Light-harvesting Complex Research Articles

Vibrational Relaxation Completes the Excitation Energy Transfer and Localization of Vibronic Excitons in Allophycocyanin α84-β84.

Phycobilisomes are light-harvesting complexes that play a key role in photosynthesis in cyanobacteria, which generate more than 40% of the world's oxygen. The near-unity excitation energy transfer efficiency from phycobilisomes to photosystems highlights its importance in understanding efficient energy transfer processes. Spectroscopic studies have shown that the 280 fs rapid excitonic downhill energy transfer within the α84-β84 chromophore dimer in allophycocyanin (APC), a subunit of phycobilisomes, is crucial to this efficiency. However, the role of strong chromophore-protein interactions and vibrational relaxation requires further exploration to fully explain this efficient downhill energy transfer. A theory is required that adequately describes exciton dynamics in an intermediate region while also incorporating vibrational relaxation mediated by protein bath modes. In this work, we incorporate vibrational relaxation into modified Redfield theory by introducing coupling fluctuation. We holistically simulate the rapid excitation energy transfer process of the α84-β84 chromophore dimer in APC and successfully model the recently observed rapid energy capture. We find that vibrational relaxation dictates capture of excitons by the localized state of the β84 chromophore. The calculated rate shows excellent agreement with previous ultrafast spectroscopic experiments. Our results show that the inclusion of vibrational relaxation is essential for systems that utilize vibronic coupling to enhance energy transfer and capture. Consequently, incorporating vibrational relaxation into Modified Redfield theory shows promise for accurately describing the excitation energy transfer process in other photosynthetic systems.

The interplay between LHCSR and PSBS proteins provides photoprotection in Chlamydomonas reinhardtii pgr5 mutant under high light

Cyclic electron transport (CET) is a vital alternative route that protects against photodamage and aids in energy production. This process depends on proton gradient regulation 5 (PGR5) and PGRL1-dependent pathways associated with CET. The exact roles of these proteins in photosystem I photochemistry under prolonged high light conditions are not fully understood. Continuous light adaptation hinges on two critical mechanisms: alterations in the proton motive force (pmf) and adjustments in the ratio of proteins activated by high light that dissipate excess light through non-photochemical quenching (NPQ). To explore this, we studied pgrl1 and pgr5 mutants to gauge their roles in balancing photochemistry and photoacclimation. These mutants showed inhibited growth, reduced photosynthetic efficiency, and a lowered pmf, leading to diminished non-photochemical energy quenching (qE) under high light. Prolonged high light exposure slowed down unregulated energy losses Y(NO), and relaxation helped regulate photosynthetic activity by increasing photoinhibitory quenching (qI), thus preventing further damage to the photosystem. The precise balance between the two pmf components, ΔpH and Δψ, is critical for controlling photochemistry and photoacclimation, yet remains elusive. In pgr5 reduced pmf led to an accumulation of cytochrome b6f under high light, and a decrease in the ΔpH component increased the Δψ component's role in photosynthetic acclimation. Notably, light-harvesting complex stress response protein 3 (LHCSR3) showed decreased expression in pgrl1, whereas pgr5 exhibited no expression of both LHCSR3 and LHCSR1 under high light conditions. Moreover, continuous increase in PSBS protein accumulation in pgr5 suggests enhanced photoprotection in the absence of LHCSR3 under high light. The study provides significant insights into how cyclic electron transport (CET) regulates photoprotective proteins LHCSR and PSBS, influencing Chlamydomonas' survival strategies.

Structural basis for molecular assembly of fucoxanthin chlorophyll a/c-binding proteins in a diatom photosystem I supercomplex

Photosynthetic organisms exhibit remarkable diversity in their light-harvesting complexes (LHCs). LHCs are associated with photosystem I (PSI), forming a PSI-LHCI supercomplex. The number of LHCI subunits, along with their protein sequences and pigment compositions, has been found to differ greatly among the PSI-LHCI structures. However, the mechanisms by which LHCIs recognize their specific binding sites within the PSI core remain unclear. In this study, we determined the cryo-electron microscopy structure of a PSI supercomplex incorporating fucoxanthin chlorophyll a/c-binding proteins (FCPs), designated as PSI-FCPI, isolated from the diatom Thalassiosira pseudonana CCMP1335. Structural analysis of PSI-FCPI revealed five FCPI subunits associated with a PSI monomer; these subunits were identified as RedCAP, Lhcr3, Lhcq10, Lhcf10, and Lhcq8. Through structural and sequence analyses, we identified specific protein–protein interactions at the interfaces between FCPI and PSI subunits, as well as among FCPI subunits themselves. Comparative structural analyses of PSI-FCPI supercomplexes, combined with phylogenetic analysis of FCPs from T. pseudonana and the diatom Chaetoceros gracilis, underscore the evolutionary conservation of protein motifs crucial for the selective binding of individual FCPI subunits. These findings provide significant insights into the molecular mechanisms underlying the assembly and selective binding of FCPIs in diatoms.

