch TCP genes, while CYC evolutionary branch genes are only found in true dicotyledons and monocotyledons (Liu et al., 2019). In addition, the rapid expansion of the TCP gene family is consistent with a polyploidy trend in land plants, with fewer tandem duplication events (Liu et al., 2019). 3R-MYB is a regulatory TF associated with drought-resistance and development. Its structure is progressively more complex in different species groups, in conjunction with a gradual increase in the number of gene family members, forming three branches (A, B, and C3) in angiosperms (Feng et al., 2017). The family of ALOG genes, which regulate reproductive growth, originated in green algae and expanded significantly in angiosperms (Naramoto et al., 2020). The YABBY and C3HDZ gene families, associated with leaf growth, have evolved in stages of biological evolution and their molecular structures have given rise to several major branches with different molecular classes exerting unique effects on leaf development (Finet et al., 2016; Vasco et al., 2016).

Moreover, the MADS and AUX/IAA gene families originated in early land plants (mosses) and expanded to encompass multiple gene sub-family classes that have shown rich functional differentiation with multiple rounds of evolutionary events (Theissen et al., 2016; Wu et al., 2017). Specifically, the MADS domains in plants originated from the transformation of topoisomerase IIA subunit A (TOPOIIA-A) into MRCA and the latter’s subsequent modification to SRF-like and MEF2-like MADS-box genes. Furthermore, in angiosperms, type II MADS-box genes mediate major evolutionary innovations in plant flowers, ovules and fruits, whereas the formation of the Mγ and interacting Mα genes (Mα*) of type I MADS-box can be traced back to the angiosperm ancestor and may be related to its heterodimeric function in angiosperm-specific embryonic trophoblast endosperm tissue (Qiu and Claudia, 2021). This evolutionary process was affected by various events, including replication and functional differentiation, resulting in the functional diversity of their regulatory properties (Ng and Yanofsky, 2001; Gramzow et al., 2010; Airoldi and Davies, 2012; Theissen et al., 2016; Schilling et al., 2020; Hsu et al., 2021; Tables 1, 2; Figure 3).

Metabolites are a direct manifestation of plant physiology. Highly specific biochemical processes that produce various metabolites have driven the formation and functional specialization of metabolic gene clusters (Duplais et al., 2020). Studies investigating the recurring events that led to the development of plant metabolic enzyme gene clusters have revealed a close relationship among the different metabolites (Duplais et al., 2020). The CYP/P450 gene family of mono-oxygenases is highly abundant in angiosperms, possibly due to multiple repeated events (polyploidy, tandem replication, and fragment repeat). They can be divided into two categories, A-type (e.g., CYP71) and non-A-type (e.g., CYP51, CYP72, CYP74, CYP85, CYP86, CYP97, CYP710, CYP711, CYP727, and CYP746), with CYP51 and CYP97 potentially representing the oldest clades (Su et al., 2021). The ACO gene families associated with respiration were almost lost early in the evolutionary path; however, they subsequently expanded and currently exist as large, functionally distinct subclasses (Wang et al., 2016; Tables 1, 2; Figure 3).

The OPR gene family of jasmonic acid biosynthesis-related enzymes doubled in number during the evolution of algae to land plants and further expanded via polyploidization and tandem duplication events. This gene family comprises seven categories. All OPR genes from green algae form subclade VII, subclade VI (present only in lower land plants), and subclade II (present in all land plants except the gymnosperm Picea sitchensis); subclade I is composed of gymnosperm and angiosperm sequences. Only monocotyledon sequences comprise subbranches III, IV, and V. The OPR gene family is particularly abundant in rice and sorghum (13 genes) (Li et al., 2009).

The HMGR gene family is associated with terpene biosynthesis and originated from bryophytes. It has only expanded in maize, soybean, cotton, and poplar, with each species containing five HMGR genes (sporophyte-specific branch, monocotyledon-specific branch HMGR III/IV, and dicotyledon-specific branch HMGR I/II) with different conserved sequences (Li et al., 2014).

