1. Introduction

Photosynthesis is a fundamental process that converts solar energy into chemical energy, thereby supporting life on Earth. It not only provides essential materials for growth, development, and reproduction, but also sustains energy flow and material cycling in both aquatic and terrestrial ecosystems (Jiang et al., 2014; Neilson and Durnford, 2010a). Photosystem (including light-harvesting complex and reaction center) serves as the core functional unit to absorb, convert, and transfer light energy through a series of complex electron transfer reactions (Buchel, 2015; Chmeliov et al., 2016; Chukhutsina et al., 2020). The primary endosymbiotic event, wherein a eukaryotic host cell engulfed a cyanobacterial ancestor, gave rise to three photosynthetic lineages: glaucophytes, red algae, and green plants (Hohmann-Marriott and Blankenship, 2011; Keeling, 2010). The secondary endosymbiosis involving a green alga gave rise to the euglenids (Keeling, 2010). The secondary and tertiary endosymbiosis of red algae led to the origin of the red plastid lineage, including cryptophytes and haptophytes and SAR supergroup: stramenopiles (e.g., diatoms and brown algae), alveolates (e.g., dinoflagellates) and rhizarians (Hohmann-Marriott and Blankenship, 2011; Keeling, 2010). These endosymbiotic events have contributed to the extensive diversity of photosynthetic organisms.

Cyanobacteria primarily depend on phycobilisomes (PBSs) to harvest light (Bag, 2021). Additionally, photosynthetic eukaryotes have evolved the light-harvesting complex (LHC) superfamily (Durnford et al., 1999; Green, 2019; Stadnichuk and Kusnetsov, 2023). The LHC superfamily encodes the light-harvesting antennas of photosystems, effectively capturing and directing light energy to the photosynthetic reaction center. In green plants, the LHC superfamily is categorized into four subfamilies: LHC, LHC-like (light-harvesting-like), PsbS (photosystem Ⅱ subunit S), and FCII (ferrochelatase Ⅱ) (Engelken et al., 2010; Jansson, 1999; Lan et al., 2022; Zou and Yang, 2019). The LHC subfamily associated with PSI and PSII is separately referred to as LHCA (LHCI) and LHCB (LHCII) (Huang et al., 2021; Jansson et al., 1999). The LHC-like subfamily includes four groups: OHP (one-helix protein), SEP (stress-enhanced protein), ELIP (early light-induced protein), and Psb33 (photosystem Ⅱ protein 33) (Engelken et al., 2010; Lan et al., 2022; Zou, 2018). In diatoms, the light-harvesting complexes incorporate fucoxanthin as the major carotenoid and are thus called fucoxanthin-chlorophyll proteins (FCPs) (Eppard et al., 2000; Nagao et al., 2019). The FCPs include the Lhcf, Lhcr, Lhcx and Lhcz subfamilies (Koziol et al., 2007; Neilson and Durnford, 2010b). Although the LHC orthologs among various photosynthetic lineages has been identified, the evolutionary scenarios of the LHC superfamily across photosynthetic organisms remains poorly understood.

The composition and architecture of both LHCI and LHCII antenna systems exhibit diversity across various photosynthetic lineages. The PSI-LHCI supercomplex of the green alga Chlamydomonas reinhardtii incorporates ten LHCA subunits organized into an extensive two-layered semicircular array (Merchant et al., 2007; Su et al., 2019). In Arabidopsis thaliana, its PSI-LHCI supercomplex comprises only four core LHCA proteins (Lhca1/Lhca4 and Lhca2/Lhca3 forming heterodimers) that assemble into a single-layered, belt-like structure (Ben-Shem et al., 2003; Pan et al., 2018). Beyond the four core antennae, Lhca5 and Lhca6 mediate the interaction between the NADH dehydrogenase-like complex and PSI, thereby assembling the PSI-NDH complexes to facilitate cyclic electron flow (Opatíková and Kouřil, 2024; Peng and Shikanai, 2011; Shen et al., 2021). In addition, the PSII-LHCII complex of C. reinhardtii forms a twofold-symmetric homodimer, comprising two copies of the PSII core alongside strongly bound (S-), moderately bound (M-), and naked (N-) LHCII trimers (Shen et al., 2019). Each of the PSII core contains one CP26 (Lhcb5) and one CP29 (Lhcb4) subunit. The S-LHCII and CP26 subunits bind directly to the CP43 side of the core, whereas M-LHCII attaches via CP29 on the CP47 side (Shen et al., 2019). In Pisum sativum, the CP24 (Lhcb6) subunit occupies a position equivalent to that of the N-LHCII trimer in green algae (Shen et al., 2019; Su et al., 2017).

