Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album

Transcriptomic Analysis of the CAM Species Kalanchoë fedtschenkoi Under Low- and High-Temperature Regimes

Temperature stress is one of the major limiting environmental factors that negatively impact global crop yields. Kalanchoë fedtschenkoi is an obligate crassulacean acid metabolism (CAM) plant species, exhibiting much higher water-use efficiency and tolerance to drought and heat stresses than C3 or C4 plant species. Previous studies on gene expression responses to low- or high-temperature stress have been focused on C3 and C4 plants. There is a lack of information about the regulation of gene expression by low and high temperatures in CAM plants. To address this knowledge gap, we performed transcriptome sequencing (RNA-Seq) of leaf and root tissues of K. fedtschenkoi under cold (8 °C), normal (25 °C), and heat (37 °C) conditions at dawn (i.e., 2 h before the light period) and dusk (i.e., 2 h before the dark period). Our analysis revealed differentially expressed genes (DEGs) under cold or heat treatment in comparison to normal conditions in leaf or root tissue at each of the two time points. In particular, DEGs exhibiting either the same or opposite direction of expression change (either up-regulated or down-regulated) under cold and heat treatments were identified. In addition, we analyzed gene co-expression modules regulated by cold or heat treatment, and we performed in-depth analyses of expression regulation by temperature stresses for selected gene categories, including CAM-related genes, genes encoding heat shock factors and heat shock proteins, circadian rhythm genes, and stomatal movement genes. Our study highlights both the common and distinct molecular strategies employed by CAM and C3/C4 plants in adapting to extreme temperatures, providing new insights into the molecular mechanisms underlying temperature stress responses in CAM species.

Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation

Baobab (Adansonia digitata) is a long-lived tree endemic to Africa with economic, ecological, and cultural importance, yet its genomic features are underexplored. Here, we report a chromosome-level reference genome anchored to 42 chromosomes for A. digitata, alongside draft assemblies for a sibling tree, two trees from distinct locations in Africa, and A. za from Madagascar. The baobab genome is uniquely rich in DNA transposons, which make up 33%, while LTR retrotransposons account for 10%. A. digitata experienced whole genome multiplication (WGM) around 30 million years ago (MYA), followed by a second WGM event 3-11 MYA, likely linked to autotetraploidy. Resequencing of 25 trees identify three subpopulations, with gene flow across West Africa distinct from East Africa. Gene enrichment and fixation index (Fst) analyses show baobab retained multiple circadian, flowering, and light-responsive genes, which likely support longevity through the UV RESISTANCE LOCUS 8 (UVR8) pathway. In sum, we provide genomic resources and insights for baobab breeding and conservation.

Multiomics unravels potential molecular switches in the C3 to CAM transition of Mesembryanthemum crystallinum

Mesembryanthemum crystallinum (common ice plant), a facultative CAM plant, shifts from C3 to CAM photosynthesis under salt stress, enhancing water use efficiency. Here we used transcriptomics, proteomics, and targeted metabolomics to profile molecular changes during the diel cycle of C3 to CAM transition. The results confirmed expected changes associated with CAM photosynthesis, starch biosynthesis and degradation, and glycolysis/gluconeogenesis. Importantly, they yielded new discoveries: 1) Transcripts displayed greater circadian regulation than proteins. 2) Oxidative phosphorylation and inositol methylation may play important roles in initiating the transition. 3) V-type H+-ATPases showed consistent transcriptional regulation, aiding in vacuolar malate uptake. 4) A protein phosphatase 2C, a major component in the ABA signaling pathway, may trigger the C3 to CAM transition. Our work highlights the potential molecular switches in the C3 to CAM transition, including the potential role of ABA signaling. SIGNIFICANCE: The common ice plant is a model facultative CAM plant, and under stress conditions it can shift from C3 to CAM photosynthesis within a three-day period. However, knowledge about the molecular changes during the transition and the molecular switches enabling the transition is lacking. Multi-omic analyses not only revealed the molecular changes during the transition, but also highlighted the importance of ABA signaling, inositol methylation, V-type H+-ATPase in initiating the shift. The findings may explain physiological changes and nocturnal stomatal opening, and inform future synthetic biology effort in improving crop water use efficiency and stress resilience.

The Cissus quadrangularis genome reveals its adaptive features in an arid habitat

Cissus quadrangularis is a tetraploid species belonging to the Vitaceae family and is known for the Crassulacean acid metabolism (CAM) pathway in the succulent stem, while the leaves perform C3 photosynthesis. Here, we report a high-quality genome of C. quadrangularis comprising a total size of 679.2 Mb which was phased into two subgenomes. Genome annotation identified 51 857 protein-coding genes, while approximately 47.75% of the genome was composed of repetitive sequences. Gene expression ratios of two subgenomes demonstrated that the sub-A genome as the dominant subgenome played a vital role during the drought tolerance. Genome divergence analysis suggests that the tetraploidization event occurred around 8.9 million years ago. Transcriptome data revealed that pathways related to cutin, suberine, and wax metabolism were enriched in the stem during drought treatment, suggesting that these genes contributed to the drought adaption. Additionally, a subset of CAM-related genes displayed diurnal expression patterns in the succulent stems but not in leaves, indicating that stem-biased expression of existing genes contributed to the CAM evolution. Our findings provide insights into the mechanisms of drought adaptation and photosynthesis transition in plants.

Bringing CAM photosynthesis to the table: Paving the way for resilient and productive agricultural systems in a changing climate

Modern agricultural systems are directly threatened by global climate change and the resulting freshwater crisis. A considerable challenge in the coming years will be to develop crops that can cope with the consequences of declining freshwater resources and changing temperatures. One approach to meeting this challenge may lie in our understanding of plant photosynthetic adaptations and water use efficiency. Plants from various taxa have evolved crassulacean acid metabolism (CAM), a water-conserving adaptation of photosynthetic carbon dioxide fixation that enables plants to thrive under semi-arid or seasonally drought-prone conditions. Although past research on CAM has led to a better understanding of the inner workings of plant resilience and adaptation to stress, successful introduction of this pathway into C3 or C4 plants has not been reported. The recent revolution in molecular, systems, and synthetic biology, as well as innovations in high-throughput data generation and mining, creates new opportunities to uncover the minimum genetic tool kit required to introduce CAM traits into drought-sensitive crops. Here, we propose four complementary research avenues to uncover this tool kit. First, genomes and computational methods should be used to improve understanding of the nature of variations that drive CAM evolution. Second, single-cell 'omics technologies offer the possibility for in-depth characterization of the mechanisms that trigger environmentally controlled CAM induction. Third, the rapid increase in new 'omics data enables a comprehensive, multimodal exploration of CAM. Finally, the expansion of functional genomics methods is paving the way for integration of CAM into farming systems.