Structural basis for molecular assembly of fucoxanthin chlorophyll a/c-binding proteins in a diatom photosystem I supercomplex.

Photosynthetic organisms exhibit remarkable diversity in their light-harvesting complexes (LHCs). LHCs are associated with photosystem I (PSI), forming a PSI-LHCI supercomplex. The number of LHCI subunits, along with their protein sequences and pigment compositions, has been found to differ greatly among the PSI-LHCI structures. However, the mechanisms by which LHCIs recognize their specific binding sites within the PSI core remain unclear. In this study, we determined the cryo-electron microscopy structure of a PSI supercomplex incorporating fucoxanthin chlorophyll a/c-binding proteins (FCPs), designated as PSI-FCPI, isolated from the diatom Thalassiosira pseudonana CCMP1335. Structural analysis of PSI-FCPI revealed five FCPI subunits associated with a PSI monomer; these subunits were identified as RedCAP, Lhcr3, Lhcq10, Lhcf10, and Lhcq8. Through structural and sequence analyses, we identified specific protein-protein interactions at the interfaces between FCPI and PSI subunits, as well as among FCPI subunits themselves. Comparative structural analyses of PSI-FCPI supercomplexes, combined with phylogenetic analysis of FCPs from T. pseudonana and the diatom Chaetoceros gracilis, underscore the evolutionary conservation of protein motifs crucial for the selective binding of individual FCPI subunits. These findings provide significant insights into the molecular mechanisms underlying the assembly and selective binding of FCPIs in diatoms.

Eustigmatophyte model of red-shifted chlorophyll a absorption in light-harvesting complexes

Photosynthetic organisms harvest light for energy. Some eukaryotic algae have specialized in harvesting far-red light by tuning chlorophyll a absorption through a mechanism still to be elucidated. Here, we combined optically detected magnetic resonance and pulsed electron paramagnetic resonance measurements on red-adapted light-harvesting complexes, rVCP, isolated from the freshwater eustigmatophyte alga Trachydiscus minutus to identify the location of the pigments responsible for this remarkable adaptation. The pigments have been found to belong to an excitonic cluster of chlorophylls a at the core of the complex, close to the central carotenoids in L1/L2 sites. A pair of structural features of the Chl a403/a603 binding site, namely the histidine-to-asparagine substitution in the magnesium-ligation residue and the small size of the amino acid at the i-4 position, resulting in a [A/G]xxxN motif, are proposed to be the origin of this trait. Phylogenetic analysis of various eukaryotic red antennae identified several potential LHCs that could share this tuning mechanism. This knowledge of the red light acclimation mechanism in algae is a step towards rational design of algal strains in order to enhance light capture and efficiency in large-scale biotechnology applications.

The thylakoid phosphatase TEF8 is involved in state transition and high light stress resistance in Chlamydomonas.

The sophisticated regulation of state transition is required to maintain optimal photosynthetic performance under fluctuating light condition, through balancing the absorbed light energy between photosystem II andphotosystem I. This exquisite process incorporates phosphorylation and dephosphorylation of light-harvesting complexes and PSII core subunits, accomplished by thylakoid membrane-localized kinases and phosphatases that have not been fully identified. In this study, one Chlamydomonas high light response gene, THYLAKOID ENRICHED FRACTION 8 (TEF8), was characterized. The Chlamydomonas tef8 mutant showed high light sensitivity and defective state transition. The enzymatic activity assays showed that TEF8 is a bona fide phosphatase localized in thylakoid membranes. Biochemical assays, including BN-PAGE, pull-down, and phosphopeptide mass spectrometry, proved that TEF8 associates with photosystem II and is involved in the dephosphorylation of D2 and CP29 subunits during state 2 to state 1 transition. Taken together, our results identified TEF8 as a thylakoid phosphatase with multiple dephosphorylation targets on photosystem II, and provide new insight into the regulatory mechanism of state transition and high light resistance in Chlamydomonas.