Beyond light harvesting, the LHC superfamily plays a crucial role in managing light energy to optimize photosynthesis and prevent damage (Scholes et al., 2011). LHC-like proteins are specifically responsible for mitigating photooxidative stress (Bassi and Dall'Osto, 2021). Under low-light conditions, the LhcSR protein of Chlamydomonas reinhardtii localizes to the stromal thylakoid membranes, distal to PSII, and remains inactive (Peers et al., 2009). Upon exposure to excessive light, thylakoid acidification and zeaxanthin accumulation activate LhcSR, prompting its migration to the grana margins and assembly into an LhcSR-CP26-LHCII quenching module for photoprotection (Bassi and Dall'Osto, 2021; Shen et al., 2019; Su et al., 2017). In Arabidopsis thaliana, PsbS remains inactive under low light but is activated upon acidification of the thylakoid lumen under high light (Li et al., 2000). The activated PsbS then binds to the CP29-CP24-M-LHCII complex, inducing its dissociation and the release of M-LHCII for energy dissipation (Bassi and Dall'Osto, 2021; Betterle et al., 2009; Drop et al., 2014). Notably, the early-branching land plant Physcomitrium patens uniquely retains both PsbS and LhcSR proteins for driving nonphotochemical quenching (NPQ) and providing robust photoprotection, crucial for its adaptation to terrestrial environments (Alboresi et al., 2010). In addition to rapid photoprotection, state transition-dependent phosphorylation of PSII-LHCII fine-tunes the photosynthetic balance between efficiency and protection. The STN7 kinase facilitates this process by phosphorylating LHCII, promoting the transfer of excitation energy towards PSI (Wunder et al., 2013). This redistribution equilibrates excitation between the photosystems and ensures a smooth delivery of electrons to PSI acceptors (Bellafiore et al., 2005; Rochaix, 2014).

Although previous studies have established the evolutionary framework of the LHC gene family in green plants, a comprehensive understanding of its functional evolution and structural variation across photosynthetic organisms remains unclear. Our study elucidates the evolutionary diversity of the LHC gene family within photosynthetic organisms and identifies four distinct subfamilies: LHCA, LHCB, LHC-like, and FCP. We demonstrate that the evolution of photosynthetic antennae from green algae to land plants involved two major shifts: a transition in gene duplication from dispersed to whole-genome duplication, and a distinct trend of structural simplification in photosynthetic antennae. Furthermore, expression profiles of LHC genes exhibit tissue-specific expression patterns. Members of the LHCA and LHCB subfamilies are upregulated in response to both biotic and abiotic stresses, indicating an adaptive regulatory strategy. This study enhances our understanding of the role of the LHC gene family in the evolution of photosynthesis.

2. Materials and methods 2.1. Identification and phylogenetic analysis of LHC superfamily

To systematically identify the homology of LHC genes across various photosynthetic organisms, we selected genomic data from 65 representative species, covering Cyanobacteria, Dinophyta, Chlorarachniophyta, Cryptophyta, Haptophyta, Ochrophyta (Phaeophyceae), Bacillariophyta, Chlorophyta, Charophyta, Glaucophyta, Rhodophyta, Pteridophyta, Lycopodiophyta, Bryophyta, Gymnosperms, and Angiosperms. The 65 genomic data were primarily obtained from Plant JGI portal and National Center for Biotechnology Information (https://ncbi.nlm.nih.gov/genome/) (Table S1). To identify homologous genes of LHC genes, we retrieved the PF00504 (Chlorophyll A–B binding protein) seed file from Pfam database (Mistry et al., 2021) and performed Hidden Markov Model (HMM) searches across the 65 genomes. We further utilized the InterProScan (Quevillon et al., 2005) and CDD database (https://ncbi.nlm.nih.gov/cdd) (Marchler-Bauer et al., 2015) to verify the presence of conserved domain. The homologous sequences were aligned using MAFFT (Katoh et al., 2005), and trimmed (-gt = 0.2) using TrimAL (Capella-Gutierrez et al., 2009). Based on the Bayesian information criterion, the optimal model LG + F + G4 was selected for constructing the maximum likelihood (ML) phylogenetic tree using IQ-TREE (v.1.6.11) (Nguyen et al., 2015), with 1000 bootstrap replicates. Protein sequences of the four monophyletic clades: LHCA, LHCB, LHC-like, and FCP, were extracted and reconstructed their orthologous trees using the above mentioned pipeline. The phylogenetic trees were visualized using iTOL (Letunic and Bork, 2021). The physicochemical properties of LHC members were analyzed using the “Protein Parameter Calc (based on ProtParam)” tool in TBtools (Chen et al., 2020).