Shifting photosynthesis between the fast and slow lane: Facultative CAM and water-deficit stress

Five decades ago, the first report of a shift from C3 to CAM (crassulacean acid metabolism) photosynthesis following the imposition of stress was published in this journal. The annual, Mesembryanthemum crystallinum (Aizoaceae), was shown to be a C3 plant when grown under non-saline conditions, and a CAM plant when exposed to high soil salinity. This observation of environmentally triggered CAM eventually led to the introduction of the term facultative CAM, which categorises CAM that is induced or upregulated in response to water-deficit stress and is lost or downregulated when the stress is removed. Reversibility of C3-to-CAM shifts distinguishes stress-driven facultative-CAM responses from purely ontogenetic increases of CAM activity. We briefly review how the understanding of facultative CAM has developed, evaluate the current state of knowledge, and highlight questions of continuing interest. We demonstrate that the long-lived leaves of a perennial facultative-CAM arborescent species, Clusia pratensis, can repeatedly switch between C3 and CAM in response to multiple wet-dry-wet cycles. Undoubtedly, this is a dedicated response to environment, independent of ontogeny. We highlight the potential for engineering facultative CAM into C3 crops to provide a flexible capacity for drought tolerance.

A chromosome-scale genome sequence of Aeonium(Aeonium arboreum 'Velour') provides novel insights into the evolution of anthocyanin synthesis

Anthocyanin glycoside is a water-soluble flavonoid compound that colors plants and aids in stress resistance. The mechanism driving the evolution of the anthocyanin synthesis pathway in plants remains unclear. Aeonium plants are highly regarded as model organisms for studying adaptive evolution. These plants can be categorized into various types, each distinguished by the content and distribution of anthocyanins in their leaves. The categories include red leaves, green leaves, black leaves, yellow leaves, and a classification known as the 'spot brocade series. In this study, we successfully assembled and annotated the genome of cultivar 'Aeonium arboreum 'Velour'' at chromosomal level. The genome size is 1,334.85 Mb containing 18 chromosomes in a single set, with a contig N50 of 23.47 Mb and a Scaffold N50 of 25.07 Mb. Through homology prediction, de novo prediction, and transcriptome prediction, we identified 166,228 coding genes, 161,656 of which were successfully annotated in the database. Comparative genomic analysis revealed that Aeonium arboreum 'Velour' underwent an independent genome-wide replication event after differentiating from Sedum album, Kalanchoe laxiflora, and Kalanchoe fedtschenkoi. It also shared a genome-wide replication event with Sedum album and Kalanchoe laxiflora. Aeonium arboreum 'Velour' exhibits a higher number of multi-copy gene families compared to other species. A total of 5,129 gene families unique to Aeonium arboreum 'Velour' were identified, primarily enriched in various metabolic pathways, including monoterpenoid biosynthesis, sesquiterpene and triterpene biosynthesis, cyanamide acid metabolism, flavonoid and flavonol biosynthesis, phosphonate and phosphinate metabolism, fatty acid degradation, biosynthesis of unsaturated fatty acid, ether lipid metabolism, tyrosine metabolism, and isoflavone biosynthesis according to the KEGG pathway analysis. Aeonium arboreum 'Velour' and Sedum album diversion dates back to approximately 43.11 million years ago during the Paleogene period, marked by the expansion of 2,807 gene families. In contrast, the divergence from Kalanchoe laxiflora and Kalanchoe fedtschenkoi began around 57.28 million years ago, with 219 gene families expanding. GO analysis highlighted that most of the expansion or contraction gene families were predominantly enriched in flower organs, leaf organ development, anthocyanin metabolism regulation, and light energy absorption and utilization. Remarkably, anthocyanin metabolism regulation is enriched to 80 expanded genes, including 36 bHLH transcription factors, possibly functioning as photosensitive pigment interaction factors (PIFs). We speculate that flavonoids play a pivotal role in the adaptation of Aeonium arboreum 'Velour' to environmental stress. Moreover, the evolution of the anthocyanin synthesis pathway is potentially driven by the plant's capability to absorb and utilize light energy, especially in high CO2 and high-temperature settings characteristic of the early Paleogene.

Insights into the Superrosids phylogeny and flavonoid synthesis from the telomere-to-telomere gap-free genome assembly of Penthorum chinense Pursh

The completion of the first telomere-to-telomere (T2T) genome assembly of Penthorum chinense Pursh (PC), a prominent medicinal plant in China, represents a significant achievement. This assembly spans a length of 257.5 Mb and consists of nine chromosomes. PC's notably smaller genome size in Saxifragales, compared to that of Paeonia ostii, can be attributed to the low abundance of transposable elements. By utilizing single-copy genes from 30 species, including 28 other Superrosids species, we successfully resolved a previously debated Superrosids phylogeny. Our findings unveiled Saxifragales as the sister group to the core rosids, with both being the sister group to Vitales. Utilizing previously characterized cytochrome P450 (CYP) genes, we predicted the compound classes that most CYP genes of PC are involved in synthesizing, providing insight into PC's potential metabolic diversity. Metabolomic and transcriptomic data revealed that the richest sources of the three most noteworthy medicinal components in PC are young leaves and flowers. We also observed higher activity of upstream genes in the flavonoid synthesis pathway in these plant parts. Additionally, through weighted gene co-expression network analysis, we identified gene regulatory networks associated with the three medicinal components. Overall, these findings deepen our understanding of PC, opening new avenues for further research and exploration.

The CAM lineages of planet Earth

BACKGROUND AND SCOPE

The growth of experimental studies of crassulacean acid metabolism (CAM) in diverse plant clades, coupled with recent advances in molecular systematics, presents an opportunity to re-assess the phylogenetic distribution and diversity of species capable of CAM. It has been more than two decades since the last comprehensive lists of CAM taxa were published, and an updated survey of the occurrence and distribution of CAM taxa is needed to facilitate and guide future CAM research. We aimed to survey the phylogenetic distribution of these taxa, their diverse morphology, physiology and ecology, and the likely number of evolutionary origins of CAM based on currently known lineages.

RESULTS AND CONCLUSIONS

We found direct evidence (in the form of experimental or field observations of gas exchange, day-night fluctuations in organic acids, carbon isotope ratios and enzymatic activity) for CAM in 370 genera of vascular plants, representing 38 families. Further assumptions about the frequency of CAM species in CAM clades and the distribution of CAM in the Cactaceae and Crassulaceae bring the currently estimated number of CAM-capable species to nearly 7 % of all vascular plants. The phylogenetic distribution of these taxa suggests a minimum of 66 independent origins of CAM in vascular plants, possibly with dozens more. To achieve further insight into CAM origins, there is a need for more extensive and systematic surveys of previously unstudied lineages, particularly in living material to identify low-level CAM activity, and for denser sampling to increase phylogenetic resolution in CAM-evolving clades. This should allow further progress in understanding the functional significance of this pathway by integration with studies on the evolution and genomics of CAM in its many forms.

