Light signaling pathways regulating early plant development: an evo-devo approach

Introduction

Light plays an inevitable role in the lifecycle of all photosynthetic organisms including plants (Sullivan and Deng, 2003). In seed plants just after germination, seedlings exhibit a dramatic difference in morphology depending on whether it perceives light or not. Seedlings that emerge in the dark, buried under layers of soil, exhibit skotomorphogenic development. Skotomorphogenesis is characterized by elongated growth of the hypocotyl enabling the plant to reach out for light. In dicots like Arabidopsis thaliana, the two cotyledons enclose the shoot apical meristem (SAM) and form an apical hook. This hook prevents damage to the SAM while the seedling tries to pierce its way through the abrasive soil particles. Once exposed to the light, seedlings orchestrate photomorphogenesis which is characterized by inhibition of hypocotyl elongation, opening of the cotyledons and formation of the chloroplasts resulting in greening. The molecular regulation of all these developmental changes in Arabidopsis thaliana is well studied and also discussed in some previous reviews (Gallego-Bartolomé et al., 2011; Abbas et al., 2013; Rehmani et al., 2023; Wang et al., 2023; Krahmer and Fankhauser, 2024). Therefore, in this review we primarily discuss some recent advancements in these fields. While the role of light in growth and development of Arabidopsis thaliana is well described, its role is less explored in primitive plants and their algal ancestors. During terrestrialization of plants, the quality and quantity of light varied significantly from water to land (Han et al., 2019; Lopez-Pozo et al., 2023). How the early land plants evolved from the aquatic algal ancestors to acclimatize to this sudden change in light quality and fluence is still not well explored. Here we attempt to comprehend the findings highlighting the role of light signaling in growth and development of the green algae Chlamydomonas reinhardtii, as well as in the non-vascular bryophytes Marchantia polymorpha and Physcomitrium patens.

Molecular regulators of the light signaling pathway

In land plants light is perceived by different classes of photoreceptors. UV-B is perceived by the UV RESISTANCE LOCUS 8 (UVR8) photoreceptor. There are several photoreceptors in plants that can detect blue light including the cryptochromes (CRYs), phototropins (PHOTs), ZEITLUPE (ZTL), FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) and LOV KELCH PROTEIN 2 (LKP2). The phytochromes are responsible for perceiving the red and far red light. The Phytochromes exist is two photo-convertible forms the P_r form and the P_fr form. The P_r form of the phytochrome perceives red light and gets converted to the P_fr form. P_fr is the active form of phytochrome that localises to the nuclei and regulates downstream signalling. P_fr form of phytochrome upon perceiving the far red light gets converted back to the inactive P_r form (Kami et al., 2010; Casal, 2013). In Arabidopsis there are five different types of phytochromes. Phytochrome A (PhyA) is light labile while the Phytochrome B (PhyB), Phytochrome C (Phy C), Phytochrome D (PhyD) and Phytochrome E (PhyE) are light stable (Li et al., 2011). PhyA plays major role in far-red light mediated responses, while PhyB is the primary player in red light response pathways. The nuclear localised P_fr form of phytochromes interact with proteins called PHYTOCHROME INTERACTING FACTORS (PIFs) and inactivate them to regulate downstream signalling (Park et al., 2012; Legris et al., 2019). The cryptochromes are known to inhibit the dark accumulated E3 Ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1) to facilitate the photomorphogenesis in the seedlings (Ponnu and Hoecker, 2021). The photoactivated monomers of UVR8 interact with the monomers of COP1 to induce UV-B photomorphogenesis (Tilbrook et al., 2013; Jenkins, 2014). Activation of the photoreceptors induce the downstream signalling cascade for gene regulation which involves key transcription factors like ELONGATED HYPOCOTYL 5 (HY5) and B-BOX (BBX) proteins (Gyula et al., 2003; Larner et al., 2018; Yadav et al., 2020b, a). In this review we primarily discuss the recent advances in the process of early seedling development.

Role of light signaling in regulation of hypocotyl elongation

The embryonic stem called hypocotyl connects the root to the cotyledons. It has a fixed number of cells at the end of the embryogenesis (Gendreau et al., 1997). Further elongation of the hypocotyl depends on the anisotropic expansion of cells, which depends on both environmental cues, such as light, and internal hormone signaling. Under dark, the germinated seedlings elongate their hypocotyl towards the soil surface. Hypocotyl elongation is driven by cell expansion by accumulating GIBBERELLIC ACID (GA) in dark, which indirectly activates auxin via PHYTOCHROME INTERACTING FACTORS (PIFs). PIFs play a major role in hypocotyl elongation, as pifq mutants exhibit a photomorphogenic phenotype in dark with a shortened hypocotyl (Shin et al., 2009). PIFs physically interact with DELLA to promote their degradation to regulate the hypocotyl elongation (Li KunLun et al., 2015; Li et al., 2016; Griffiths et al., 2024). DE-ETIOLATED 1 (DET1) also increases the abundance of PIFs in dark by negatively regulating the DELLA (Dong et al., 2014). In the dark PIFs transcriptionally activate auxin biosynthesis and auxin-regulated genes like SMALL AUXIN UP-RNAs (SAUR)s including (SAUR19) (Figure 1) (Spartz et al., 2012; Sun et al., 2016). These SAURs inhibit PROTEIN PHOSPHATASE 2C.D (PP2C.D) and activate H⁺- ATPase which leads to the cell wall matrix acidification. This further activates EXPANSINs (EXPs) and XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE (XTH18,19) leading to hypocotyl cell elongation (Wolf et al., 2012). Auxin also induces the interaction between Transmembrane kinase (TMK) and H⁺-ATPase and promotes TMK-dependent phosphorylation of the H⁺-ATPase to promote cell elongation in the dark (Lin et al., 2021) (Figure 1). BR also positively regulates hypocotyl elongation by activating PIFs. In dark, COP1 is nuclear localised and plays a multifaceted roles by interacting and degrading the pathway components of different phytohormones. COP1 degrades the phosphorylated form of BES1 (BRASSINOSTEROID INSENSITIVE 1-EMS-SUPPRESSOR 1), increasing the active form of BZR1 (BRASSINAZOLE RESISTANCE 1) and BES1. BZR1/BES1 interact with PIFs to regulate cell elongation (Oh et al., 2012; Yang et al., 2017). COP1 promotes GA accumulation and GA increases PIF activity by causing GIBBERELLIN INSENSITIVE DWARF 1 (GID1) to degrade the GA inhibitor DELLA proteins (Blanco-Touriñán et al., 2020). In addition, COP1/DET1 negatively regulate HY5 protein, to promote hypocotyl elongation in the dark (Figure 1).