Design principles for energy transfer in the photosystem II supercomplex from kinetic transition networks

Photosystem II (PSII) has the unique ability to perform water-splitting. With light-harvesting complexes, it forms the PSII supercomplex (PSII-SC) which is a functional unit that can perform efficient energy conversion, as well as photoprotection, allowing photosynthetic organisms to adapt to the naturally fluctuating sunlight intensity. Achieving these functions requires a collaborative energy transfer network between all subunits of the PSII-SC. In this work, we perform kinetic analyses and characterise the energy landscape of the PSII-SC with a structure-based energy transfer model. With first passage time analyses and kinetic Monte Carlo simulations, we are able to map out the overall energy transfer network. We also investigate how energy transfer pathways are affected when individual protein complexes are removed from the network, revealing the functional roles of the subunits of the PSII-SC. In addition, we provide a quantitative description of the flat energy landscape of the PSII-SC. We show that it is a unique landscape that produces multiple kinetically relevant pathways, corresponding to a high pathway entropy. These design principles are crucial for balancing efficient energy conversion and photoprotection.

Revisiting the early light-induced protein hypothesis in the sustained thermal dissipation mechanism in yew leaves.

Overwintering evergreen trees in boreal regions continuously convert absorbed light energy into heat through a process known as 'sustained thermal dissipation'. To better understand this mechanism, this study examined the alterations in the photosynthetic apparatus and transcriptomes of yew (Taxus cuspidata) leaves throughout the year, comparing sun-exposed and shaded leaves. The Y(II) parameter, conventionally used to estimate the quantum yield of photosystem II (PSII), suggests the occurrence of temperature-dependent thermal dissipation during winter. On the other hand, the levels of photosystem subunits, including the D1 subunit of the PSII reaction center, remain relatively stable year-round, suggesting that typical photoinhibition is unlikely to occur. Time-resolved chlorophyll fluorescence analysis revealed that heat dissipation at the PSII antenna is prominent in winter. Winter transcriptomes are notably characterized by a predominance of Elip transcripts encoding early light-induced protein (ELIP), which constitute 20% of the total transcripts, as deduced from RNA-seq analysis. Furthermore, ELIP protein concentration increases to nearly half that of the major light-harvesting complexes. The predicted structure of ELIP includes potential chlorophyll a and carotenoid binding sites. Considering a previous report showing ELIP's capacity for energy dissipation, these findings lead to a reevaluation of its significant role in sustained thermal dissipation.

Mpsqd: A matrix product state based Python package to simulate closed and open system quantum dynamics.

We introduce a Python package based on matrix product states (MPS) to simulate both the time-dependent Schrödinger equation (TDSE) and the hierarchical equations of motion (HEOM). The wave function in the TDSE or the reduced density operator/auxiliary density operators in the HEOM are represented using MPS. A matrix product operator (MPO) is then constructed to represent the Hamiltonian in the TDSE or the generalized Liouvillian in the HEOM. The fourth-order Runge-Kutta method and the time-dependent variational principle are used to propagate the MPS. Several examples, including the nonadiabatic interconversion dynamics of the pyrazine molecule, excitation energy transfer dynamics in molecular aggregates and photosynthetic light-harvesting complexes, the spin-boson model, a laser driven two-state model, the Holstein model, and charge transport in the Anderson impurity model, are presented to demonstrate the capability of the package.

Structure-based validation of recombinant light-harvesting complex II.

Light-harvesting complex II (LHCII) captures sunlight and dissipates excess energy to drive photosynthesis. To elucidate this mechanism, the individual optical properties of pigments in the LHCII protein must be identified. In vitro reconstitution with apoproteins synthesized by Escherichia coli and pigment-lipid mixtures from natural sources is an effective approach; however, the local environment surrounding each pigment within reconstituted LHCII (rLHCII) has only been indirectly estimated using spectroscopic and biochemical methods. Here, we used cryo-electron microscopy to determine the 3D structure of the rLHCII trimer and found that rLHCII exhibited a structure that was virtually identical to that of native LHCII, with a few exceptions: some C-terminal amino acids were not visible, likely due to aggregation of the His-tags; a carotenoid at the V1 site was not visible; and at site 614 showed mixed occupancy by both chlorophyll a and b molecules. Our observations confirmed the applicability of the in vitro reconstitution technique.