2.2. Expansion mechanism analysis of LHC in green plants

To elucidate the expansion mechanism of LHC gene family, we conducted gene duplication and synteny analyses across eight representatives of green plants with chromosome-level genomes: green algae (Chlamydomonas reinhardtii, Chromochloris zofingiensis and Prasinoderma colonial), bryophytes (Physcomitrella patens), ferns (Alsophila spinulosa), gymnosperms (Cycas panzhihuaensis) and angiosperms (Arabidopsis thaliana and Oryza sativa). The MCScanX (Wang et al., 2012) was utilized for collinearity analysis, and genes were classified into five categories: single, dispersed, proximal, tandem, and segmental/whole-genome duplication (WGD). The genomic locations of LHC genes were visualized using TBtools (Chen et al., 2020).

2.3. Structural analyses of PSI-LHCI and PSII-LHCII between green algae and land plants

The structural models of PSI-LHCI and PSII-LHCII were obtained from the RCSB Protein Data Bank (https://www.rcsb.org/). The retrieved structural models of representatives include PSI-LHCI (PDB ID: 6IJO) and PSII-LHCII (PDB ID: 6KAF) from Chlamydomonas reinhardtii, PSI-LHCI (PDB ID: 6L35) and PSII-LHCII (PDB ID: 5XNM) from Physcomitrium patens, and PSI-LHCI from Pisum sativum (PDB ID: 4XK8). Comparison and visualization of these complex structures was performed using the UCSF Chimera tool (Pettersen et al., 2004).

2.4. Gene expression analysis

The FPKM values for members of the LHC gene family in Arabidopsis thaliana and Oryza sativa were obtained from the PlantRNADB database (https://plantrnadb.com/) (Zhang et al., 2020). This dataset encompasses expression profiles across various tissues (roots, leaves, seedlings, stems, etc.) under different stress conditions (salt, drought, heat, etc.). For each gene, expression values from all biological replicates under the same condition were averaged to generate the final dataset for plotting. Using the pheatmap package in R, we analyzed the expression patterns of LHC gene family members in both tissue-specific contexts and under biotic and abiotic stress conditions.

3. Results and discussion 3.1. Phylogenetic and structural analyses of LHCA and LHCB

Among 65 photosynthetic organisms, a total of 1922 LHC proteins were identified and classified into four clades: LHCA, LHCB, LHC-like and FCP (Fig. S1). LHCA subfamily only existed in green plants and was categorized into 12 branches. Among these, Lhca7, Lhca8, and Lhca9 are green algae-specific clades (Fig. 1A). The Lhcp clade, located at the base of LHCA subfamily, is exclusively found in chlorophytes and charophytes (Mesostigma viride) (Fig. 1A). The LHCB subfamily is also unique to green plants and has 7 branches. Among them, the LHCBM in green algae forms a stable monophyletic group (Fig. 1B). CP29 and CP24 phylogenetically clustered within the LHCA clade, sharing conserved gene structures and regulatory sequences with LHCA members, suggesting that CP29, CP24, and LHCA members shared a common ancestors (Chukhutsina et al., 2020).