In light, phototropin1 (PHOT1) plays a rapid role in inhibiting cell elongation below the hypocotyl apex, mainly by inhibiting the activation of H⁺-ATPases in the elongating cells (Zhao et al., 2013). CRY1 inhibits elongation in the apical zone by interacting with and stabilizing AUX/IAA proteins to suppress auxin signaling (Bustamante et al., 2025). Exposure to light decreases the GA accumulation in the hypocotyl. Under light CRY1 physically interacting with GID1 which might attenuate GID1-DELLA interaction and promote the DELLA-mediated inhibition of PIFs (Zhong et al., 2021). In red light, phyB gets activated and degrades PIFs (Park et al., 2018). It also stabilizes HEMERA (HMR) to degrade PIF1/3 in photobodies (Galvão et al., 2012). Green light regulates hypocotyl elongation through brassinosteroid signaling, however its regulation needs further investigation (Hao et al., 2023). HY5 is a positive regulator of photomorphogenesis and hy5 mutants exhibit elongated hypocotyl (Oyama et al., 1997). HY5 competes with PIFs for binding to the promoters of auxin-producing genes like YUC8 at E/G-box elements (Chen et al., 2013; Gangappa and Kumar, 2017). By decreasing the acetylation of HISTONE4 (H4), HY5 recruits HISTONE DE ACETYLASE 15 (HDA15) and other chromatin modifiers to suppress genes involved in auxin signaling and cell wall organization, while increased H3K27me3 levels suppress hypocotyl elongation (Zhao et al., 2019). Together with HY5, several BBXs also play a role in hypocotyl development, depending upon environmental cues. Cao et al., 2023, have summarized the role of BBXs in hypocotyl development. Here we primarily discuss the reports characterising the role of BBXs reported afterwards. BBX14/15/16 function redundantly to regulate hypocotyl elongation through the PIFs/HY5-GLK module, where HY5 and PIFs form a feedback regulatory loop to antagonistically regulate hypocotyl elongation in the presence of light via auxin and BR-responsive genes (Nasim et al., 2024) (Figure 1). In red light phyB interacts with BBX9, and promotes its stabilisation. BBX9 interacts with PIFs and represses their transcriptional activities in the promoter of SAUR genes, e.g.- SAUR24/29 and IAA29. Interaction between BBX9 and BBX21, a previously identified cofactor of HY5, forms a positive regulatory loop to promote photomorphogenesis under light (Song et al., 2024)(Figure 1).

Light signal transduction during cotyledon opening and greening

De-etiolation is marked by the unfolding and expansion of cotyledon as well as the establishment of the photosynthetic apparatus. This transition is essential for seedling survival and photoautotrophic growth. Cotyledon opening is one of the most prominent morphological changes during de-etiolation. While the complete understanding of the mechanism involved in opening and expansion of the cotyledons is still missing, several reviews have nicely summarized this process (Yang et al., 2020; Wei et al., 2023; Reyes-Hernández, 2025). In the dark, after germination, cotyledons remain small and closed primarily due to the action of COP1 and PIFs which are major inhibitors of light signaling. cop1 and pifq mutants exhibit open and expanded cotyledons in the dark suggesting that COP1 and the PIF proteins inhibit cotyledon opening in dark. Studies suggest, PIF1 and PIF3 play a major role in cotyledon closure as the pif1pif3 double mutant displays partially open cotyledons in dark (Shin et al., 2009). Additionally, PIF3 also negatively regulates cotyledon opening under red and far-red light (Kim et al., 2003; Xin et al., 2018).

SAURs are known for their role in promoting cell expansion and are reported to be the direct target of PIFs (Spartz et al., 2014; Sun et al., 2016). SAUR17 is identified to be highly expressed in the cotyledons and the hook regions of etiolated seedlings and responsible for maintaining the apical hook and the closed cotyledons (Wang et al., 2020). SAUR6, SAUR12, SAUR14, SAUR16, and SAUR50 are part of a subgroup of SAUR genes called lirSAUR (light-induced in cotyledons and/or repressed in hypocotyls SAUR), whose expression is oppositely affected by light in cotyledons and hypocotyls (Sun et al., 2016). LirSAURs mainly represented by SAUR16 and SAUR50, on the contrary, act antagonistically to SAUR17 and promote hook and cotyledon opening by inhibiting PP2C-D1. SAUR17 has high affinity for PP2C-D1 which inhibits SAUR50 from binding to PP2C-D1 thereby suppressing cell expansion and maintaining skotomorphogenesis under dark (Wang et al., 2020).

TEOSINTE BRANCHED1, CYCLOIDEA, and PCF (TCP) family of plant-specific transcription factors are known to be developmental regulators. CIN-like clade of TCP genes, including TCP4-like genes (TCP3, TCP4, and TCP10), were predominantly expressed in cotyledons and promotes cotyledon opening by directly regulating the expression of SAUR16 and SAUR50 (Figure 1). PIF3, which accumulates in the dark, functions to antagonize TCP4’s binding to the promoter of SAUR genes (Dong et al., 2019). TCP15, a member of class I TCP proteins, is also known to participate in regulating cotyledon opening but through different mechanisms. TCP15 requires GLK1 for efficient cotyledon opening and induction of SAUR and EXPANSIN genes involved in cell expansion and chloroplast biogenesis (Alem et al., 2025). Class II TEOSINTE BRANCHED1, CYCLOIDEA, and PCF (TCP) TCP10 are induced upon light perception which act together with GOLDEN2-LIKE1 (GLK1) to promote cotyledon de-etiolation (Figure 1). TCP15 also associates with the transcriptional loop between TCP10 and GLK1 through GLK1, which induces cell expansion (SMALL AUXIN UP RNA, EXPANSIN) and photosynthesis-associated nuclear genes (Alem et al., 2025).

Brassinosteroid (BR) is a steroidal hormone and acts antagonistic to light to regulate cotyledon opening (Wang et al., 2012). Central transcription factors, including HY5, PIFs, and BZR1, regulate downstream genes involved in cell expansion and organ movement. BZR1 induces auxin-related genes such as LAX3, WAG2, PIN1, and ACS5 to suppress cotyledon opening (Figure 1) (Li and He, 2016). In contrast, HY5 inhibits the activity of BZR1 and prevents its binding to the promoters of the above mentioned genes, thereby promoting the photomorphogenesis. B-box proteins (BBXs) function as critical integrators of light and hormonal signaling in seedlings. Studies have shown that BBX32 is expressed in cotyledons, induced by BR, and physically interacts with both BZR1 and PIF3 to suppress cotyledon opening in darkness. BBX32 thus integrates light and BR pathways to regulate cotyledon opening during the dark-to-light transition (Figure 1) (Ravindran et al., 2021). In contrast, BZS1 (BBX20) enhances light signaling but represses BR signaling. It interacts with COP1 and undergoes COP1-mediated degradation. A gain-of-function allele, BZS1-D, partially suppresses the phenotype of the constitutively active bzr1-1D mutant, and BZS1 represses numerous BR-activated genes (Fan et al., 2012). Similarly, BBX28 and BBX29 positively regulate BR signaling in Arabidopsis thaliana (Figure 1). BR treatment stabilizes these proteins in a BRI1 and BIN2 dependent manner. The mutant seedlings bbx28bbx29 display enhanced cotyledon opening in darkness when treated with brassinazole, whereas overexpression of BBX28/29 can partially rescue BR-deficient phenotypes in bri1–5 and bin2–1 mutants (Cao et al., 2022). Recent studies have shown that jasmonate, which is a major defence hormone, promotes cotyledon opening in etiolated seedlings by inhibiting COP1 activity and stabilizing HY5 and PAR1/PAR2 (Zheng et al., 2017).