Acidisoma cladoniae sp. nov., an acidotolerant bacterium isolated from an Antarctic lichen.

Gram-staining-negative, aerobic, white-cream-pearly colony, coccobacilli, and non-motile bacterial strain, PAMC 29798T was isolated from an Antarctic lichen. The strain was acidotolerant and psychrotolerant growing at pH 4.0-7.5 (optimally at pH 4.0-6.5) and 0-25°C (optimally at 10-20°C). The major fatty acids are Summed Feature 8, C18:1 2OH, and C19:0 cyclo ω8c. The major respiratory quinone was Q-10. Phylogenetic and phylogenomic analyses indicated that strain PAMC 29798T belonged to the genus Acidisoma and 16S rRNA gene sequences of PAMC 29798T were closely related to Acidisoma silvae (97.7% sequence similarity), Acidisoma cellulosilyticum (96.5%), Acidisoma tundrae (96.5%), and Acidisoma sibiricum (96.3%). Genomic relatedness analyses showed that strain PAMC 29798T was clearly distinguished from type strains of the genus Acidisoma based on values of average nucleotide identity (< 75%) and the digital DNA-DNA hybridization (< 19.6%). Genome analysis revealed that the genome size of PAMC 29798T is approximately 5.0 Mb with a G+C content of 63.4%. The complete genome comprises 5 contigs containing 4636 protein-coding genes, 46 tRNA genes, and 2 rRNA operons. The genome possesses genes for light-harvesting complexes, type-II photosynthetic reaction center, and C-P lyase to solubilize organic phosphates, while genes encoding nitrogenase iron protein involved in the nitrogen fixation were not present. Based on the results of phylogenetic, genome-based relatedness, and physiological and genomic analyses, strain PAMC 29798T is proposed to represent a novel species of the genus Acidisoma, with the name Acidisoma cladoniae. The type strain is PAMC 29798T (= KCTC 82159T = JCM 35634T).

Chromatic acclimation in cyanobacteria renders robust photosynthesis and fitness in dynamic light environment: Recent advances and future perspectives.

Cyanobacteria are photoautotrophic organisms that use light and water as a source of energy and electrons, respectively, to fix atmospheric carbon dioxide and release oxygen as a by-product during photosynthesis. However, photosynthesis and fitness of organisms are challenged by seasonal and diurnal fluctuations in light environments. Also, the distribution of cyanobacteria in a water column is subject to changes in the light regime. The quality and quantity of light change significantly in low and bright light environments that either limit photochemistry or result in photoinhibition due to an excess amount of light reaching reaction centers. Therefore, cyanobacteria have to adjust their light-harvesting machinery and cell morphology for the optimal harvesting of light. This adjustment of light-harvesting involves remodeling of the light-harvesting complex called phycobilisome or incorporation of chlorophyll molecules such as chlorophyll d and f into their light-harvesting machinery. Thus, photoacclimation responses of cyanobacteria at the level of pigment composition and cell morphology maximize their photosynthetic ability and fitness under a dynamic light environment. Cyanobacteria exhibit different types of photoacclimation responses that are commonly known as chromatic acclimation (CA). In this work, we discuss different types of CA reported in cyanobacteria and present a molecular mechanism of well-known type 3 CA where phycoerythrin and phycocyanin of phycobilisome changes according to light signals. We also include other aspects of type 3 CA that have been recently studied at a molecular level and highlight the importance of morphogenes, cytoskeleton, and carboxysome proteins. In summary, CA gives a unique competitive benefit to cyanobacteria by increasing their resource utilization ability and fitness.

Fine-Tuning the Microstructure and Photophysical Characteristics of Fluorescent Conjugated Copolymers Using Photoalignment and Liquid-Crystal Ordering.