Prospects and perspectives: inferring physiological and regulatory targets for CAM from molecular and modelling approaches

BACKGROUND AND SCOPE

This review summarizes recent advances in our understanding of Crassulacean Acid Metabolism (CAM) by integrating evolutionary, ecological, physiological, metabolic and molecular perspectives. A number of key control loops which moderate the expression of CAM phases, and their metabolic and molecular control, are explored. These include nocturnal stomatal opening, activation of phosphoenolpyruvate carboxylase by a specific protein kinase, interactions with circadian clock control, as well as daytime decarboxylation and activation of Rubisco. The vacuolar storage and release of malic acid and the interplay between the supply and demand for carbohydrate reserves are also key metabolic control points.

FUTURE OPPORTUNITIES

We identify open questions and opportunities, with experimentation informed by top-down molecular modelling approaches allied with bottom-up mechanistic modelling systems. For example, mining transcriptomic datasets using high-speed systems approaches will help to identify targets for future genetic manipulation experiments to define the regulation of CAM (whether circadian or metabolic control). We emphasize that inferences arising from computational approaches or advanced nuclear sequencing techniques can identify potential genes and transcription factors as regulatory targets. However, these outputs then require systematic evaluation, using genetic manipulation in key model organisms over a developmental progression, combining gene silencing and metabolic flux analysis and modelling to define functionality across the CAM day-night cycle. From an evolutionary perspective, the origins and function of CAM succulents and responses to water deficits are set against the mesophyll and hydraulic limitations imposed by cell and tissue succulence in contrasting morphological lineages. We highlight the interplay between traits across shoots (3D vein density, mesophyll conductance and cell shrinkage) and roots (xylem embolism and segmentation). Thus, molecular, biophysical and biochemical processes help to curtail water losses and exploit rapid rehydration during restorative rain events. In the face of a changing climate, we hope such approaches will stimulate opportunities for future research.

Gene duplications facilitate C4-CAM compatibility in common purslane

Common purslane (Portulaca oleracea) integrates both C4 and crassulacean acid metabolism (CAM) photosynthesis pathways and is a promising model plant to explore C4-CAM plasticity. Here, we report a high-quality chromosome-level genome of nicotinamide adenine dinucleotide (NAD)-malic enzyme (ME) subtype common purslane that provides evidence for 2 rounds of whole-genome duplication (WGD) with an ancient WGD (P-β) in the common ancestor to Portulacaceae and Cactaceae around 66.30 million years ago (Mya) and another (Po-α) specific to common purslane lineage around 7.74 Mya. A larger number of gene copies encoding key enzymes/transporters involved in C4 and CAM pathways were detected in common purslane than in related species. Phylogeny, conserved functional site, and collinearity analyses revealed that the Po-α WGD produced the phosphoenolpyruvate carboxylase-encoded gene copies used for photosynthesis in common purslane, while the P-β WGD event produced 2 ancestral genes of functionally differentiated (C4- and CAM-specific) beta carbonic anhydrases involved in the C4 + CAM pathways. Additionally, cis-element enrichment analysis in the promoters showed that CAM-specific genes have recruited both evening and midnight circadian elements as well as the Abscisic acid (ABA)-independent regulatory module mediated by ethylene-response factor cis-elements. Overall, this study provides insights into the origin and evolutionary process of C4 and CAM pathways in common purslane, as well as potential targets for engineering crops by integrating C4 or CAM metabolism.

Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids

Some of the most vexing problems of deep level relationship that remain in angiosperms involve the superrosids. The superrosid clade contains a quarter of all angiosperm species, with 18 orders in three subclades (Vitales, Saxifragales and core rosids) exhibiting remarkable morphological and ecological diversity. To help resolve deep-level relationships, we constructed a high-quality chromosome-level genome assembly for Tiarella polyphylla (Saxifragaceae) thus providing broader genomic representation of Saxifragales. Whole genome microsynteny analysis of superrosids showed that Saxifragales shared more synteny clusters with core rosids than Vitales, further supporting Saxifragales as more closely related with core rosids. To resolve the ordinal phylogeny of superrosids, we screened 122 single copy nuclear genes from genomes of 36 species, representing all 18 superrosid orders. Vitales were recovered as sister to all other superrosids (Saxifragales + core rosids). Our data suggest dramatic differences in relationships compared to earlier studies within core rosids. Fabids should be restricted to the nitrogen-fixing clade, while Picramniales, the Celastrales-Malpighiales (CM) clade, Huerteales, Oxalidales, Sapindales, Malvales and Brassicales formed an "expanded" malvid clade. The Celastrales-Oxalidales-Malpighiales (COM) clade (sensu APG IV) was not monophyletic. Crossosomatales, Geraniales, Myrtales and Zygophyllales did not belong to either of our well-supported malvids or fabids. There is strong discordance between nuclear and plastid phylogenetic hypotheses for superrosid relationships; we show that this is best explained by a combination of incomplete lineage sorting and ancient reticulation.

Diel dynamics of multi-omics in elkhorn fern provide new insights into weak CAM photosynthesis

Crassulacean acid metabolism (CAM) has high water-use efficiency (WUE) and is widely recognized to have evolved from C3 photosynthesis. Different plant lineages have convergently evolved CAM, but the molecular mechanism that underlies C3-to-CAM evolution remains to be clarified. Platycerium bifurcatum (elkhorn fern) provides an opportunity to study the molecular changes underlying the transition from C3 to CAM photosynthesis because both modes of photosynthesis occur in this species, with sporotrophophyll leaves (SLs) and cover leaves (CLs) performing C3 and weak CAM photosynthesis, respectively. Here, we report that the physiological and biochemical attributes of CAM in weak CAM-performing CLs differed from those in strong CAM species. We investigated the diel dynamics of the metabolome, proteome, and transcriptome in these dimorphic leaves within the same genetic background and under identical environmental conditions. We found that multi-omic diel dynamics in P. bifurcatum exhibit both tissue and diel effects. Our analysis revealed temporal rewiring of biochemistry relevant to the energy-producing pathway (TCA cycle), CAM pathway, and stomatal movement in CLs compared with SLs. We also confirmed that PHOSPHOENOLPYRUVATE CARBOXYLASE KINASE (PPCK) exhibits convergence in gene expression among highly divergent CAM lineages. Gene regulatory network analysis identified candidate transcription factors regulating the CAM pathway and stomatal movement. Taken together, our results provide new insights into weak CAM photosynthesis and new avenues for CAM bioengineering.