The KCS gene family, which is involved in ultra-long-chain fatty acid synthesis, is divided into five main sub-clades (A, B, C, D, and E) with the number of genes in this family gradually increasing from one in algae to eleven in angiosperms, and with an apparent trend in the expansion of related polyploid species (Little et al., 2018).

Proteins with roles in cell wall formation and other aspects of cell structure are important for plant morphogenesis and can have basic enzymatic reactions. These proteins tend to have a low probability of gene loss, but they can accumulate a high degree of functional differentiation throughout a long evolutionary process, as observed within the CesA family of cellulose synthases (Little et al., 2018). The PSBP gene, encoding the light-harvesting protein complex PSII, only exists in the green plants of polymorphic biological groups that consist of few members with obvious structural differences (Ifuku et al., 2008). Cell cycle-related Cyc genes are divided into ten branches, most of which existed before green algae and became widely expanded during the transition to angiosperms (Boscolo-Galazzo et al., 2021). DLC genes associated with the dynein system are derived from DLC-VIII genes of green algae. With the gradual expansion of DLC genes along the evolutionary path, each plant type produced unique molecules (e.g., algae: DLC-VIII, bryophyte: DLC-VII, fern: DLC-IV, monocotyledon: DLC-I/II, dicotyledon: II/V), with a common branch in seed plants (DLC-VI) (Cao et al., 2017). The actin-associated Myo gene produces Myo-XI (A) in green algae and gradually extends into ten branches (Peremyslov et al., 2011). The aquaporin-encoding gene AQP developed from the LIPS type gene in green algae and gradually diverged into eight significantly different AQP genes (GIPS, LIPS, HIPS, XIPS, SIPS, PIPS, TIPS, and NIPS) in various plants, including soybean, upland cotton, and oilseed rape (Hussain et al., 2020). The RNA splice component NSR/RBP was slightly extended in soybean but contained differences in its conserved motifs (Lucero et al., 2020; Tables 1, 2; Figure 3).

The SH3P gene family, associated with cell plate formation, may have originated from the SH3P1-like ancestor of Charophyta and gradually expanded during the transition to mosses and angiosperms (Forero and Cvrckova, 2019). The cellulose synthase superfamily CesA, associated with cell wall formation, developed several branches among different species (CSLA and its developed branches CSLC and CESA, CSLB/H and its developed branches CSLF, CSLJ/M, CSLG, and CSLE). Moreover, the different subfamilies exhibit obvious selection for sugar synthesis. For example, certain members of the CSLJ subfamily may mediate (1, 3;1, 4)-β-glucan biosynthesis (Little et al., 2018). The FT/TFLL gene family, associated with flowering time, developed from MFT-like in angiosperms and contains several members (6) (Jin et al., 2021). The OFP gene family, associated with fruit shape, may have originated from the ancestors of land plants. Different species have varying numbers of these genes, which have been divided into 11 classes, due to numerous copy-number loss events (Liu et al., 2014). HAM gene families associated with tissue formation were generated from bryophytes and exhibit several molecular differences among different plant classes, where each family formed one branch. These gene families expanded in seed plants and ultimately evolved into two angiosperm branches (Type-I and Type-II) (Geng et al., 2021; Tables 1, 2; Figure 3).