Etiolated seedlings emerging from the soil strictly control chlorophyll biosynthesis and chloroplast development to harvest light energy and sustain growth, which is essential for the transition from heterotrophic to autotrophic growth. Greening of the cotyledons primarily involves the biosynthesis of chlorophyll in the chloroplasts. Chlorophyll biosynthesis is a multistep process, which starts with the conversion of glutamate to 5-aminolevulinic acid (5-ALA) via the activity of glutamyl-tRNA reductase, which eventually converts into protoporphyrin IX via the tetrapyrrole biosynthetic pathway (von Wettstein, 1991; Tanaka and Tanaka, 2007) These steps are similar to the biosynthesis of heme and phytochromobilin. The first committed step towards chloroplast biosynthesis is when Mg-chelatase acts on protoporphyrin IX to form Mg-protoporphyrin IX which is further converted to protochlorophyllide (Pchlide) (Kobayashi and Masuda, 2016). In dark-grown seedling plastids exist as etioplasts, which accumulate protochlorophyllide. Upon light exposure, there is a transition of etioplast to chloroplast, which is catalyzed by protochlorophyllide oxidoreductase (POR) enzymes. The Pchlide pool must be stoichiometrically controlled, as upon light exposure excess protochlorophyllide can accumulate large amounts of reactive oxygen species (ROS), causing photooxidative damage or even cell death (Reinbothe et al., 1996; Wagner et al., 2004; Buhr et al., 2008).

Chlorophyll biosynthesis is tightly regulated at post-translational level and transcriptional level to avoid photooxidative stress (Matsumoto et al., 2004; Mochizuki et al., 2010; Kobayashi and Masuda, 2016; Zhang et al., 2022b). FLU (fluorescence) plays an important role during post translational regulation as it forms a protein complex with a subunit of the Mg-protoporphyrin IX monomethyl ester oxidative cyclase (CHL27), PORB, and PORC and is involved in the feedback control of glutamyl tRNA reductase (GluTR) by inhibiting 5-aminolevulinic acid (ALA) synthesis (Meskauskiene et al., 2001; op den Camp et al., 2003; Mochizuki et al., 2010; Kauss et al., 2012). Thus, dark-grown fluorescence (flu) mutants lead to rapid photobleaching due to excessive Pchlide accumulation. During transcriptional regulation, several transcription factors are involved that regulate the expression of photosynthesis-associated nuclear genes (PhANGs). PHYTOCHROME-INTERACTING FACTORs (PIFs) are known to be primarily involved in cotyledon greening by negatively regulating the expression of a number of tetrapyrrole biosynthetic genes including CHLOROPHYLLIDE a OXYGENASE (CAO), GLUTAMYL-tRNA REDUCTASE 1 (HEMA1), GENOMES UNCOUPLED 4 (GUN4), and GUN5 to repress chlorophyll biosynthesis. They also activate the transcription of ROS-responsive genes like ASCORBATE PEROXIDASE 2 (APX2) and ZAT ZINC FINGER PROTEIN 10 (ZAT10), thereby enhancing ROS scavenging and preventing cell death during seedling de-etiolation (Monte et al., 2004; Stephenson et al., 2009). Dark grown pif mutants accumulate excessive Pchlide but low activity of POR enzymes causing photooxidative damage upon light exposure (Monte et al., 2004; Stephenson et al., 2009).

In light conditions, ELONGATED HYPOCOTYL5 (HY5), GOLDEN2-LIKE (GLK), GATA NITRATE-INDUCIBLE CARBON-METABOLISM-INVOLVED (GNC), CYTOKININ-RESPONSIVE GATA1 (CGA1)/GNC-LIKE (GNL), and MYB-related transcription factors (MYBS1/2) individually enhance PhANG expression, chlorophyll biosynthesis, and chloroplast development (Figure 2) (Lee et al., 2007; Waters et al., 2009; Wang et al., 2013; Hernández-Muñoz et al., 2024). BBX11 has been reported to regulate protochlorophyllide levels by acting downstream of PIF3 in the dark. Upon light exposure HY5 binds to the promoter of BBX11 and activates it to promote photomorphogenesis (Job and Datta, 2021). Recently, BBX10 has also been reported for its role in cotyledon greening. In darkness it inhibits the accumulation of protochlorophyllide which leads to reduced ROSs upon light irradiation ultimately promoting greening during de-etiolation. BBX10 directly interacts with PIF1 and enhances its biochemical activities toward target genes GUN5 and APX2 (Zhou et al., 2025). GLKs are acknowledged as the key regulators of chloroplast development and have been studied across multiple species. In Arabidopsis thaliana, GLK1 and GLK2 operate redundantly to induce the expression of photosynthesis-associated nuclear genes (PhANGs) by binding to their promoter regions under light. Under light or BR deficiency, BRZ-INSENSITIVE-PALE GREEN 4 (BPG4) expression is transcriptionally upregulated. It acts as a chloroplast homeostasis factor, which interacts with GLKs and suppresses their transcriptional activity to promote the expression of PhANGs, thereby causing a decrease in the amounts of chlorophylls and the size of light-harvesting complexes. BPG4-deficient mutants cause enhanced reactive oxygen species (ROS) generation and damage to photosynthetic activity under excessive/high intensity light conditions. PIFs are suggested to be involved in the transcriptional activation of BPG4 in the light, but further research needs to be done for better understanding (Tachibana et al., 2024). In Arabidopsis, BPG4 has 3 paralogs: BPG4 HOMOLOGOUS GENE 1, 2, and 3, which correspond to BGH1, BGH2, and BGH3, respectively. BGH2 is accumulated under dark by transcriptional activation by PIFs, and it suppresses excessive proto chlorophilide accumulation via interaction with GOLDEN2-LIKE 1 (GLK1) and GLK2 promoting cotyledon greening during de-etiolation (Figure 2) (Tachibana et al., 2025).