Replicating the microstructural basis and the near 100% excitation energy transfer efficiency in naturally occurring light-harvesting complexes (LHCs) remains challenging in synthetic energy-harvesting devices. Biological photosynthesis regulates active ensembles of light-absorbing and funneling chlorophylls in proteins in response to fluctuating sunlight. Here, use of long-range liquid crystal (LC) ordering to tailor chain orientation and packing structure in liquid crystalline conjugated polymer (LCCP) layers for bio-mimicry of certain structural basis and light-harvesting properties of LHCs is reported. It is found that long-range orientational ordering in an LC phase of poly(9,9-dioctylfluorene-co-benzothiadiazole) (F8BT) copolymer stabilizes a small fraction of randomly-oriented F8BT nanocrystals dispersed in an amorphous matrix of F8BT chains, resembling a self-doped host-guest system whereby excitation energy funneling and photoluminescence quantum efficiencies are enhanced significantly by triggering 3D donor-to-acceptor Förster resonance energy transfer (FRET) and dominant intrachain emission in the nano-crystal acceptor. Further, photoalignment of nematic F8BT layers is combined with LC orientational ordering to fabricate large-area-extended monodomains exhibiting >60% crystallinity and ≈20nm-long interchain packing order. Remarkably, these monodomains demonstrate strong linearly polarized emission, whilst also promoting a new band-edge absorption species and an extra emissive interchain excited state as compared to the non-aligned films.

Incoherent ultrafast energy transfer in phycocyanin 620 from Thermosynechococcus vulcanus revealed by polarization-controlled two dimensional electronic spectroscopy.

Phycocyanin 620 (PC620) is the outermost light-harvesting complex in phycobilisome of cyanobacteria, engaged in light collection and energy transfer to the core antenna, allophycocyanin. Recently, long-lived exciton-vibrational coherences have been observed in allophycocyanin, accounting for the coherent energy transfer [Zhu et al., Nat. Commun. 15, 3171 (2024)]. PC620 has a nearly identical spatial location of three α84-β84 phycocyanobilin pigment pairs to those in allophycocyanin, inferring an existence of possible coherent energy transfer pathways. However, whether PC620 undergoes coherent or incoherent energy transfer remains debated. Furthermore, accurate determination of energy transfer rates in PC620 is still necessary owing to the spectral overlap and broadening in conventional time-resolved spectroscopic measurements. In this work, the energy transfer process within PC620 was directly resolved by polarization-controlled two dimensional electronic spectroscopy (2DES) and global analysis. The results show that the energy transfer from α84 to the adjacent β84 has a lifetime constant of 400fs, from β155 to β84 of 6-8ps, and from β155 to α84 of 66ps, fully conforming to the Förster resonance energy transfer mechanism. The circular dichroism spectrum also reveals that the α84-β84 pigment pair does not form excitonic dimer, and the observed oscillatory signals are confirmed to be vibrational coherence, excluding the exciton-vibrational coupling. Nodal line slope analysis of 2DES further reveals that all the vibrational modes participate in the energy dissipation of the excited states. Our results consolidate that the ultrafast energy transfer process in PC620 is incoherent, where the twisted conformation of α84 is suggested as the main cause for preventing the formation of α84-β84 excitonic dimer in contrast to allophycocyanin.

Cavity-Mediated Enhancement of the Energy Transfer in the Reduced Fenna-Matthews-Olson Complex.

Strong light-matter interaction leads to the formation of hybrid polariton states and can alter the light-harvesting properties of natural photosynthetic systems without modifying their chemical structure. In the present study, we computationally investigate the effect of the resonant cavity on the efficiency and the rate of the population transfer in a quantum system coupled to the cavity and the dissipative environment. The parameters of the model system were chosen to represent the Fenna-Matthews-Olson natural light-harvesting complex reduced to the three essential sites. The dynamics of the total system was propagated using the hierarchical equations of motion. Our results show that the strong light-matter interaction can accelerate the population transfer process compared to the cavity-free case but at the cost of lowering the transfer efficiency. The transition to the strong coupling regime was found to coincide with the degeneracy of polariton eigenvalues. Our findings indicate the potential and the limit of tuning the energy transfer in already efficient natural light-harvesting systems.

Integrated transcriptomic and metabolomic analysis reveals the effects and potential mechanism of hydrogen peroxide on pigment metabolism in postharvest broccoli.