High-quality Cymbidium mannii genome and multifaceted regulation of crassulacean acid metabolism in epiphytes

Epiphytes with crassulacean acid metabolism (CAM) photosynthesis are widespread among vascular plants, and repeated evolution of CAM photosynthesis is a key innovation for micro-ecosystem adaptation. However, we lack a complete understanding of the molecular regulation of CAM photosynthesis in epiphytes. Here, we report a high-quality chromosome-level genome assembly of a CAM epiphyte, Cymbidium mannii (Orchidaceae). The 2.88-Gb orchid genome with a contig N50 of 22.7 Mb and 27 192 annotated genes was organized into 20 pseudochromosomes, 82.8% of which consisted of repetitive elements. Recent expansions of long terminal repeat retrotransposon families have made a major contribution to the evolution of genome size in Cymbidium orchids. We reveal a holistic scenario of molecular regulation of metabolic physiology using high-resolution transcriptomics, proteomics, and metabolomics data collected across a CAM diel cycle. Patterns of rhythmically oscillating metabolites, especially CAM-related products, reveal circadian rhythmicity in metabolite accumulation in epiphytes. Genome-wide analysis of transcript and protein level regulation revealed phase shifts during the multifaceted regulation of circadian metabolism. Notably, we observed diurnal expression of several core CAM genes (especially βCA and PPC) that may be involved in temporal fixation of carbon sources. Our study provides a valuable resource for investigating post-transcription and translation scenarios in C. mannii, an Orchidaceae model for understanding the evolution of innovative traits in epiphytes.

Sedum Growth Patterns under Different Pedoclimatic Conditions

This research paper presents a case study analysis of the behavior of three Sedum varieties and their growth in three different types of substrates without additional watering or fertilizing. The study aims to identify a suitable substrate for propagation and to provide insight into the plant's growth patterns. By analyzing the growth of the Sedum species and varieties-SS'PW', SS'CB', and SS'P'-without intervening in their growth process, we were able to identify factors that play a more crucial role in promoting root growth, plant growth, aesthetic value, and use. Over a 20-month period, various technical tools were employed to conduct observations and measurements for both plants and weather conditions. The type of substrate significantly affected plant growth, with the green roof substrate exhibiting the highest overall average monthly root growth rate (0.92 ± 0.05 d, 1.01 ± 0.05 b, 0.96 ± 0.05 c) while in the case of stem growth, among all three varieties, the best results were obtained in the commercial mix (0.87 ± 0.04 a, 0.40 ± 0.02 c, 0.35 ± 0.02 d). Based on the morphological analyses, all values were significantly lower than the control. Best results for leaf weight and surface area were noticed in the green roof substrate with an average growth of 46%, 53%, 55%, and for stem weight, length, and thickness in the commercial mix with 64%, 61%, and 55% compared to the control, respectively. Leaves had varying morphological characteristics, but the chromatic characteristics were preserved. The plants had an overall poor growth which may not be desirable in landscape designs. The findings of this study are applicable in the planning and execution of eco-friendly infrastructure initiatives, leading to the development of more robust and environmentally friendly urban settings.

Time of Day Analysis over a Field Grown Developmental Time Course in Rice

Plants integrate time of day (TOD) information over an entire season to ensure optimal growth, flowering time, and grain fill. However, most TOD expression studies have focused on a limited number of combinations of daylength and temperature under laboratory conditions. Here, an Oryza sativa (rice) expression study that followed TOD expression in the field over an entire growing season was re-analyzed. Similar to Arabidopsis thaliana, almost all rice genes have a TOD-specific expression over the developmental time course. As has been suggested in other grasses, thermocycles were a stronger cue for TOD expression than the photocycles over the growing season. All the core circadian clock genes display consistent TOD expression over the season with the interesting exception that the two grass paralogs of EARLY FLOWERING 3 (ELF3) display a distinct phasing based on the interaction between thermo- and photo-cycles. The dataset also revealed how specific pathways are modulated to distinct TOD over the season consistent with the changing biology. The data presented here provide a resource for researchers to study how TOD expression changes under natural conditions over a developmental time course, which will guide approaches to engineer more resilient and prolific crops.

Comparative genomics analysis of drought response between obligate CAM and C3 photosynthesis plants

Crassulacean acid metabolism (CAM) plants exhibit elevated drought and heat tolerance compared to C₃ and C₄ plants through an inverted pattern of day/night stomatal closure and opening for CO₂ assimilation. However, the molecular responses to water-deficit conditions remain unclear in obligate CAM species. In this study, we presented genome-wide transcription sequencing analysis using leaf samples of an obligate CAM species Kalanchoë fedtschenkoi under moderate and severe drought treatments at two-time points of dawn (2-h before the start of light period) and dusk (2-h before the dark period). Differentially expressed genes were identified in response to environmental drought stress and a whole genome wide co-expression network was created as well. We found that the expression of CAM-related genes was not regulated by drought stimuli in K. fedtschenkoi. Our comparative analysis revealed that CAM species (K. fedtschenkoi) and C₃ species (Arabidopsis thaliana, Populus deltoides 'WV94') share some common transcriptional changes in genes involved in multiple biological processes in response to drought stress, including ABA signaling and biosynthesis of secondary metabolites.

Core circadian clock and light signaling genes brought into genetic linkage across the green lineage

The circadian clock is conserved at both the level of transcriptional networks as well as core genes in plants, ensuring that biological processes are phased to the correct time of day. In the model plant Arabidopsis (Arabidopsis thaliana), the core circadian SHAQKYF-type-MYB (sMYB) genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and REVEILLE (RVE4) show genetic linkage with PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7, respectively. Leveraging chromosome-resolved plant genomes and syntenic ortholog analysis enabled tracing this genetic linkage back to Amborella trichopoda, a sister lineage to the angiosperm, and identifying an additional evolutionarily conserved genetic linkage in light signaling genes. The LHY/CCA1-PRR5/9, RVE4/8-PRR3/7, and PIF3-PHYA genetic linkages emerged in the bryophyte lineage and progressively moved within several genes of each other across an array of angiosperm families representing distinct whole-genome duplication and fractionation events. Soybean (Glycine max) maintained all but two genetic linkages, and expression analysis revealed the PIF3-PHYA linkage overlapping with the E4 maturity group locus was the only pair to robustly cycle with an evening phase, in contrast to the sMYB-PRR morning and midday phase. While most monocots maintain the genetic linkages, they have been lost in the economically important grasses (Poaceae), such as maize (Zea mays), where the genes have been fractionated to separate chromosomes and presence/absence variation results in the segregation of PRR7 paralogs across heterotic groups. The environmental robustness model is put forward, suggesting that evolutionarily conserved genetic linkages ensure superior microhabitat pollinator synchrony, while wide-hybrids or unlinking the genes, as seen in the grasses, result in heterosis, adaptation, and colonization of new ecological niches.