During seedling establishment, ethylene, which is a gaseous hormone, is triggered as a response to the mechanical pressure experienced by the seedlings. ETHYLENE-INSENSITIVE 3/1 (EIN3/EIL1) are key regulators of chlorophyll biosynthesis, which are regulated by ethylene via EIN2 and ETHYLENE-INSENSITIVE-BINDING F BOX PROTEIN 1/2 (EBF1/2). In the dark, EIN3 and EIL1 markedly repress accumulation of Pchlide and directly associate with the promoters of PORA and PORB to prevent cotyledons from photooxidative damage. Ethylene suppresses the activity of EBF1/EBF2 to stabilize EIN3 and activate ethylene responses. Upon light perception, active phyB directly associates with EIN3 and targets it to the E3 Ubiquitin ligase EBF1/2, which rapidly degrades it. EIN3 and PIF3 act interdependently in regulating the chloroplast development by inhibiting the transcription of most LIGHT HARVESTING COMPLEX (LHC) genes to repress chloroplast development. Recently, BBX32 has been identified as an important regulator that protects seedlings against severe photobleaching damage. Upon light perception, BBX32 directly interacts with EIN3, PIF3, and EBF1/2 and reduces the interactions of EIN3 and PIF3 with their E3 ligase EBF1/2, thus attenuating degradation (Wang et al., 2025). Also, BBX32 has been reported to enhance seedling soil emergence by enhancing PIF3 on HLS1 (HOOKLESS1) promoter (Ravindran et al., 2025). Taken together, while the molecular knowhow about cotyledon opening and greening has expanded we still need a better understanding of the whole process. We have summarized the identified molecular components regulating the early seedling development in Arabidopsis in Figure 3 depicting the possible connection and crosstalk between the signaling molecules regulated by light and phytohormones.

Light signaling in early land plants: Chlamydomonas reinhardtii

Chlamydomonas reinhardtii belongs to the division chlorophyta in Kingdom Plantae which serves as a unicellular model organism for studying photosynthesis, the development and function of cilia/flagella, and evolution of the complex structure of the chloroplast. Its haploid genome makes it an ideal candidate for genetic studies (Salomé and Merchant, 2019). Light signalling in Chlamydomonas reinhardtii is coordinated via a specialized organelle called the eyespot and an array of photoreceptors like channel rhodopsins, cryptochromes, UVR8 photoreceptors, phototropins. These help the algae to sense the photon stimulus and regulate its physiological and developmental processes in response to changes in light intensity and direction. Chlamydomonas reinhardtii can show either positive phototaxis (movement towards light source) or negative phototaxis (movement away from light source) and these movements are caused due to change in flagellar motion upon perception of light by eyespot (Hegemann, 2008). These changes in flagellar motion are primarily caused due to plasma membrane depolarization mediated by influx of cations through channel rhodopsins (Hegemann, 2008).

Chlamydomonas reinhardtii possesses two channel rhodopsin proteins (CHR1 and CHR2) localised in the eyespot where they function as light gated ion channels mediating phototaxic and photophobic responses (Hegemann, 2008). Both of them possess distinct spectral responsiveness with CHR1 showing maximum absorption in the green region of the spectrum and CHR2 shows maximum absorption in the blue region of spectrum (Hegemann, 2008). Activated CHR1 causes influx of cations leading to depolarisation causing light triggered changes in flagellar motion that enable directional movement in response to light (Hegemann, 2008). CHR2 similarly functions as a light gated cation selective ion channel that is involved in the photoreception specifically under low light intensities (Nagel et al., 2003). Moreover at higher intensities CHR1 gets degraded leaving CHR2 as a major contributor to photocurrent generation under these climatic conditions (Nagel et al., 2003).

Beyond the realm of visible light signalling, Chamydomonas reinhardtii displays UVB signalling transduction mechanism which is conserved in accordance with complex life forms like angiosperms (Tilbrook et al., 2016). It possesses an UV-B sensing protein called Cr-UVR8 which contains crucial tryptophan residues for UV-B perception, similar to the AtUVR8. When exposed to UV-B, Cr-UVR8 monomerizes to interact with Cr-COP closely paralleling the UV-B signalling mechanism described for angiosperms (Tilbrook et al., 2016) (Figure 4). The ability of Cr-UVR8 to functionally complement UV-B mediated signaling in Atuvr8 null mutants further supports the functional conservation (Tilbrook et al., 2016). In Arabidopsis thaliana, downstream to AtUVR8 and AtCOP1, AtHY5 acts as key transcription factor to promote UV responsive genes but the role of downstream components in the UV signalling pathway is not well explored in Chlamydomonas (Tilbrook et al., 2016).

Chlamydomonas reinhardtii possess both plant-like and animal-like cryptochromes and two DASH cryptochromes which makes it a suitable model for studying cryptochrome evolution and function (Müller et al., 2017). The gene CPH1 (CHLAMYDOMONAS PHOTOLYASE HOMOLOG 1) encodes a putative plant-like cryptochrome protein of 867 amino acids with a predicted molecular mass of 91 kD (Small et al., 1995; Reisdorph and Small, 2004). This Cr-CPH1 gets accumulated under dark and as soon as it is exposed to blue or red light, it starts getting degraded which suggests a light dependent regulation of CrCPH1 (Reisdorph and Small, 2004). Functionally CrCPH1 is shown to be a positive regulator of zygote germination but a negative regulator of mating indicating its dual role in the sexual life cycle ( (Müller et al., 2017). On the other hand, aCRY (an animal-like cryptochrome of Chlamydomonas reinhardtii) shows broad spectral responsiveness as it can respond to more than one wavelength, such as blue and red light (Beel et al., 2012). Interestingly, aCRY can exist in three redox states, a feature that might be responsible for its ability to respond to multiple wavelengths. Expression of aCRY is found to be dynamically regulated throughout the life cycle playing an important role in sexual reproduction. It positively influences the germination of the alga, during which the zygote undergoes meiosis, akin to the regulation by blue light receptors such as phototropin and plant cryptochrome (pCRY). Nonetheless, aCRY functions alongside pCRY as a negative regulator for both mating capability and mating persistence, contrasting with the role of phototropin in these processes (Zou et al., 2017) (Figure 4). aCRY role has also been found in DNA repair (Franz et al., 2018).

Out of the two CrCRY-DASH proteins identified in C.reinhardtii CRY-DASH1 shows similarity to DASH-cryptochrome subfamily members like CrCRY3 of Arabidopsis (Rredhi et al., 2021). It is localised in the plastid and does maximum absorption in the UV-A range with MTHF(5,10-methenyltetrahydrofolate) serving as its chromophore. Functional analysis of cry-dash1 mutants show increased stacking of thylakoids and increased levels of chlorophyll and carotenoid suggesting a probable role in preventing excess grana formation and regulating pigmentation (Rredhi et al., 2021).