Studies on signal transduction-related gene families showed that the number of PAB gene families, which are involved in promoting mRNA stability and protein translation, varies significantly among different groups. These gene families are divided into three groups (Class I: PAB1/PAB3/PAB5, Class II: PAB2/PAB4/PAB8, and Class III: PAB6/PAB7); however, their individual evolutionary routes remain unknown (Gallie and Liu, 2014). In seed plants, small peptide signal-related CEP gene families may have significantly expanded via WGD, especially in the Gramineae and Solanaceae (Ogilvie et al., 2014). The CNGC gene family, which act in calcium-gating, are divided into five classes (Groups I, II, III, IVA, and IVB), and the number of members within each class varies considerably (Saand et al., 2015). Auxin response factors are classified into three classes and seven groups (Class A: ARF5/7, ARF6/8; Class B: ARF1, ARF2, ARF3/4, ARF9; and Class C: ARF10/16/17) and were formed through the evolution of three bryophyte proteins (Finet et al., 2013). The alkalization factor RALF genes are divided into ten classes and may have developed from two primitive ancestors (Cao and Shi, 2012; Tables 1, 2; Figure 3).

The number of CBL, CIPK, CDPK, and CRK gene members associated with calcium signaling differs significantly across evolutionary stages (during the transition from lower plants to core angiosperms), and this phenomenon may be due to the abundant occurrence of WGD events and gene loss at these evolutionary stages. These polyploidy events then promoted the functional differentiation of corresponding proteins (Xiao et al., 2017; Zhang X. X. et al., 2020). Although only two PEBP genes, which are bind phospholipids and have roles in signal transduction, have been characterized in gymnosperms, they are particularly abundant in angiosperms, and their secondary expansion appears to be related to the formation of seed plants and angiosperms (Hedman et al., 2009; Karlgren et al., 2011). GPAT genes, which are associated with glycerol 3-phosphate biosynthesis, emerged earlier than those present in green algae, from which GPAT and GPAT9 developed into several GPAT genes in land plants (Waschburger et al., 2018; Tables 1, 2; Figure 3).

During evolution, other plant gene families have generated a high number of members with functional differentiation. In the salt or nutrient signaling pathways, the phosphorus transporter-encoding gene (PHO) contains obvious differences in copy number [from 0/1 when developed in green algae to two gradually more complex branches (C-1 and C-2) in land plants], protein structure, and number of introns (He et al., 2013). The ion transduction VP gene is divided into two branches, II and I, which originated from red algae and green algae, respectively. These branches were affected by polyploidy and were expanded in angiosperms (Zhang Y. M. et al., 2020). The plant ferritin Fer gene was already present in red algae and marginally increased in copy number in the later clades. Notably, the Fer gene of the monocotyledonous plant Lycoris aurea (Asparagales) appears more comparable to that of dicotyledonous plants (Strozycki et al., 2010). VIT genes encoding iron transporters consist of five ancient branches; however, two duplication events and six loss events led to substantial contraction of non-angiosperm VIT genes, and a subsequent expansion in copy number in angiosperms (Cao, 2019). Meanwhile, there is no significant difference in the number of methionine biosynthesis-related gene family (CIMS) members among green plants; however, multiple gene loss and gene duplication events occurred. In addition, WGT (wide-genome triploidy) led to the expansion of CIMS genes in soybean and alfalfa (Rody and de Oliveira, 2018; Tables 1, 2; Figure 3).

There has been obvious expansion and gene loss of the β-glucohydrolase (BAM) gene in different groups of hydrolases, which were divided into eight branches (Bam1, Bam10, Bam3, Bam4, Bam9, Bam5/6, Bam2/7, and Bam8) that existed before the formation of land plants. However, significant gene losses have occurred in basal land plants (Thalmann et al., 2019). The SUS gene family, which is involved in glycolysis, can be divided into three groups containing members that may have developed from WGD and that have also undergone obvious expansion in certain higher plants (Xu et al., 2019). Among the genes related to epigenetic factors, the methylation-related HMT family has two branches (Class 1 and Class 2) in land plants, especially in seed plants, indicating that the HMT genes underwent two separate functional differentiation events (Zhao et al., 2018). The ubiquitin-related FBP family that originated in green algae has undergone significant expansion in lower plants, monocotyledons, and dicotyledons, such as Brassicaceae (Navarro-Quezada et al., 2013; Tables 1, 2; Figure 3).