Chloroplasts in C3 grasses move in response to blue-light

Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, Scaevola taccada and S. hainanensis-Insight into Adaptation Outside of the Common Range

While most of the species in Goodeniaceae family, excluding the Scaevola genus, are endemic to Australasia, S. taccada and S. hainanensis have expanded their distribution range to the tropical coastlines of the Atlantic and Indian Oceans. S. taccada appears to be highly adapted to coastal sandy lands and cliffs, and it has become invasive in places. S. hainanensis is found mainly in salt marshes near mangrove forests, and is at risk of extinction. These two species provide a good system to investigate adaptive evolution outside the common distribution range of this taxonomic group. Here, we report their chromosomal-scale genome assemblies with the objective of probing their genomic mechanisms related to divergent adaptation after leaving Australasia. The scaffolds were assembled into eight chromosome-scale pseudomolecules, which covered 90.12% and 89.46% of the whole genome assembly for S. taccada and S. hainanensis, respectively. Interestingly, unlike many mangroves, neither species has undergone whole-genome duplication. We show that private genes, specifically copy-number expanded genes are essential for stress response, photosynthesis, and carbon fixation. The gene families that are expanded in S. hainanensis and contracted in S. taccada might have facilitated adaptation to high salinity in S. hainanensis. Moreover, the genes under positive selection in S. hainanensis have contributed to its response to stress and its tolerance of flooding and anoxic environments. In contrast, compared with S. hainanensis, the more drastic copy number expansion of FAR1 genes in S. taccada might have facilitated its adaptation to the stronger light radiation present in sandy coastal lands. In conclusion, our study of the chromosomal-scale genomes of S. taccada and S. hainanensis provides novel insights into their genomic evolution after leaving Australasia.

Molecular insights into the phototropin control of chloroplast movements

Chloroplast movements are controlled by ultraviolet/blue light through phototropins. In Arabidopsis thaliana, chloroplast accumulation at low light intensities and chloroplast avoidance at high light intensities are observed. These responses are controlled by two homologous photoreceptors, the phototropins phot1 and phot2. Whereas chloroplast accumulation is triggered by both phototropins in a partially redundant manner, sustained chloroplast avoidance is elicited only by phot2. Phot1 is able to trigger only a small, transient chloroplast avoidance, followed by the accumulation phase. The source of this functional difference is not fully understood at either the photoreceptor or the signalling pathway levels. In this article, we review current understanding of phototropin functioning and try to dissect the differences that result in signalling to elicit two distinct chloroplast responses. First, we focus on phototropin structure and photochemical and biochemical activity. Next, we analyse phototropin expression and localization patterns. We also summarize known photoreceptor systems controlling chloroplast movements. Finally, we focus on the role of environmental stimuli in controlling phototropin activity. All these aspects impact the signalling to trigger chloroplast movements and raise outstanding questions about the mechanism involved.

Enhancement of photosynthesis efficiency and yield of strawberry (Fragaria ananassa Duch.) plants via LED systems

Due to advances in the industrial development of light-emitting diodes (LEDs), much research has been conducted in recent years to get a better understanding of how plants respond to these light sources. This study investigated the effects of different LED-based light regimes on strawberry plant development and performance. The photosynthetic pigment content, biochemical constituents, and growth characteristics of strawberry plants were investigated using a combination of different light intensities (150, 200, and 250 μmol m^-2 s^-1), qualities (red, green, and blue LEDs), and photoperiods (14/10 h, 16/8 h, and 12/12 h light/dark cycles) compared to the same treatment with white fluorescent light. Plant height, root length, shoot fresh and dry weight, chlorophyll a, total chlorophyll/carotenoid content, and most plant yield parameters were highest when illuminated with LM7 [intensity (250 μmol m^-2 s^-1) + quality (70% red/30% blue LED light combination) + photoperiod (16/8 h light/dark cycles)]. The best results for the effective quantum yield of PSII photochemistry Y(II), photochemical quenching coefficient (qP), and electron transport ratio (ETR) were obtained with LM8 illumination [intensity (250 μmol m^-2 s^-1) + quality (50% red/20% green/30% blue LED light combination) + photoperiod (12 h/12 h light/dark cycles)]. We conclude that strawberry plants require prolonged and high light intensities with a high red-light component for maximum performance and biomass production.