Chlamydomonas reinhardtii contains a single phototropin gene CrPhot which shows high sequence similarity with arabidopsis PHOT1 and PHOT2 consisting of two LIGHT, OXYGEN and VOLTAGE domains (LOVE1 and LOVE2) at its N-terminal and a ser/thr kinase domain at C-terminal (Huang et al., 2002). CrPhot is important for sexual reproduction in Chlamydomonas reinhardtii. Its life cycle involves germination of a zygote to give rise to four independent vegetative cells. These vegetative cells develop as pre-gametes upon nitrogen starvation under dark. Further, these cells turn into mature gametes upon blue light illumination, indicating the importance of blue light in sexual reproduction. These gametes lose their mating competence under dark but this is photo-reversible. CrPhot is essential for all these three processes: gamete formation, the maintenance of mating competence in gametes, and zygote germination,. Knock down of CrPhot results in defects in all these three events. Taken together CrPhot has a pivotal role in Chlamydomonas reinhardtii sexual reproduction. Chlamydomonas reinhardtii accumulates starch during the day, and breaks it down at night. Light regulates the starch metabolism as well. In a recent study, blue light mediated starch metabolism has been uncovered. PHOTOTROPIN-MEDIATED SIGNALING KINASE 1 (PMSK1) in its phosphorylated state promotes GLYCERALDEHYDE- 3-PHOSPHATE DEHYDROGENASE (GAP1) which in turn leads to starch accumulation (Figure 4). Blue light activated CrPhot dephosphorylates the PMSK1 which further inhibits GAP1 to reduce the starch accumulation. Hence the crphot mutants are hyper starch accumulators (Yuan et al., 2025). CrPhot has its own mark in dynamic maintenance of the eyespot size. Dark increases the eyespot size whereas light decreases it. The knockout strain lacking CrPhot has a larger eyespot irrespective of presence or absence of light. CrPhot regulates channelrhodopsin-1(ChR1) levels which is a key receptor in the eye spot for tuning photo-taxis (Trippens et al., 2012). CrPhot localises in the axoneme of flagella to serve as a cargo mediating the intra-flagellar transport (Huang et al., 2004). Taken together the light signalling components for UVB signalling, cryptochromes, and phototropins are well conserved in Chlamydomonas but the phytochromes are not reported yet. Table 1 contains the light signaling genes characterised in Chlamydomonas. Apart from these photoreceptors, Chlamydomonas also possess channel rhodopsins to facilitate its locomotion towards the light.

Table 1. Light signalling factors in Chlamydomonas reinhardtii.

Light signaling mechanisms regulating growth and development of Marchantia polymorpha

Marchantia polymorpha is considered to be an ideal model system to study the signaling mechanisms among the thallophytes. Sequenced genome of Tak-1 contains 8 pairs of autosomes and a single X/Y sex chromosome. Its haploid dominant phase in the lifecycle is one of the greatest advantages of studying Marchantia. Marchantia polymorpha has only one copy for most of the light signaling factors studied in Arabidopsis like a single copy for cryptochrome (MpCRY), phytochrome (MpPHY) and for UVR8 (MpUVR8) (Inoue et al., 2016; Zhang et al., 2022; Liang et al., 2025). MpCRY protein forms homodimers under blue light (Figure 5). MpCRY inhibits ABA signaling genes that inhibit gemma dormancy in blue light (Figure 5) (Liao et al., 2023). Blue light also promotes several secondary metabolites accumulation in Marchantia by enhancing the expression of chalcone synthase (CHS), cellulose synthase (CELL), and L-ascorbate peroxidase (APOX3) (Zhang et al., 2022a). Downstream to MpCRY, the MpCOP1-MpSPA complex acts as a central regulatory network for skotomorphogenic responses (Figure 5). MpSPA knockout mutants exhibit asymmetrical thallus growth. MpCRY knockout mutant mimics the MpSPA knockout mutant phenotype with respect to thallus asymmetric growth. MpSPA interacts with MpCRY in a blue light independent way whereas MpSPA interacts with MpCOP1 in a blue light dependent way. MpCOP1 along with MpSPA ubiquitinates MpHY5 (Figure 5). In Arabidopsis, CRY1 and CRY2 inhibit COP1-SPA mediated ubiquitination of HY5, whereas in Marchantia, MpCRY does not regulate the MpCOP1-MpSPA mediated MpHY5 ubiquitination (Figure 5). This suggests that the COP1/SPA mediated HY5 regulation is conserved in Marchantia polymorpha but MpCRY does not inhibit the MpHY5 ubiquitination under blue light (Figure 5) (Zhang et al., 2022a). In Marchantia, MpHY5 also regulates chloroplast development although there is still a lot to be explored (Yelina et al., 2024). Marchantia perceives blue light by phototropins (MpPHOT) as well. Phototropins are known to regulate chloroplast movement in angiosperms. Under low blue light, phototropins enhance chloroplast accumulation to maximise the photosynthesis while high intensity blue light promotes chloroplast avoidance for phoptoprotection. This mechanism is conserved in Marchantia which has a single copy of the phototropin gene, MpPHOT. MpPHOT knock out mutants don’t show any chloroplast movements. MpPHOT successfully rescued chloroplast movement defects in fern Adiantum capillus-veneris and also the angiosperm Arabidopsis thaliana. In Marchantia, MpPHOT undergoes cis-autophosphorylation that leads to the chloroplast accumulation under low blue light;whereas it undergoes both cis-autophosphorylation and trans-autophosphorylation ultimately leading to chloroplast avoidance response under high light and cold stress (Komatsu et al., 2014; Noguchi et al., 2025).

MpHY5 regulates only a few genes in the UV-B signaling pathway in Marchantia polymorpha, whereas in Arabidopsis HY5/HYH module regulate the majority of UV-B signaling genes (Liang et al., 2025). Marchantia polymorpha possesses a single ortholog of AtUVR8 i.e. MpUVR8. MpUVR8 also forms UV-B mediated homodimers similar to AtUVR8. MpUVR8 monomers interact with MpCOP1 in nuclei under UV-B irradiation. MpRUP favours MpUVR8 dimerization to inhibit the signaling. Interestingly, Mpspa mutants are hyper-responsive to UV-B, indicating MpSPA act divergently from Arabidopsis (Liang et al., 2025). Upon exposure to the red or far-red (R/FR) light, Marchantia phytochrome (MpPHY) shows photo-reversibility between P_r and P_fr forms (Figure 5). In Marchantia the gemma germination is red light dependent and MpPHY is required for the gemma germination (Inoue et al., 2016, 2019) (Figure 5). Constitutive expression of MpPHY enhances the gemmae germination. Downstream to MpPHY, there is only a single copy of PIF, MpPIF. MpPIF acts as a negative factor and inhibits germination and under light MpPHY causes the degradation of MpPHY, similar to that of Arabidopsis (Figure 5) (Inoue et al., 2019). This indicates the PHY-PIF module is functionally conserved in the liverworts. MpPIF also inhibits the expression of light responsive genes e.g. - LIGHT- HARVESTING CHLOROPHYLL A/B BINDING PROTEIN (MpLHCB) and PROTOCHLOROPHYLLIDE OXIDOREDUCTASE (MpPOR) in Marchantia (Inoue et al., 2016).