To determine how structure relates to function in these LHC members, we conducted comparative structural analyses of PSI-LHCI and PSII-LHCII complexes. In Chlamydomonas reinhardtii, PSI-LHCI forms a two-layer crescent structure, with the P1–P4 sites occupied by Lhca1, 8, 7, 3 (inner) and Lhca1, 4, 6, 5 (outer) (Fig. 1C). The C. reinhardtii Lhca2 (hereafter CrLhca2) and CrLhca9 proteins, located at the P5 and P6 sites respectively, forming a heterodimer (Fig. 1C) (Huang et al., 2021). CrLhca3, CrLhca8, and CrLhca7 were classified in the Lhca3/5/7/8 clade, while CrLhca4, CrLhca6, and CrLhca5 were assigned to the Lhca2/4/6 clade (Fig. 1C), The sister-clade divergence of LHCA proteins in the phylogeny corresponds directly to their spatial layering in the PSI peripheral antenna complex. In contrast, the PSI-LHCI complex in Physcomitrium patens and Pisum sativum only possess a single-layer LHCA protein occupying the P1–P4 sites (Fig. 1C). Notably, the P2 site exhibits differences between the two species. In P. sativum, this position is occupied by Lhca4 (Qin et al., 2015). In P. patens, earlier work suggested it was Lhca5, but recent structural evidence identifies it as a unique paralogue, Lhca2b, forming a distinctive Lhca1-Lhca2b-Lhca2a-Lhca3 antenna. The other three subunits remain conserved (Gorski et al., 2022; Iwai et al., 2024; Liu et al., 2025; Yan et al., 2021). These two dimers exhibit distinct functional characteristics: the Lhca1-Lhca4 dimer in P. sativum specifically binds chlorophyll a (Chla 614) and lutein (LUT 320), whereas the Lhca1-Lhca5 dimer in P. patens lacks this ability (Mazor et al., 2017). Although both dimers contain proteins from the Lhca1 clade, Lhca4 is classified under the Lhca2/4/6 clade, whereas Lhca5 belongs to the Lhca3/5/7/8 clade. We hypothesize that clade-specific residue variations in the pigment-binding pockets could underlie the observed differences in pigment binding between Lhca4-and Lhca5-containing dimers. In contrast to the LHCI complexes found in green plants and algae, the PSI-LHCI complex in the red alga Cyanidioschyzon merolae exhibits a significantly simpler architecture. Comparative studies indicate that it lacks PsaG and retains only three Lhcr subunits, resulting in a vacancy at the Lhca1 binding site (Fig. S4) (Antoshvili et al., 2019; Kumazawa and Ifuku, 2024).

The LHCII antenna system, the primary light-harvesting complex of PSII, is organized as trimers at the periphery of core PSII complex (Fig. 1D). These trimers are predominantly composed of Lhcb1, Lhcb2, and Lhcb3, conserved across land plants. However, other peripheral antenna organization differs fundamentally between green algae and angiosperms. In Chlamydomonas reinhardtii, the antenna comprises three LHCII trimers associated with CP26 and CP29, while in angiosperms, the N-LHCII trimer is replaced by CP24, leading to a simplified monomeric arrangement (Fig. 1D). This divergence in peripheral antenna architecture likely reflects adaptations to distinct environments. The more complex antenna in C. reinhardtii, which features an additional trimer with CP26/CP29, may enhance light harvesting under fluctuating aquatic light conditions (Li and Dohlman, 2023). Conversely, in angiosperms, the incorporation of CP24 and the loss of trimers potentially optimize energy transfer and photoprotection in stable, high light intensities characteristic of terrestrial habitats (Suga and Shen, 2020). These variations highlight how the organization of PSII antennae is tailored to meet specific environmental demands across different photosynthetic lineages.