Genome-Wide Identification and Expression of FAR1 Gene Family Provide Insight Into Pod Development in Peanut (Arachis hypogaea)

The far-red-impaired response 1 (FAR1) transcription family were initially identified as important factors for phytochrome A (phyA)-mediated far-red light signaling in Arabidopsis; they play crucial roles in controlling the growth and development of plants. The reported reference genome sequences of Arachis, including A. duranensis, A. ipaensis, A. monticola, and A. hypogaea, and its related species Glycine max provide an opportunity to systematically perform a genome-wide identification of FAR1 homologous genes and investigate expression patterns of these members in peanut species. Here, a total of 650 FAR1 genes were identified from four Aarchis and its closely related species G. max. Of the studied species, A. hypogaea contained the most (246) AhFAR1 genes, which can be classified into three subgroups based on phylogenic relationships. The synonymous (Ks) and non-synonymous (Ka) substitution rates, phylogenetic relationship and synteny analysis of the FAR1 family provided deep insight into polyploidization, evolution and domestication of peanut AhFAR1 genes. The transcriptome data showed that the AhFAR1 genes exhibited distinct tissue- and stage-specific expression patterns in peanut. Three candidate genes including Ahy_A10g049543, Ahy_A06g026579, and Ahy_A10g048401, specifically expressed in peg and pod, might participate in pod development in the peanut. The quantitative real-time PCR (qRT-PCR) analyses confirmed that the three selected genes were highly and specifically expressed in the peg and pod. This study systematically analyzed gene structure, evolutionary characteristics and expression patterns of FAR1 gene family, which will provide a foundation for the study of genetic and biological function in the future.

Cross-species transcriptomic analyses reveals common and opposite responses in Arabidopsis, rice and barley following oxidative stress and hormone treatment

BACKGROUND

For translational genomics, a roadmap is needed to know the molecular similarities or differences between species, such as model species and crop species. This knowledge is invaluable for the selection of target genes and pathways to alter downstream in response to the same stimuli. Here, the transcriptomic responses to six treatments including hormones (abscisic acid - ABA and salicylic acid - SA); treatments that cause oxidative stress (3-amino-1,2,4-triazole - 3AT, methyl viologen - MV); inhibit respiration (antimycin A - AA) or induce genetic damage (ultraviolet radiation -UV) were analysed and compared between Arabidopsis (Arabidopsis thaliana), barley (Hordeum vulgare) and rice (Oryza sativa).

RESULTS

Common and opposite responses were identified between species, with the number of differentially expressed genes (DEGs) varying greatly between treatments and species. At least 70% of DEGs overlapped with at least one other treatment within a species, indicating overlapping response networks. Remarkably, 15 to 34% of orthologous DEGs showed opposite responses between species, indicating diversity in responses, despite orthology. Orthologous DEGs with common responses to multiple treatments across the three species were correlated with experimental data showing the functional importance of these genes in biotic/abiotic stress responses. The mitochondrial dysfunction response was revealed to be highly conserved in all three species in terms of responsive genes and regulation via the mitochondrial dysfunction element.

CONCLUSIONS

The orthologous DEGs that showed a common response between species indicate conserved transcriptomic responses of these pathways between species. However, many genes, including prominent salt-stress responsive genes, were oppositely responsive in multiple-stresses, highlighting fundamental differences in the responses and regulation of these genes between species. This work provides a resource for translation of knowledge or functions between species.

Photosynthetic performance of rocket (Eruca sativa. Mill.) grown under different regimes of light intensity, quality, and photoperiod

In recent years, much effort has been devoted to understanding the response of plants to various light sources, largely due to advances in industry light-emitting diodes (LEDs). In this study, the effect of different light modes on rocket (Eruca sativa. Mill.) photosynthetic performance and other physiological traits was evaluated using an orthogonal design based on a combination between light intensity, quality, and photoperiod factors. Some morphological and biochemical parameters and photosynthetic efficiency of the plants were analyzed. Plants grew in a closed chamber where three light intensities (160, 190, and 220 μmol m-2 s-1) provided by LEDs with a combination of different ratios of red, green, and blue (R:G:B- 7:0:3, 3:0:7, and 5:2:3) and three different photoperiods (light/dark -10/14 h, 12/12 h, and 14/10 h) were used and compared with white fluorescent light (control). This experimental setup allowed us to study the effect of 9 light modes (LM) compared to white light. The analyzes performed showed that the highest levels of chlorophyll a, chlorophyll b, and carotenoids occurred under LM4, LM3, and LM1, respectively. Chlorophyll a fluorescence measurement showed that the best effective quantum yield of PSII photochemistry Y(II), non-photochemical quenching (NPQ), photochemical quenching coefficient (qP), and electron transport ratio (ETR) were obtained under LM2. The data showed that the application of R7:G0:B3 light mode with a shorter photoperiod than 14/10 h (light/dark), regardless of the light intensity used, resulted in a significant increase in growth as well as higher photosynthetic capacity of rocket plants. Since, a clear correlation between the studied traits under the applied light modes was not found, more features should be studied in future experiments.