The thallus architecture of Marchantia is tightly regulated by its meristem activity. The active meristem develops dichotomous branching in Marchantia. Interestingly, the light signalling components especially MpPIF signals the meristem activity to control overall architecture of Marchantia. Clade III SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor MpSPL1 promotes meristem dormancy to orchestrate the apical branching in liverworts (Streubel et al., 2023) (Figure 5). A liverwort-specific Mpo-MR13, miRNA inhibits MpSPL1. Mp-MR13 is further negatively controlled by the MpPIF (Figure 5). Under white light, lower levels of MpPIF leads to the accumulation of Mp-MR13 which strongly inhibits MpSPL1 that breaks the meristem dormancy and promotes branching (Streubel et al., 2023) (Figure 5). Under shade conditions, MpPIF levels are up and strongly inhibits MP-MR13 which favours the accumulation of MpSPL1. This promotes meristem dormancy and inhibits branching. Hence, light modulates meristem dormancy to control MpPHY-MpPIF mediated branching through Mpo-MR-13 and MpSPL1 cascade (Streubel et al., 2023).

The MpPHY-MpPIF module is also required for the FR responses. One of such FR response is, MpPIF positively regulates GA biosynthetic genes like (MpCPS) COPALYL DIPHOSPHATE SYNTHASE, (MpKAOL1) KAURENOIC ACID OXIDASE-LIKE PROTEIN 1 under FR enriched conditions (Sun et al., 2023). MpPIF also interacts with a major gibberellic acid signaling inhibitor MpDELLA to regulate growth under stress. Oxidative stress induces the accumulation of MpDELLA that inhibits MpPIF to promote sexual reproduction. MpPIF also favours gemma dormancy under stress to halt the growth. It inhibits production of the flavonoids which are required for stress tolerance (Hernández-García et al., 2021). Additionally, MpPHY regulates chloroplast development under FR enriched conditions. It promotes agranal chloroplasts with starch content which results in reduction in photosynthetic efficiency of the thalli (Pashkovskiy et al., 2023). Another FR-HIR (FAR RED-HIGH IRRADIANCE RESPONSE) response is gametangiophore formation, which is a sign of induction of sexual reproduction. Apart from its canonical role, MpPHY along with MpFHY1 (FAR-RED ELONGATED HYPOCOTYL1) regulate induction of the sexual reproduction program in Marchantia. Knockout of MpPIF, abolished the FR-HIR-dependent gametangiophore formation, while its overexpression enhances this response. This indicates that a single MpPHY mediates both LFR and FR-HIR response (Inoue et al., 2019).

During spore germination, light promotes anisotropic division in early meristem to build auxin minima in the upper cell mass. This favours the prothallus development. In the absence of light, early cell mass undergoes isotropic cell division which disrupts the lower auxin minimum in upper cell mass which ultimately aborts the growth (Wallner et al., 2025). Further investigations to uncover the involvement of any specific monochromatic light in the vegetative and reproductive development are required. We have concisely mentioned the light signalling factors and their involvement in the molecular mechanisms regulating growth and development in Marchantia in Table 2.

Table 2. Light signaling factors and their identified roles in Physcomitrium and Marchantia.

Light signaling components regulating growth and development in Physcomitrium patens

Physcomitrium patens is one of the well-studied model Bryophytes. Its life cycle oscillates between dominant haploid gametophytic phase and a diploid sporophytic stage. They undergo various developmental changes during their life cycle which are light regulated. P. patens has phytochromes and cryptochromes whose amino acid sequences are highly homologous to their counterparts in A. thaliana, suggesting conserved light-sensing mechanisms in the plant kingdom (Yamawaki et al., 2011). It has two orthologs of cryptochrome e.g.- PpCRY1a and PpCRY1b, seven orthologs of phytochrome (PpPHY1, PpPHY2, PpPHY3, PpPHY4 and PpPHY5a/b/c), nine orthologs of COP1 PpCOP1a/b/c/d/e/f/g/h/i, two orthologs of SPA1 (PpSPAa and PpSPAb)and two orthologs of HY5 i.e. PpHY5a and PpHY5b (Yamawaki et al., 2011).

Phytochromes in P. patens are grouped into 3 clades i.e. PHY1/3, PHY2/4 and PHY5a/b/c (Yuan et al., 2023). Phytochromes regulate various aspects of development in P. patens such as and protonemal branching in juvenile phase and gametophore growth, induction in later stages of development (Yuan et al., 2023). PpPHYs show sensitivity to both red (20uM/m²sec) and blue (12uM/m²sec) light (Yuan et al., 2023). In the wild type (Grandsen) moss grown under blue and white light, the number of gametophores is more and protonemal filaments are green. However, phytochrome septuple mutant shows decrease in number of gametophores and a brown appearance (Yuan et al., 2023). The Phy5abc triple mutants show reduced induction of gametophores while Ppphy1234 quadruple mutants showed a reduction in protonemata growth under blue light (Yuan et al., 2023). These suggest a crucial role of phytochromes in gametophore development and chlorophyll biosynthesis under blue light. PpPHY5abc clade is primarily responsible for mediating red light triggered responses (Figure 6) as the mutants for the other phytochromes i.e. Ppphy1/3 and Ppphy2/4 do not show any phenotype under red light conditions. But in the PpPHY5abc mutants reduction in the number of gametophores induced were low, protonemal branching is also inhibited and the chloronema to caulonema transition hampered as well under red light, suggesting their major role in perception of red light (Yuan et al., 2023). Among the members of PpPHY5 clade, PpPHY5a is the central player and required for the red and blue light triggered responses, studies carried out with single and double mutants showed that PpPHY5a/b/c play a redundant role (Yuan et al., 2023). PHY1/3 are responsible for perceiving far-red light (Figure 6) and regulate the branching of protonemata and induction of gametophore under far-red light (Yuan et al., 2023). Physcomitrium patens respond to the canopy shade conditions as well, by elongating the gametophores. PpPHY1/2/3/4 play a redundant role in sensing low red: far-red ratio in light and elongating the gametophores. The nuclear localisation of the PpPHYs are conserved in Physcomitrium patens as PpPHY1/2/3/4 get localised to the nuclei upon exposure to light, while PpPHY1 requires FAR-RED ELONGATED HYPOCOTYL 1 (PpFHY1) for getting localised to the nucleus (Possart and Hiltbrunner, 2013) (Figure 6). In the perspective of evolutionary conserved roles PpPHYs stand out as they respond to the blue light irradiations while their role in regulating protonema growth and branching, chloronema to caulonema transition as well as responsiveness to the shade conditions are well conserved in other organisms. PpPHYs are also responsible for red light mediated movement in Physcomitrium patens (Kasahara et al., 2004).