A genome for Cissus illustrates features underlying its evolutionary success in dry savannas

Cissus is the largest genus in Vitaceae and is mainly distributed in the tropics and subtropics. Crassulacean acid metabolism (CAM), a photosynthetic adaptation to the occurrence of succulent leaves or stems, indicates that convergent evolution occurred in response to drought stress during species radiation. Here we provide the chromosomal level assembly of Cissus rotundifolia (an endemic species in Eastern Africa) and a genome-wide comparison with grape to understand genome divergence within an ancient eudicot family. Extensive transcriptome data were produced to illustrate the genetics underpinning C. rotundifolia's ecological adaption to seasonal aridity. The modern karyotype and smaller genome of C. rotundifolia (n = 12, 350.69 Mb/1C), which lack further whole-genome duplication, were mainly derived from gross chromosomal rearrangements such as fusions and segmental duplications, and were sculpted by a very recent burst of retrotransposon activity. Bias in local gene amplification contributed to its remarkable functional divergence from grape, and the specific proliferated genes associated with abiotic and biotic responses (e.g. HSP-20, NBS-LRR) enabled C. rotundifolia to survive in a hostile environment. Reorganization of existing enzymes of CAM characterized as diurnal expression patterns of relevant genes further confer the ability to thrive in dry savannas.

Differential timing of gene expression and recruitment in independent origins of CAM in the Agavoideae (Asparagaceae)

Crassulacean acid metabolism (CAM) photosynthesis has evolved repeatedly across the plant tree of life, however our understanding of the genetic convergence across independent origins remains hampered by the lack of comparative studies. Here, we explore gene expression profiles in eight species from the Agavoideae (Asparagaceae) encompassing three independent origins of CAM. Using comparative physiology and transcriptomics, we examined the variable modes of CAM in this subfamily and the changes in gene expression across time of day and between well watered and drought-stressed treatments. We further assessed gene expression and the molecular evolution of genes encoding phosphoenolpyruvate carboxylase (PPC), an enzyme required for primary carbon fixation in CAM. Most time-of-day expression profiles are largely conserved across all eight species and suggest that large perturbations to the central clock are not required for CAM evolution. By contrast, transcriptional response to drought is highly lineage specific. Yucca and Beschorneria have CAM-like expression of PPC2, a copy of PPC that has never been shown to be recruited for CAM in angiosperms. Together the physiological and transcriptomic comparison of closely related C₃ and CAM species reveals similar gene expression profiles, with the notable exception of differential recruitment of carboxylase enzymes for CAM function.

Evolution of Crassulacean acid metabolism in response to the environment: past, present, and future

Crassulacean acid metabolism (CAM) is a mode of photosynthesis that evolved in response to decreasing CO2 levels in the atmosphere some 20 million years ago. An elevated ratio of O2 relative to CO2 caused many plants to face increasing stress from photorespiration, a process exacerbated for plants living under high temperatures or in water-limited environments. Today, our climate is again rapidly changing and plants' ability to cope with and adapt to these novel environments is critical for their success. This review focuses on CAM plant responses to abiotic stressors likely to dominate in our changing climate: increasing CO2 levels, increasing temperatures, and greater variability in drought. Empirical studies that have assessed CAM responses are reviewed, though notably these are concentrated in relatively few CAM lineages. Other aspects of CAM biology, including the effects of abiotic stress on the light reactions and the role of leaf succulence, are also considered in the context of climate change. Finally, more recent studies using genomic techniques are discussed to link physiological changes in CAM plants with the underlying molecular mechanism. Together, the body of work reviewed suggests that CAM plants will continue to thrive in certain environments under elevated CO2. However, how CO2 interacts with other environmental factors, how those interactions affect CAM plants, and whether all CAM plants will be equally affected remain outstanding questions regarding the evolution of CAM on a changing planet.

As right as rain: deciphering drought-related metabolic flexibility in the C4-CAM Portulaca

This article comments on: Ferrari RC, Kawabata AB, Ferreira SS, Hartwell J, Freschi L. 2022. A matter of time: regulatory events behind the synchronization of C₄ and crassulacean acid metabolism gene expression in Portulaca oleracea. Journal of Experimental Botany 73,4867–4885.

Gene co-expression reveals the modularity and integration of C4 and CAM in Portulaca

C4 photosynthesis and Crassulacean acid metabolism (CAM) have been considered as largely independent adaptations despite sharing key biochemical modules. Portulaca is a geographically widespread clade of over 100 annual and perennial angiosperm species that primarily use C4 but facultatively exhibit CAM when drought stressed, a photosynthetic system known as C4 + CAM. It has been hypothesized that C4 + CAM is rare because of pleiotropic constraints, but these have not been deeply explored. We generated a chromosome-level genome assembly of Portulaca amilis and sampled mRNA from P. amilis and Portulaca oleracea during CAM induction. Gene co-expression network analyses identified C4 and CAM gene modules shared and unique to both Portulaca species. A conserved CAM module linked phosphoenolpyruvate carboxylase to starch turnover during the day-night transition and was enriched in circadian clock regulatory motifs in the P. amilis genome. Preservation of this co-expression module regardless of water status suggests that Portulaca constitutively operate a weak CAM cycle that is transcriptionally and posttranscriptionally upregulated during drought. C4 and CAM mostly used mutually exclusive genes for primary carbon fixation, and it is likely that nocturnal CAM malate stores are shuttled into diurnal C4 decarboxylation pathways, but we found evidence that metabolite cycling may occur at low levels. C4 likely evolved in Portulaca through co-option of redundant genes and integration of the diurnal portion of CAM. Thus, the ancestral CAM system did not strongly constrain C4 evolution because photosynthetic gene networks are not co-regulated for both daytime and nighttime functions.

Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C4 and crassulacean acid metabolism plants

Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C₄and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulting in the convergent evolution of C₄ and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remain poorly understood. In the present study, we identified the members of PEPC gene family across green plants with seventeen genomic datasets, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructing PEPC gene family tree and reconciled with species tree, we found PEPC genes underwent 71 gene duplication events and 16 gene loss events, which might result from whole-genome duplication events in plants. Based on the phylogenetic tree of the PEPC gene family, we detected four convergent evolution sites of PEPC in C₄ species but none in CAM species. The PEPC gene family was ubiquitous and highly conservative in green plants. After originating from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that might facilitate the convergent evolution of C₄ photosynthesis in Angiosperms. However, there was no evidence for convergent molecular evolution of PEPC genes between CAM plants. Our findings help to understand the origin and convergent evolution of C₄ and CAM plants and shed light on the adaptation of plants in dry, hot environments.