Genome-Wide Identification and Characterization of the CsFHY3/FAR1 Gene Family and Expression Analysis under Biotic and Abiotic Stresses in Tea Plants (Camellia sinensis)

The FHY3/FAR1 transcription factor family, derived from transposases, plays important roles in light signal transduction, and in the growth and development of plants. However, the homologous genes in tea plants have not been studied. In this study, 25 CsFHY3/FAR1 genes were identified in the tea plant genome through a genome-wide study, and were classified into five subgroups based on their phylogenic relationships. Their potential regulatory roles in light signal transduction and photomorphogenesis, plant growth and development, and hormone responses were verified by the existence of the corresponding cis-acting elements. The transcriptome data showed that these genes could respond to salt stress and shading treatment. An expression analysis revealed that, in different tissues, especially in leaves, CsFHY3/FAR1s were strongly expressed, and most of these genes were positively expressed under salt stress (NaCl), and negatively expressed under low temperature (4 °C) stress. In addition, a potential interaction network demonstrated that PHYA, PHYC, PHYE, LHY, FHL, HY5, and other FRSs were directly or indirectly associated with CsFHY3/FAR1 members. These results will provide the foundation for functional studies of the CsFHY3/FAR1 family, and will contribute to the breeding of tea varieties with high light efficiency and strong stress resistance.

Blue Light Mediates Chloroplast Avoidance and Enhances Photoprotection of Vanilla Orchid

Vanilla orchid, which is well-known for its flavor and fragrance, is cultivated in tropical and subtropical regions. This shade-loving plant is very sensitive to high irradiance. In this study, we show that vanilla chloroplasts started to have avoidance movement when blue light (BL) was higher than 20 μmol m-2s-1 and significant avoidance movement was observed under BL irradiation at 100 μmol m-2s-1 (BL100). The light response curve indicated that when vanilla was exposed to 1000 μmol m-2s-1, the electron transport rate (ETR) and photochemical quenching of fluorescence (qP) were significantly reduced to a negligible amount. We found that if a vanilla orchid was irradiated with BL100 for 12 days, it acquired BL-acclimation. Chloroplasts moved to the side of cells in order to reduce light-harvesting antenna size, and chloroplast photodamage was eliminated. Therefore, BL-acclimation enhanced vanilla orchid growth and tolerance to moderate (500 μmol m-2s-1) and high light (1000 μmol m-2s-1) stress conditions. It was found that under high irradiation, BL-acclimatized vanilla maintained higher ETR and qP capacity than the control without BL-acclimation. BL-acclimation induced antioxidant enzyme activities, reduced ROS accumulation, and accumulated more carbohydrates. Moreover, BL-acclimatized orchids upregulated photosystem-II-associated marker genes (D1 and PetC), Rubisco and PEPC transcripts and sustained expression levels thereof, and also maximized the photosynthesis rate. Consequently, BL-acclimatized orchids had higher biomass. In short, this study found that acclimating vanilla orchid with BL before transplantation to the field might eliminate photoinhibition and enhance vanilla growth and production.

Blue Light Acclimation Reduces the Photoinhibition of Phalaenopsis aphrodite (Moth Orchid)

The moth orchid is an important ornamental crop. It is very sensitive to high light irradiation due to photoinhibition. In this study, young orchid tissue culture seedlings and 2.5” potted plants pretreated under blue light (BL, λ_max = 450 nm) at 100 µmol m⁻² s⁻¹ for 12 days (BL acclimation) were found to have an increased tolerance to high light irradiation. After BL acclimation, orchids had an increased anthocyanin accumulation, enhanced chloroplast avoidance, and increased chlorophyll fluorescence capacity whenever they were exposed to high light of 1000 μmol m⁻² s⁻¹ for two weeks (HL). They had higher Fv/Fm, electron transport rate (ETR), chlorophyll content, catalase activity and sucrose content when compared to the control without BL acclimation. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that transcript levels of phototropins, D1, RbcS, PEPCK, Catalase and SUT2 were upregulated in the BL-acclimated orchids. Consequently, BL acclimation orchids had better growth when compared to the control under long-term high light stress. In summary, this study provides a solution, i.e., BL acclimation, to reduce moth orchid photoinhibition and enhance growth before transplantation of the young tissue culture seedlings and potted plants into greenhouses, where they usually suffer from a high light fluctuation problem.