In Physcomitrium patens, there are two orthologs of AtCRYs i.e. PpCRY1a and PpCRY1b. Both PpCRY1a and PpCRY1b contain nuclear localization signals (NLS) at their C-terminus and localise to the nucleus (Imaizumi et al., 2002) (Figure 6). PpCRY1a and PpCRY1b play redundant role in regulating certain developmental steps throughout the moss life cycle, including induction of side branching on protonema as well as the gametophore induction and development (Imaizumi et al., 2002). PpCRYs inhibit the auxin signaling leading to the regulation of developmental steps (Imaizumi et al., 2002). PpCrys negatively regulate SQUAMOSA PROMOTER BINDING PROTEIN (SBP) domain transcription factors PpSBP1and PpSBP4, which act as negative regulators of side branch formation in the protonema.

Four orthologs of AtPHOTs are identified in Physcomitrium patens and are grouped into two categories PpPHOTA1, PpPHOTA2 and PpPHOTB1, PpPHOTB2 on the basis of their amino acid sequences (Kasahara et al., 2004)(Figure 6). PpPHOTA2, PpPHOTB1 and PpPHOTB2 are expressed under both light and dark conditions. Expression of PpPHOTA1 is specific to blue light illumination and gets inhibited under dark (Kasahara et al., 2004). PpphotA2–1 mutants lack the chloroplast avoidance movement in the basal cells of protonema while the tip cells of protonema lacked chloroplast movement in PpphotA1PpphotA2-1, suggesting that the group PpPHOTA is responsible for mediating photo avoidance response under blue light and are the functional ortholog of AtPHOT2 (Kasahara et al., 2004). At higher fluence rates photB1B2 double mutants showed avoidance response indicating a functional redundancy (Kasahara et al., 2004). Phototropins also have a role in mediating phytochrome dependent chloroplast movements as PpphotA2PpphotB1PpphotB2 triple mutants lack red light driven avoidance and accumulation response (Kasahara et al., 2004). Since PpPHY5abc are mainly responding to red light, it is speculated that PpPHOTA2,PpPHOTB1 and PpPHOTB2 are downstream to unexplored pathway involving PHYabc.

The two orthologs of HY5 in Physcomitrium patens i.e. PpHY5a and PpHY5b play crucial role in caulonemal cells development under light and dark conditions as the double mutants for PpHY5a/b are defective in caulonemal development (Yamawaki et al., 2011). Examination of diurnal transcriptional profiles revealed that expression of PpHY5a was light inducible, and it also showed strong induction when exposed to red and blue light after a brief incubation in dark (Yamawaki et al., 2011). Although both the orthologs are share their amino acid sequence similarity, but differ in terms of expression upon exposure to light. This suggests PpHY5a is more important for light signaling. Overexpressing PpHY5a in A. thaliana recovered the elongated hypocotyl phenotype of Athy5 mutants suggesting functional redundancy and evolutionary conservation between AtHY5 and PpHY5a. Further studies can unravel the signaling mechanism connecting PpHY5 and PpPHYs as well as PpCRYs.

(Kreiss et al., 2023) COP1 orthologs in Physcomitrium (PpCOP1a/b/c/d/e/f/g/h/i) share approximately 54-64% sequence similarity with AtCOP1 and have at least one ring finger motif, coiled coiled domain and WD40 repeat domain. Out of the 9 orthologs COP1a is the closest ortholog of AtCOP1 (Ranjan et al., 2014). PpCOP1a is only able to partially rescue the constitutive photomorphogenic phenotype shown by Atcop1-4 (Ranjan et al., 2014). The phenotype of Ppcop1 nonuple mutants resembles that of Ppspa mutants (Kreiss et al., 2023). Most importantly, both mutants produce green chloroplasts in complete darkness. They also exhibit dwarfed gametophores, disturbed branching of protonemata under different light conditions. PpCOP1 and PpSPA proteins form a complex and they interact via their WD repeat domains, also both show interaction with PpCRY1b under blue light (Kreiss et al., 2023). This suggests that PpCOP1/PpSPA complex regulates various developmental and physiological aspects in Physcomitrium patens such as branching and greening of protonema and gametophore development in blue light dependent manner downstream to CRY1b (Figure 6). This resembles the interaction of AtSPA1 with AtCRY1 (Lian et al., 2011). Ppcop1 nonuple mutants continued normal gametophore growth in dark and grew to a larger size than wildtype with leaflets that were slightly expanded than wildtype and Ppspa mutant (Kreiss et al., 2023). RNA-sequencing (RNA-seq) analysis of wild-type, Ppcop1_9x, and Ppspa_ab mutant grown in darkness or subjected to 24 hours of white light indicated that PpCOP1 and PpSPA repress light-responsive genes in darkness. However, light-regulated gene expression in Ppcop1 and Ppspa is only partially constitutive, suggesting that PpCOP1 and PpSPA proteins may not be the sole repressor of light-responsive genes in darkness (Kreiss et al., 2023).

The predicted domain structures of Physcomitrium SPA proteins are similar to SPA proteins in Arabidopsis. They both contain an N-terminal kinase-like domain, a coiled-coil domain, and seven WD40-repeats. Both PpSPAa and PpSPAb show similarity to AtSPA1 (Ranjan et al., 2014). However, PpSPAb gene driven by AtSPA1 and AtSPA4 promoters failed to rescue the phenotype of Atspa1/3/4 triple mutant and Atspa1/2/3 triple mutants (Ranjan et al., 2014). PpSPAa and PpSPAb double mutants develope smaller gametophores than wildtype while PpSPAa single mutants also show reduction in the length of the gametophores (Artz et al., 2019). This suggests that PpSPA genes contribute to gametophore development redundantly with PpSPAa being the major contributor as the mutants of PpSPAb exhibited insignificant dwarfing of gametophores. In Ppspaa/b double mutants, the leaflet formation is impaired hence show an etiolated phenotype which is strikingly different from spaQ which shows constitutive photomorphogenesis. The protonema grows faster in Ppspaa/b double mutant, suggesting that PpSPA genes negatively regulate protonemal growth (Artz et al., 2019). Transcriptomic analysis carried out in Ppspaa/b background for 3 strongly light regulated genes PpPOR, PpFNR and PpFEDa also confirmed that partial constitutive light signaling prevails in Ppspa double mutants which can be due to the action of COP1 orthologs in P. patens (Artz et al., 2019).