3.2. Phylogeny of LHC-like and FCP subfamily among photosynthetic organisms

The single-helix HLIP in cyanobacteria serves as the structural prototype of LHC family, from which eukaryotes have evolved more complex variants: the dual-helix SEP, the triple-helix ELIP, and the quadruple-helix PsbS (Fig. 2A and C). Notably, OHP1 and OHP2, the eukaryotic homologs of HLIP, have retained the single-helix architecture and diverged into two functionally distinct clades (Fig. 2A). SEP is widely distributed within the green lineage and facilitates NPQ by promoting direct energy transfer from chlorophyll a to lutein (Levin and Schuster, 2023). ELIP, the most abundant member of LHC-like branch, accumulates under high light stress, binding to chlorophyll a and lutein, effectively eliminating excited-state chlorophyll and thereby preventing the formation of ROS (Hutin et al., 2003). PsbS is present in green plants, typically existing as a single copy in most species (Fig. 2A). It acts as a key regulator of pH-dependent photoprotection in land plants, undergoing conformational changes that enhance its interaction with other LHC proteins, such as CP29, thus facilitating energy quenching (Levin and Schuster, 2023). This indicates that PsbS likely originated prior to the aquatic-terrestrial split, but its central role in photoprotection was refined during the evolution of land plants.

The FCP clade comprises four subtypes: Lhcx (LhcSR), Lhcf, Lhcr, and Lhcz. Lhcx (LhcSR) is widely distributed among Chlorophytes, Charophytes, Bryophytes, and the SAR group, as well as Haptophytes. This subtype forms a stable monophyletic group and serves as the executor of NPQ in green algae. However, it is absent in angiosperms, where its function is replaced by PsbS. In contrast, Lhcf, Lhcr, and Lhcz are specifically found in unequal flagellates, fixed flagellates, and cryptophytes (Fig. 2B). These organisms contain fucoxanthin, as FCP specifically bind this pigment to facilitate light harvesting, and these species possess multiple copies of FCP to support this function. All members of the FCP family exhibit a triple helix structure (Fig. 2D). This structural combination provides the FCP complex with a significant competitive advantage, enabling it to efficiently absorb and utilize the most penetrating blue light (450–550 nm) and green light (500–580 nm) wavelengths in marine surface environments, where chlorophyll b and carotenoids in green plants exhibit relatively weak absorption capabilities (Wang et al., 2019).

The phylogeny of the LHC superfamily elucidates its intricate evolutionary trajectory, characterized by multiple endosymbiotic events, gene duplications, and gene losses (Fig. 2E). The LHC-like proteins represent the earliest diverging members within the LHC superfamily. Red algae acquired ancestral OHP, SEP, and ELIP proteins from their cyanobacterial endosymbiont, evolving from HLIP precursors. Through gene duplication, these proteins diversified into two functional groups: the OHP/SEP/ELIP proteins for photoprotection, and specialized Lhcr proteins for light harvesting (Fig. 2E). In contrast, green algae acquired OHP, SEP, ELIP, and PsbS proteins, while their repertoire of light-harvesting genes further diversified into Lhcx, Lhcf, Lhca1-9, and Lhcb4/5/7. Among the secondary endosymbiotic groups of green algae, the chlorarachniophyta acquired the Lhcb4/5 proteins while losing the Lhcb7 protein. The secondary endosymbiotic group of red algae, known as cryptoalgae, obtained ELIP, Lhcr, and Lhcz proteins. For instance, Lhcf and Lhcr originated from red algal endosymbionts, whereas Lhcz is specific to cryptophytes and may have been transferred to haptophytes. Ultimately, OHP, ELIP, Lhcf, and Lhcr proteins were acquired from dinoflagellates that originated through symbiosis across four levels (Fig. 2E). Within the LHC-like subfamily, the nuclear-encoded OHP gene evolved from the ancestral HLIP gene of cyanobacteria. Through gene duplication, proteins such as SEP, PsbS, and ELIP emerged, exhibiting diverse structures and functions. This phenomenon illustrates the functional transitions followed by structural evolution (Hohmann-Marriott and Blankenship, 2011; Neilson and Durnford, 2010a).

3.3. High diversity of LHC revealed by molecular characteristics

We conducted a statistical analysis to investigate the molecular variation of LHC superfamily across photosynthetic organisms. LHCA and LHCB are predominantly found in green algae, charophytes, and vascular plants, with LHCB consistently outnumbering LHCA in these lineages (Fig. 3A). The coefficient of variation (CV) for LHC-like subfamily is 91.5%, which is more than twice that of LHCA (42%) and LHCB (58%), reflecting differential evolutionary constraints among these subfamilies. The FCP subfamily exhibits a more extreme distribution pattern: it is particularly found in SAR superclusters. The coefficient of variation for FCP is 191%, indicating the highest variability among all LHC family members (Fig. 3A).