Genome-wide profiling of drought-tolerant Arabidopsis plants over-expressing chickpea MT1 gene reveals transcription factors implicated in stress modulation

Drought, a major abiotic limiting factor, could be modulated with in-built reprogramming of plants at molecular level by regulating the activity of plant developmental processes, stress endurance and adaptation. The transgenic Arabidopsis thaliana over-expressing metallothionein 1 (MT1) gene of desi chickpea (Cicer arietinum L.) was subjected to transcriptome analysis. We evaluated drought tolerance of 7 days old plants of Arabidopsis thaliana in both wild-type (WT) as well as transgenic plants and performed transcriptome analysis. Our analysis revealed 24,737 transcripts representing 24,594 genes out of which 5,816 were differentially expressed genes (DEGs) under drought conditions and 841 genes were common in both genotypes. A total of 1251 DEGs in WT and 2099 in MT1 were identified in comparison with control. Out of the significant DEGs, 432 and 944 were upregulated, whereas 819 and 1155 were downregulated in WT and MT1 plants, respectively. The physiological and molecular parameters involving germination assay, root length measurements under different stress treatments and quantitative expression analysis of transgenic plants in comparison to wild-type were found to be enhanced. CarMT1 plants also demonstrated modulation of various other stress-responsive genes that reprogrammed themselves for stress adaptation. Amongst various drought-responsive genes, 24 DEGs showed similar quantitative expression as obtained through RNA sequencing data. Hence, these modulatory genes could be used as a genetic tool for understanding and delineating the mechanisms for fine-tuning of stress responses in crop plants.

Rewilding staple crops for the lost halophytism: Toward sustainability and profitability of agricultural production systems

Abiotic stress tolerance has been weakened during the domestication of all major staple crops. Soil salinity is a major environmental constraint that impacts over half of the world population; however, given the increasing reliance on irrigation and the lack of available freshwater, agriculture in the 21st century will increasingly become saline. Therefore, global food security is critically dependent on the ability of plant breeders to create high-yielding staple crop varieties that will incorporate salinity tolerance traits and account for future climate scenarios. Previously, we have argued that the current agricultural practices and reliance on crops that exclude salt from uptake is counterproductive and environmentally unsustainable, and thus called for a need for a major shift in a breeding paradigm to incorporate some halophytic traits that were present in wild relatives but were lost in modern crops during domestication. In this review, we provide a comprehensive physiological and molecular analysis of the key traits conferring crop halophytism, such as vacuolar Na⁺ sequestration, ROS desensitization, succulence, metabolic photosynthetic switch, and salt deposition in trichomes, and discuss the strategies for incorporating them into elite germplasm, to address a pressing issue of boosting plant salinity tolerance.

CAM photosynthesis: the acid test

There is currently considerable interest in the prospects for bioengineering crassulacean acid metabolism (CAM) photosynthesis - or key elements associated with it, such as increased water-use efficiency - into C₃ plants. Resolving how CAM photosynthesis evolved from the ancestral C₃ pathway could provide valuable insights into the targets for such bioengineering efforts. It has been proposed that the ability to accumulate organic acids at night may be common among C₃ plants, and that the transition to CAM might simply require enhancement of pre-existing fluxes, without the need for changes in circadian or diurnal regulation. We show, in a survey encompassing 40 families of vascular plants, that nocturnal acidification is a feature entirely restricted to CAM species. Although many C₃ species can synthesize malate during the light period, we argue that the switch to night-time malic acid accumulation requires a fundamental metabolic reprogramming that couples glycolytic breakdown of storage carbohydrate to the process of net dark CO₂ fixation. This central element of the CAM pathway, even when expressed at a low level, represents a biochemical capability not seen in C₃ plants, and so is better regarded as a discrete evolutionary innovation than as part of a metabolic continuum between C₃ and CAM.

Changes in crassulacean acid metabolism expression, chloroplast ultrastructure, photochemical and antioxidant activity in the Aloe vera during acclimation to combined drought and salt stress

We determined time course changes of photochemical and antioxidant activity during the induction of strong crassulacean acid metabolism (CAM) in Aloe vera L. plants grown under salt and drought stress. We found that the strong CAM was induced during 25-30days of drought alone treatment. After 25-30days, we showed the withdrawal of strong CAM back to constitutive CAM background under the combination of simultaneous drought and salt stress, which coincided with the accumulation of malondialdehyde, and the decrease in the contents of endogenous nitric oxide (NO) and non-enzymatic antioxidants. At the same time, the chloroplast ultrastructure was damaged with a parallel accumulation of reactive oxygen species, and the whole photosynthetic electron transport flux was impaired by combined stress treatment. In conclusion, the changes in CAM expression parameters was attended by a similar pattern of antioxidant and photochemical change in Aloe plants subjected to only drought or combined stress.

Underwater CAM photosynthesis elucidated by Isoetes genome

To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation to low CO2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has hindered comparison between aquatic and terrestrial CAM. Here, we investigate underwater CAM in Isoetes taiwanensis by generating a high-quality genome assembly and RNA-seq time course. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, we identify several key differences. Notably, Isoetes may have recruited the lesser-known 'bacterial-type' PEPC, along with the 'plant-type' exclusively used in other CAM and C4 plants for carboxylation of PEP. Furthermore, we find that circadian control of key CAM pathway genes has diverged considerably in Isoetes relative to flowering plants. This suggests the existence of more evolutionary paths to CAM than previously recognized.

Drought resistance mechanisms of Phedimus aizoon L

Phedimus aizoon L. is a drought-resistant Chinese herbal medicine and vegetable. However, its drought tolerant limit and the mechanism of drought tolerance are unknown, which restricts the promotion of water-saving cultivation of Phedimus aizoon L. in arid areas. To solve the above problem, we carried out a 30-day-long drought stress experiment in pots that presented different soil water contents and were divided into four groups: control check, 75-80% of the maximum water-holding capacity (MWHC); mild drought, 55-60%; moderate drought, 40-45%; and severe drought, 20-25%. The dynamic changes in both plant physiological indexes from 10 to 30 days and leaf anatomical structure on the 30th day of stress were recorded. The results show that Phedimus aizoon L. grew normally under mild drought stress for 30 days, but the growth of the plants became inhibited after 20 days of severe drought and after 30 days of moderate drought. At the same time, Phedimus aizoon L. physiologically responded to cope with drought stress: the growth of the root system accelerated, the waxy layer of the leaves thickened, and the dark reactions of the plants transformed from those of the C3 cycle to CAM. The activity of antioxidant enzymes (SOD, POD and CAT) continuously increased to alleviate the damage caused by drought stress. To ensure the relative stability of the osmotic potential, the contents of osmoregulatory substances such as proline, soluble sugars, soluble protein and trehalose increased correspondingly. Although Phedimus aizoon L. has strong drought stress resistance, our experimental results show that the soil available water content should not be less than 27% during cultivation.