Physcomitrium patens contains four orthologs for PIFs named PpPIF1/2/3/4 (Possart et al., 2017). There exist some significant variations in the PpPIFs for motif-dependent PHY interaction, similar to AtPIFs in terms of protein domain structure, molecular characteristics, and physiological consequences (Possart et al., 2017). Physcomitrium patens contains potential PIF homologues and they complement the constitutively photomorphogenic phenotype of the pifQ mutant in Arabidopsis (Xu et al., 2020). PpPIFs have a function in the expression of light-regulated genes, similar to PIFs in Arabidopsis thaliana. PpPIF1/3/4 interact with PpPHY1/3/2/4 in a light dependent manner suggesting that the function of PIFs in phytochrome downstream signaling might be conserved in land plants (Possart et al., 2017).This interaction prevents PpPIF mediated transcriptional regulation but. On analyzing the gametophore induction and development in different Pppif mutants, no significant deviation from the wild type was observed (Xu et al., 2020). These genes are down regulated in both wild-type and mutant under continuous white light conditions. This suggests that PpPIFs have discrete roles to play in light mediated responses under specific conditions. We have concisely mentioned all the light signalling factors in Physcomitrium in Table 2. A recent report identifies that blue light facilitates the regeneration in P. patens, this cellular reprogramming is mediated through SHMT1, which accumulate more under bluelight (Zhao et al., 2025). Though the photoreceptors, and their downstream components are identified but there exist a few non canonical functions such as both red and blue light perception by PpPHYs, red light mediated chloroplast movement and etiolated phenotypes of Ppspaa/b mutants. However further studies can reveal the complete understanding of the mechanisms.

Concluding remarks

Light is one of the external cues regulating growth and development of terrestrial plants. While the light signaling mechanism regulating early plant development is well studied in Arabidopsis thaliana, its role in early plant development is increasingly being investigated. In Arabidopsis the activation of the light signaling takes place by the light perception by the photoreceptors. The downstream signaling cascades involve PIFs, HY5, COP-DET-FUS etc. signalling components which regulate a wide range of physiological functions including seed germination, apical hook opening, hypocotyl elongation, cotyledon opening and greening (Figure 3). The temporal and spatial localization of some of the key regulators mentioned above and their stability modulate the transcription of the downstream genes. The connection between the light signaling and phytohormones regulating the early seedling establishment continuously expanding. The hypocotyl length regulation by the BBXs (BBX14/15/16), the CRY-mediated regulation of auxin and GA signaling and the SAURs interaction with TMK regulating the alkalization of the extracellular matrix are a few examples of novel findings in this area.

There are many studies that identified light perception and phototactic behaviour in Chlamydomonas reinhardtii. It utilizes the light cues by converting light as an electrical signal to orchestrate the flagella beating pattern. Using the model organisms Marchantia polymorpha and Physcomitrium patens scientists have recently started developing a better understanding of the light signaling mechanisms in bryophytes. The core module of light perception, signal transduction and response seems to be quite conserved throughout the lineage starting from Chlamydomonas, Marchantia, Physcomitrium and Arabidopsis. However, presence or absence of photoreceptors and some downstream components and responses are quite divergent. In Chlamydomonas, light perception takes place by the eyespot, and the membrane localized photoreceptors. Channel rhodopsins which act as ion channels causing depolarisation of membranes, perceive blue and green light to mediate the phototactic movements. It also possesses orthologs of cryptochromes, and a single copy of phototropin for the blue light perception and signalling. In addition to photosynthesis, light regulates sexual reproduction, starch biosynthesis and UV acclimatation. The established mechanisms of CrPhot mediated regulation of PMSK1 in starch biosynthesis and CrUVR8 mediated promotion of UV acclimatation by CrCOP1 accumulation is established but the downstream HY5 mediated gene networking is not well explored in Chlamydomonas. Orthologs of AtRUP1 and AtRUP2 also need to be characterised in Chlamydomonas.

In Marchantia, light perception shares both similarities as well as differences from Physcomitrium and Arabidopsis. The conventional phytochrome P_r and P_fr conversion is well conserved in Marchantia. Since Marchantia has single phytochrome, it takes over both red and far-red light perception and signaling mechanisms which is different from Physcomitrium and Arabidopsis. Downstream to MpPHY, MpPIF regulates gemma germination, sexual reproduction and meristem dormancy. In case of blue light perception and signaling, the CRY mediated inhibition of COP1 is absent in Marchantia. However, MpCRY inhibits ABA responsive genes to inhibit gemma dormancy. Further studies are required in Marchantia to completely understand light signaling in this liverwort.

In Physcomitrium patens, the genome is more complex than Chlamydomonas, and Marchantia. It has multiple copies of photoreceptors and light signaling genes. It has even higher copies of genes than Arabidopsis for some of the signaling pathways particularly light signaling. Red light is perceived by PpPHYabc whereas far red light is perceived by the PpPHY1/3. Blue light is perceived by PpPHOTs and PpCRYs. CRY mediated inhibition of HY5 by COP1 is conserved in Physcomitrium patens. PpCOP has nine copies in Physcomitrium whereas there is only one AtCOP1. However, interestingly Physcomitrium has only two SPA proteins, but Arabidopsis has 4 SPAs. And COP and SPA proteins are not solely skotomorphogenic promoters in Physcomitrium, since the absence of COP and SPA could not abolish expression of all light regulated genes in dark. Also, Ppcopn develop green chloroplast in dark which is not usual in the Arabidopsis. Physcomitrium possess four orthologs of photropins which mediate red and blue light mediated chloroplast movements. Interestingly PHYabc are mainly responsible for perceiving red light therefore we speculate that PpPHOTA2, PpPHOTB1, PpPHOTB2 are key players of red light mediated chloroplast movements involving PHYabc since the triple mutants for the above mentioned three phototropins don’t show red light mediated chloroplast movements. All these together suggest that while the core light perception and signaling is well conserved among these species there is a lot of difference in the number copies of the light signaling genes and their functional divergence during evolution.

Genes regulating the photoreceptors and other light signaling pathway components have evolved during the process of land invasion by plants. Further characterization of the light signaling components in green algae, and bryophytes like Physcomitrium and Marchantia will enhance our understanding of the role of light in shaping plant development over time. The use of technologies like single cell and spatial transcriptomics, long-read RNA sequencing, live imaging methods and hormonal bio-sensors might help enhance our knowledge about the evolution of light signaling in plants. These studies might further facilitate the use of optogenetic methods and genome editing tools in modulating light-mediated development for enhanced resilience under changing climatic conditions.

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Footnotes

Edited by: Jay Prakash Maurya, Banaras Hindu University, India

Reviewed by: Ye Zhao, Beijing Forestry University, China

Miroslava Rakocevic, State University of Northern Rio de Janeiro, Brazil

Junjie Ling, Anhui Agricultural University, China