Physicochemical property characteristics of LHC superfamily demonstrated evident differences in amino acid length, molecular weight, and isoelectric point (pI) among distinct subfamilies (Fig. 3B). LHCB subfamily exhibits molecular weight ranging from 24 to 31 kDa. In contrast, the LHC-like subfamily displays the broadest range of molecular weights, spanning from 18 to 35 kDa, and includes the highest observed molecular weight of 35 kDa among all groups. This observation is consistent with its sequence divergence. Both LHCA (pI 5.2–6.0) and LHCB (pI 4.8–5.7) subfamily members are classified as weakly acidic, which facilitates their binding to PSI and PSII. In contrast, FCP subfamily has the lowest pI (3.9–5.1). The LHC-like family exhibits the largest variation in pI (from 7.3 to 10.0, with a difference of 2.7) (Fig. 3B). In terms of protein length, LHCB exhibits the longest mean length, whereas LHC-like demonstrates the shortest mean length (Fig. 3B).

We identified two highly conserved motifs within LHC superfamily, which share a common conserved region characterized by ‘ExxNxRxAM’ (Fig. 3C). These two highly conserved motifs mainly localize in functional domains involved in chlorophyll ligation and exciton transfer. Purifying selection maintains the conservation of these motifs because they constitute key pigment-binding sites indispensable for light-harvesting function (Li and Dohlman, 2023). Comparative sequence analysis of Lhca1-4 and Lhcb1/Lhcb4-6 proteins revealed highly conserved structural features at most pigment-binding sites. Specific variations were observed at certain positions. For instance, in M. commoda Lhca1, glutamine is replaced by glutamate (Q to E) at the Chl613 ligand position. Similarly, in C. reinhardtii Lhca2, histidine is substituted with asparagine (H to N) at the Chl603 coordination site (Figs. S8–15 and Tables S2–S8). These specific modifications represent adaptive changes that maintain core pigment-binding functionality while enabling localized structural optimization. Such variations facilitate precise tuning of protein-pigment interactions without compromising the fundamental light-harvesting capabilities of the complex (Su et al., 2019).

3.4. Gene duplication and synteny analysis of LHC superfamily

To elucidate the evolutionary dynamics of LHC superfamily across green plants, we systematically analyzed their genomic distribution and duplication patterns in six representative species: Arabidopsis thaliana, Oryzia sativa, Cycas panzhihuaensis, Alsophila spinulosa, Physcomitrium patens and Chlamydomonas. Ranging from green algae to angiosperms, all identified LHC family members showed widespread and uneven distribution patterns across chromosomes (Fig. 4). Synteny analysis indicated that WGD events were absent in green algae, dispersed duplication accounts for the majority of LHC gene copies (Fig. 4A and Fig. S5). In P. patens and A. spinulosa, WGD events resulted in an overall doubling of its genome, simultaneously increasing the number of WGD-type LHC genes, meanwhile, the number of dispersed duplicate genes also increased (Fig. 4B and C and Table 1). In C. panzhihuaensis, LHC genes predominantly experienced dispersed-type and tandem-type duplications, with the tandem-type duplications significantly enriched on chromosome 7 (Fig. 4D and Table 1). Eight of the nine tandem-type LHC gene copies are localized on chromosome 7, underscoring a chromosomal preference for tandem duplication events. These results suggested that chromosome 7 of C. panzhihuaensis may serve as a lineage-specific hotspot for the expansion of LHC genes through localized replication mechanisms. Although WGD events have been observed in angiosperms, dispersed type LHC genes were the most prevalent, separately comprising 48% and 67% of their LHC gene copies (Fig. 4E and F; Table 1). This observation indicates that, following these WGD events, dispersed-type LHC genes have maintained a quantitative dominance.

Our analysis revealed a distinct expansion pattern: green algae primarily rely on dispersed duplication, whereas vascular plants synergistically employ WGD and dispersed duplication. Especially, the dispersed patterns found in angiosperms may represent an evolutionary mode aimed at preserving functional diversity following WGD (Wang et al., 2011). These differences likely reflect distinct selective pressures encountered during terrestrial adaptation (Van de Peer et al., 2017).