Research advances in and prospects of ornamental plant genomics

The term 'ornamental plant' refers to all plants with ornamental value, which generally have beautiful flowers or special plant architectures. China is rich in ornamental plant resources and known as the "mother of gardens". Genomics is the science of studying genomes and is useful for carrying out research on genome evolution, genomic variations, gene regulation, and important biological mechanisms based on detailed genome sequence information. Due to the diversity of ornamental plants and high sequencing costs, the progress of genome research on ornamental plants has been slow for a long time. With the emergence of new sequencing technologies and a reduction in costs since the whole-genome sequencing of the first ornamental plant (Prunus mume) was completed in 2012, whole-genome sequencing of more than 69 ornamental plants has been completed in <10 years. In this review, whole-genome sequencing and resequencing of ornamental plants will be discussed. We provide analysis with regard to basic data from whole-genome studies of important ornamental plants, the regulation of important ornamental traits, and application prospects.

The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes

Dragon fruits are tropical fruits economically important for agricultural industries. As members of the family of Cactaceae, they have evolved to adapt to the arid environment. Here we report the draft genome of Hylocereus undatus, commercially known as the white-fleshed dragon fruit. The chromosomal level genome assembly contains 11 longest scaffolds corresponding to the 11 chromosomes of H. undatus. Genome annotation of H. undatus found ~29,000 protein-coding genes, similar to Carnegiea gigantea (saguaro). Whole-genome duplication (WGD) analysis revealed a WGD event in the last common ancestor of Cactaceae followed by extensive genome rearrangements. The divergence time between H. undatus and C. gigantea was estimated to be 9.18 MYA. Functional enrichment analysis of orthologous gene clusters (OGCs) in six Cactaceae plants found significantly enriched OGCs in drought resistance. Fruit flavor-related functions were overrepresented in OGCs that are significantly expanded in H. undatus. The H. undatus draft genome also enabled the discovery of carbohydrate and plant cell wall-related functional enrichment in dragon fruits treated with trypsin for a longer storage time. Lastly, genes of the betacyanin (a red-violet pigment and antioxidant with a very high concentration in dragon fruits) biosynthetic pathway were found to be co-localized on a 12 Mb region of one chromosome. The consequence may be a higher efficiency of betacyanin biosynthesis, which will need experimental validation in the future. The H. undatus draft genome will be a great resource to study various cactus plants.

Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control

Rootless plants in the genus Wolffia are some of the fastest growing known plants on Earth. Wolffia have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas, which has the smallest genome size in the genus at 357 Mb and has a reduced set of predicted protein-coding genes at about 15,000. Comparison between multiple high-quality draft genome sequences from W. australiana clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. Wolffia has also lost most of the conserved nucleotide-binding leucine-rich repeat (NLR) genes that are known to be involved in innate immunity, as well as those involved in terpene biosynthesis, while having a significant overrepresentation of genes in the sphingolipid pathways that may signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ∼40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The Wolffia genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.

Comparison of CAM expression, photochemistry and antioxidant responses in Sedum album and Portulaca oleracea under combined stress

Previous studies of crassulacean acid metabolism (CAM) pathway during stress have been directed at individual drought and salinity stress, here, we studied the effects of a combination of drought and salt on CAM expression, chlorophyll fluorescence and antioxidant parameters in the C₃ -CAM facultative Sedum album and C₄ -CAM facultative Portulaca oleracea plants. While salinity alone was not able to induce functional CAM expression in P. oleracea leaves, we showed that salinity induced low level of nocturnal acid accumulation in S. album species. After 20 d of exposure to the combination of simultaneous salt and drought stress, P. oleracea plants exhibited more resistance to photoinhibition as compared to S. album plants. The decrease of maximum quantum yield (F_v /F_m ) in S. album leaves under combined stress was in parallel with the largest suppression of CAM expression of >50%, probably displaying the withdrawal of functional CAM back to C₃ pathway. However, under drought treatment alone, S. album plants exhibited higher photosynthetic flexibility, which was associated with the up-regulation of antioxidant enzymes activities and maintenance of glutathione (GSH) pool, and consequently higher photochemical functioning. The levels of nitric oxide (NO) correlated well with CAM expression, which was observed only in S. album, suggesting that NO acts in a different way in C₃ and C₄ species during CAM induction. Additionally, in both species, over the course of CAM induction, the changes in CAM expression parameters exhibited a similar pattern to that of antioxidant capacity and photochemical functioning parameters.

Alternative Crassulacean Acid Metabolism Modes Provide Environment-Specific Water-Saving Benefits in a Leaf Metabolic Model

Crassulacean acid metabolism (CAM) evolved in arid environments as a water-saving alternative to C₃ photosynthesis. There is great interest in engineering more drought-resistant crops by introducing CAM into C₃ plants. However, it is unknown whether full CAM or alternative water-saving modes would be more productive in the environments typically experienced by C₃ crops. To study the effect of temperature and relative humidity on plant metabolism in the context of water saving, we coupled a time-resolved diel (based on a 24-h day-night cycle) model of leaf metabolism to an environment-dependent gas-exchange model. This combined model allowed us to study the emergence of CAM as a trade-off between leaf productivity and water saving. We show that vacuolar storage capacity in the leaf is a major determinant of the extent of CAM. Moreover, our model identified an alternative CAM cycle involving mitochondrial isocitrate dehydrogenase as a potential contributor to initial carbon fixation at night. Simulations across a range of environmental conditions show that the water-saving potential of CAM strongly depends on the daytime weather conditions and that the additional water-saving effect of carbon fixation by isocitrate dehydrogenase can reach 11% total water saving for the conditions tested.

Crassulacean acid metabolism

Gilman and Edwards introduce crassulacean acid metabolism and highlight how recent advances in molecular biology are deepening our knowledge of CAM evolution.

Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation

Plants are continuously exposed to diurnal fluctuations in light and temperature, and spontaneous changes in their physical or biotic environment. The circadian clock coordinates regulation of gene expression with a 24 h period, enabling the anticipation of these events. We used RNA sequencing to characterize the Brachypodium distachyon transcriptome under light and temperature cycles, as well as under constant conditions. Approximately 3% of the transcriptome was regulated by the circadian clock, a smaller proportion than reported in most other species. For most transcripts that were rhythmic under all conditions, including many known clock genes, the period of gene expression lengthened from 24 to 27 h in the absence of external cues. To functionally characterize the cyclic transcriptome in B. distachyon, we used Gene Ontology enrichment analysis, and found several terms significantly associated with peak expression at particular times of the day. Furthermore, we identified sequence motifs enriched in the promoters of similarly phased genes, some potentially associated with transcription factors. When considering the overlap in rhythmic gene expression and specific pathway behavior, thermocycles was the prevailing cue that controlled diurnal gene regulation. Taken together, our characterization of the rhythmic B. distachyon transcriptome represents a foundational resource with implications in other grass species.