To understand the effects and related potential mechanism of H2O2 on pigment metabolism in postharvest broccoli, an integrated analysis of transcriptome and metabolome was performed. Results suggested that 65 differentially expressed genes and 26 differentially accumulated metabolites involved in chlorophyll, carotenoid, and flavonoid metabolism were identified. H2O2 treatment delayed the decrease of chlorophyll content by upregulating the expressions of chlorophyll synthetic genes, thylakoid synthetic genes, and 15 light-harvesting complex genes compared with the control and diphenylene iodonium treatments. H2O2 treatment decreased the accumulation of 11 flavonoids and 5 flavonols by downregulating the flavonoid synthetic genes. In addition, H2O2 treatment promoted carotenoid biosynthesis to eliminate reactive oxygen species in thylakoids, thereby protecting chlorophyll molecules from degradation. The inhibition of flavonoids and flavonols accumulation and chlorophyll decrease was the crucial reason for the delayed yellowing in H2O2 treatment. This study provides a new method and theoretical support for delaying the yellowing process in postharvest broccoli.

The Unusual Functional Role of Protein Flexibility in Photosynthetic Light Harvesting: Protein Dynamics Studied Using Neutron Scattering

In addition to investigations of the three-dimensional protein structure, information on the dynamical properties of proteins is indispensable for an understanding of protein function in general. Correlations between protein dynamics and function are typically anticipated when both molecular mobility and function are concurrently affected under specific temperatures or hydration conditions. In contrast, excitation energy transfer within the major photosynthetic light-harvesting complex II (LHC II) presents an atypical case, as it remains fully operational even at cryogenic temperatures, primarily depending on the interactions between electronic states and involving harmonic protein vibrations only. This review summarizes recent work on vibrational and conformational protein dynamics of LHC II and directly relates these findings to its light-harvesting function. In addition, we give a comprehensive introduction into the use of neutron spectroscopy and molecular dynamics simulations to investigate the protein dynamics of photosynthetic protein complexes in solution, which is information complementary to that obtained by protein crystallography.

Photo-induced dynamics with continuous and discrete quantum baths.

The ultrafast quantum dynamics of photophysical processes in complex molecules is an extremely challenging computational problem with a broad variety of fascinating applications in quantum chemistry and biology. Inspired by recent developments in open quantum systems, we introduce a pure-state unraveled hybrid-bath method that describes a continuous environment via a set of discrete, effective bosonic degrees of freedom using a Markovian embedding. Our method is capable of describing both, a continuous spectral density and sharp peaks embedded into it. Thereby, we overcome the limitations of previous methods, which either capture long-time memory effects using the unitary dynamics of a set of discrete vibrational modes or use memoryless Markovian environments employing a Lindblad or Redfield master equation. We benchmark our method against two paradigmatic problems from quantum chemistry and biology. We demonstrate that compared to unitary descriptions, a significantly smaller number of bosonic modes suffices to describe the excitonic dynamics accurately, yielding a computational speed-up of nearly an order of magnitude. Furthermore, we take into account explicitly the effect of a δ-peak in the spectral density of a light-harvesting complex, demonstrating the strong impact of the long-time memory of the environment on the dynamics.

An Unexpected Water Channel in the Light-Harvesting Complex of a Diatom: Implications for the Switch between Light Harvesting and Photoprotection

An Unexpected Water Channel in the Light-Harvesting Complex of a Diatom: Implications for the Switch between Light Harvesting and Photoprotection

The Chrysosplenium sinicum genome provides insights into adaptive evolution of shade plants

Chrysosplenium sinicum, a traditional Tibetan medicinal plant, can successfully thrive in low-light environments for long periods of time. To investigate the adaptive evolution of shade plants in low-light environments, we generated a chromosome-scale genome assembly (~320 Mb) for C. sinicum by combining PacBio sequencing and Hi-C technologies. Based on our results, gene families related to photosynthesis and cell respiration greatly expanded and evolved in C. sinicum genome due to intracellular DNA transfer from organelle genome to nuclear genome. Under positive selective pressure, adaptive evolution of light-harvesting complex II (LHCII) component protein CsLhcb1s resulted in the expansion of threonine residues at the phosphorylation site of STN7 kinase, potentially establishing a crucial genomic foundation for enhancing C. sinicum’s adaptability in low-light environments. Through transcriptome and metabolome analysis, we identified chrysosplenol and chrysosplenoside as predominant flavonoid metabolites of C. sinicum and predicted their synthesis pathways. In addition, analysis of alternative splicing (AS) revealed that AS events help regulate state transition and flavonoid biosynthesis. The present study provides new insights into the genomes of shade plants exposed to low-light conditions and adaptive evolution of these genomes; in addition, the results improve our current knowledge on the biosynthetic and regulatory processes of chrysosplenol and chrysosplenoside.