3.5. Expression patterns of LHC in Arabidopsis thaliana and Oryza sativa

To explore the potential functions of LHC superfamily members, we analyzed the expression patterns of LHC genes under various stress conditions in A. thaliana and O. sativa. The LHC superfamily members exhibited tissue-specific expression patterns (Fig. 5A and D). LHCA and LHCB subfamilies are constitutively highly expressed in photosynthetic tissues (such as leaf, meristem), reflecting their functions in formation photosynthetic antenna systems. The variability in expression levels among different tissues for LHCB subfamily members is greater than LHCA subfamily members. In contrast, LHC-like subfamily members displayed unique pattern: specifically expressed in seedlings and stems of A. thaliana, and predominantly expressed in stem and panicle tissues of O. sativa. The expression abundance of LHC-like subfamily members was not directly correlating with the photosynthetically active tissues (Fig. 5A and D).

LHCA and LHCB subfamily members exhibited consistent upregulation under salt, drought, and heat stresses (Fig. 5B and E), whereas LHC-like subfamily showed species-specific patterns in response to different stresses. In Arabidopsis thaliana, LHC-like subfamily members were specifically induced by oxidative and irradiated stress. In Oryza sativa, only water deficit triggered the induction of LHC-like subfamily members, with no significant response to dark, shade and cold stressors (Fig. 5E). This contrast reveals that the core photosynthetic components (LHCA/B) and LHC-like subfamily of the LHC superfamily have evolved distinct functional roles. In response to biotic stress, both LHCA and LHCB subfamilies showed marked upregulation, with their expression levels increased by approximately 2- to 3-fold compared to constitutive expression levels. Conversely, LHC-like genes maintained consistently lower expression levels compared to LHCA and LHCB, mirroring their minimal responsiveness to abiotic stressors observed previously (Fig. 5C and F). This persistent expression dichotomy suggests distinct functional specialization within the LHC superfamily. These results demonstrate that LHCA and LHCB subfamily maintain stable photosynthetic protection across abiotic and biotic stresses, while LHC-like members exhibit species-specific responses. These findings offer molecular evidence for comprehending the functional diversity of the LHC superfamily in the context of plant evolution and adaptations.

In summary, this study systematically investigates the evolutionary dynamics of the LHC superfamily across 65 photosynthetic organisms, revealing new insights into phylogenetic diversification, structural adaptation, and functional specialization. Our phylogenetic analyses classify LHC proteins into four major clades: LHCA, LHCB, LHC-like, and FCP, with LhcSR belonging to the FCP subfamily. Primary endosymbiosis introduced ancestral proteins, and secondary endosymbiosis drove lineage-specific gains and losses. Green algae primarily rely on dispersed duplication for the expansion of LHC, whereas land plants increasingly employ WGD during terrestrial adaptation. Expression profiling further demonstrates functional diversification: core LHCA and LHCB genes exhibit constitutive expression in photosynthetic tissues with strong induction under biotic and abiotic stresses, confirming their conserved role in maintaining photosynthetic activity. These findings elucidate how the structural and functional diversification of LHC underpin photosynthetic adaptations to various environments, providing a framework for future studies on LHC-mediated stress tolerance mechanism and photosynthetic efficiency enhancement.

Acknowledgements

This work was supported by the National Natural Science Foundation of China (32370228, W2511024 and 32470232) (B.Z. and Z.Z.); the Natural Science Foundation of Jiangsu Province (BK20250004) (B.Z.); the Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (B.Z.); the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) (B.Z.).

CRediT authorship contribution statement

Kexin Cai: Writing-review & editing, Writing-original draft, Visualization, Project administration, Funding acquisition, Formal analysis, Data curation, Conceptualization. Runjie Diao, Zhihang Zhao, Yannan Liu and Zhenhua Zhang: Writing-original draft, Resources, Formal analysis. Bojian Zhong: Writing-original draft, Project administration, Investigation, Conceptualization.

Data availability statement

The datasets presented in this study can be found in online repositories: https://figshare.com/articles/dataset/LHC_phylogeny_data/29939495?file=57277457.

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Appendix A. Supplementary data

Supplementary data to this article can be found online at https://doi.org/10.1016/j.pld.2026.01.004.