Pseudomonas fluorescens promote photosynthesis, carbon fixation and cadmium phytoremediation of hyperaccumulator Sedum alfredii

Plant growth-promoting bacteria (PGPB) can promote photosynthesis and biomass production of hyperaccumulators, achieving enhanced phytoremediation efficiency of cadmium (Cd). A better understanding of the mechanisms controlling photosynthesis of hyperaccumulating plants by PGPB is necessary for developing strategies that promote the practical phytoextraction of Cd-polluted soils. In this study, chlorophyll fluorescence, gas exchange, and transcriptome sequencing were conducted to evaluate the physiological and transcriptional changes on photosynthesis and carbon fixation in hyperaccumulator Sedum alfredii after inoculation with PGPB Pseudomonas fluorescens. The results showed that bacterial inoculation significantly enhanced maximum quantum yield of PS II (Fv/Fm), effective quantum yield of PS II (ΦPSII), photochemical quenching (qP) and chlorophyll concentration, while reduced non-photochemical quenching (NPQ) of S. alfredii. Further, inoculation resulted in an increased net photosynthetic rates (Pn), intercellular CO₂ concentration (Ci), transpiration rate (Tr) and stomatal conductance (Gs) of the studied plant. At the transcriptional level, 70 photosynthetic genes and 42 C4-pathway carbon fixation related genes were significantly up-regulated in response to inoculation, which could be the reason for enhanced photosynthesis and dry biomass. To sum up, this P. fluorescens strain can simultaneously promote growth and Cd uptake of S. alfredii, which can be a promising bacterial agent applied to Cd phytoremediation practices.

Kalanchoë PPC1 Is Essential for Crassulacean Acid Metabolism and the Regulation of Core Circadian Clock and Guard Cell Signaling Genes

Unlike C3 plants, Crassulacean acid metabolism (CAM) plants fix CO2 in the dark using phosphoenolpyruvate carboxylase (PPC; EC 4.1.1.31). PPC combines phosphoenolpyruvate with CO2 (as HCO3 -), forming oxaloacetate. The oxaloacetate is converted to malate, leading to malic acid accumulation in the vacuole, which peaks at dawn. During the light period, malate decarboxylation concentrates CO2 around Rubisco for secondary fixation. CAM mutants lacking PPC have not been described. Here, we employed RNA interference to silence the CAM isogene PPC1 in Kalanchoë laxiflora Line rPPC1-B lacked PPC1 transcripts, PPC activity, dark period CO2 fixation, and nocturnal malate accumulation. Light period stomatal closure was also perturbed, and the plants displayed reduced but detectable dark period stomatal conductance and arrhythmia of the CAM CO2 fixation circadian rhythm under constant light and temperature free-running conditions. By contrast, the rhythm of delayed fluorescence was enhanced in plants lacking PPC1 Furthermore, a subset of gene transcripts within the central circadian oscillator was upregulated and oscillated robustly in this line. The regulation of guard cell genes involved in controlling stomatal movements was also perturbed in rPPC1-B These findings provide direct evidence that the regulatory patterns of key guard cell signaling genes are linked with the characteristic inverse pattern of stomatal opening and closing during CAM.

C4 and crassulacean acid metabolism within a single leaf: deciphering key components behind a rare photosynthetic adaptation

Although biochemically related, C₄ and crassulacean acid metabolism (CAM) systems are expected to be incompatible. However, Portulaca species, including P. oleracea, operate C₄ and CAM within a single leaf, and the mechanisms behind this unique photosynthetic arrangement remain largely unknown. Here, we employed RNA-seq to identify candidate genes involved exclusively or shared by C₄ or CAM, and provided an in-depth characterization of their transcript abundance patterns during the drought-induced photosynthetic transitions in P. oleracea. Data revealed fewer candidate CAM-specific genes than those recruited to function in C₄ . The putative CAM-specific genes were predominantly involved in night-time primary carboxylation reactions and malate movement across the tonoplast. Analysis of gene transcript-abundance regulation and photosynthetic physiology indicated that C₄ and CAM coexist within a single P. oleracea leaf under mild drought conditions. Developmental and environmental cues were shown to regulate CAM expression in stems, whereas the shift from C₄ to C₄ -CAM hybrid photosynthesis in leaves was strictly under environmental control. Moreover, efficient starch turnover was identified as part of the metabolic adjustments required for CAM operation in both organs. These findings provide insights into C₄ /CAM connectivity and compatibility, contributing to a deeper understanding of alternative ways to engineer CAM into C₄ crop species.

Model approaches to advance crassulacean acid metabolism system integration

This review summarises recent progress in understanding crassulacean acid metabolism (CAM) systems and the integration of internal and external stimuli to maximise water-use efficiency. Complex CAM traits have been reduced to their minimum and captured as computational models, which can now be refined using recently available data from transgenic manipulations and large-scale omics studies. We identify three key areas in which an appropriate choice of modelling tool could help capture relevant comparative molecular data to address the evolutionary drivers and plasticity of CAM. One focus is to identify the environmental and internal signals that drive inverse stomatal opening at night. Secondly, it is important to identify the regulatory processes required to orchestrate the diel pattern of carbon fluxes within mesophyll layers. Finally, the limitations imposed by contrasting succulent systems and associated hydraulic conductance components should be compared in the context of water-use and evolutionary strategies. While network analysis of transcriptomic data can provide insights via co-expression modules and hubs, alternative forms of computational modelling should be used iteratively to define the physiological significance of key components and informing targeted functional gene manipulation studies. We conclude that the resultant improvements of bottom-up, mechanistic modelling systems can enhance progress towards capturing the physiological controls for phylogenetically diverse CAM systems in the face of the recent surge of information in this omics era.

Comparative genomics can provide new insights into the evolutionary mechanisms and gene function in CAM plants

Crassulacean acid metabolism (CAM) photosynthesis is an important biological innovation enabling plant adaptation to hot and dry environments. CAM plants feature high water-use efficiency, with potential for sustainable crop production under water-limited conditions. A deep understanding of CAM-related gene function and molecular evolution of CAM plants is critical for exploiting the potential of engineering CAM into C3 crops to enhance crop production on semi-arid or marginal agricultural lands. With the newly emerging genomics resources for multiple CAM species, progress has been made in comparative genomics studies on the molecular basis and subsequently on the evolution of CAM. Here, recent advances in CAM comparative genomics research in constitutive and facultative CAM plants are reviewed, with a focus on the analyses of DNA/protein sequences and gene expression to provide new insights into the path and driving force of CAM evolution and to identify candidate genes involved in CAM-related biological processes. Potential applications of new computational and experimental technologies (e.g. CRISPR/Cas-mediated genome-editing technology) to the comparative and evolutionary genomics research on CAM plants are offered.