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The NADP-ME type of C4 pathway in sorghum and maize. CA, carboxylating anhydrase; MDH, malate dehydrogenase; ME, malic enzyme; OAA, oxaloacetate; PEPC, phosphoenolpyruvate carboxylase; PPCK, PEPC kinase; PPDK, pyruvate orthophosphate dikinase; PPDK-RP, PPDK regulatory protein; TP, transit peptide.
Source publication
Sorghum is the first C4 plant and the second grass with a full genome sequence available. This makes it possible to perform a whole-genome-level exploration of C4 pathway evolution by comparing key photosynthetic enzyme genes in sorghum, maize (C4) and rice (C3), and to investigate a long-standing hypothesis that a reservoir of duplicated genes is...
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As compared to C3, C4 plants have higher photosynthetic rates and better tolerance to high temperature and drought. These traits are highly beneficial in the current scenario of global warming. Interestingly, all the genes of the C4 photosynthetic pathway are present in C3 plants, although they are involved in diverse non-photosynthetic functions....
We have identified an efficient filamentous marine cyanobacterium, Phormidium valderianum BDU 20041, which was adaptive to different concentrations of CO2. In our study, P. valderianum BDU 20041 was grown under ambient (0.04) and elevated (2, 3, 4, 5, 10, and 15%) CO2 concentration. Its optimal growth occurred at 3% CO2 supply. P. valderianum displ...
Citations
... These include genes related to root development and salt tolerance that enhance plant adaptive response to intertidal zones. In relationship to photosynthesis traits, several studies, including those by Wang et al. (2009b) and Hoang et al. (2023), showed the contribution of WGD to the evolution of C 4 photosynthesis from the C 3 ancestral state in two evolutionarily distant families, Poaceae and Cleomaceae, respectively. Our results on retained WGT genes and their sub-genome dominance, especially those related to plant response to endogenous stimuli, morphogenesis, development, organelle organization, chloroplast-targeted pathways and photosynthesis, might reflect important gene families that were involved in the evolution that led to the high-photosynthesis traits at high light intensity in H. incana. ...
Background and Aims
The Brassiceae tribe encompasses many economically important crops and exhibits high intraspecific and interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event (Br-α, ~15.9 million years ago), differential lineage diversification and genomic changes contributed to an array of divergence in morphology, biochemistry, and physiology underlying photosynthesis-related traits. Here, the C3 species Hirschfeldia incana is studied as it displays high photosynthetic rates under high-light conditions. Our aim was to elucidate the evolution that gave rise to the genome of H. incana and its high-photosynthesis traits.
Methods
We reconstructed a chromosome-level genome assembly for H. incana (Nijmegen, v2.0) using nanopore and chromosome conformation capture (Hi-C) technologies, with 409Mb in size and an N50 of 52Mb (a 10× improvement over the previously published scaffold-level v1.0 assembly). The updated assembly and annotation was subsequently employed to investigate the WGT history of H. incana in a comparative phylogenomic framework from the Brassiceae ancestral genomic blocks and related diploidized crops.
Key Results
Hirschfeldia incana (x=7) shares extensive genome collinearity with Raphanus sativus (x=9). These two species share some commonalities with Brassica rapa and B. oleracea (A genome, x=10 and C genome, x=9, respectively) and other similarities with B. nigra (B genome, x=8). Phylogenetic analysis revealed that H. incana and R. sativus form a monophyletic clade in between the Brassica A/C and B genomes. We postulate that H. incana and R. sativus genomes are results of hybridization or introgression of the Brassica A/C and B genome types. Our results might explain the discrepancy observed in published studies regarding phylogenetic placement of H. incana and R. sativus in relation to the "Triangle of U" species. Expression analysis of WGT retained gene copies revealed sub-genome expression divergence, likely due to neo- or sub-functionalization. Finally, we highlighted genes associated with physio-biochemical-anatomical adaptive changes observed in H. incana which likely facilitate its high-photosynthesis traits under high light.
Conclusions
The improved H. incana genome assembly, annotation and results presented in this work will be a valuable resource for future research to unravel the genetic basis of its ability to maintain a high photosynthetic efficiency in high-light conditions and thereby improve photosynthesis for enhanced agricultural production.
... These include genes related to root development and salt tolerance that enhance plant adaptive response to intertidal zones. In relationship to photosynthesis traits, several studies, including those by Wang et al. (2009b) and Hoang et al. (2023), showed the contribution of WGD to the evolution of C 4 photosynthesis from the C 3 ancestral state in two evolutionarily distant families, Poaceae and Cleomaceae, respectively. Our results on retained WGT genes and their sub-genome dominance, especially those related to plant response to endogenous stimuli, morphogenesis, development, organelle organization, chloroplast-targeted pathways and photosynthesis, might reflect important gene families that were involved in the evolution that led to the high-photosynthesis traits at high light intensity in H. incana. ...
Background and Aims
The Brassiceae tribe encompasses many economically important crops and exhibits high intraspecific and interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event (Br-α, ~15.9 million years ago), differential lineage diversification and genomic changes contributed to an array of divergence in morphology, biochemistry, and physiology underlying photosynthesis-related traits. Here, the C3 species Hirschfeldia incana is studied as it displays high photosynthetic rates under high-light conditions. Our aim was to elucidate the evolution that gave rise to the genome of H. incana and its high-photosynthesis traits.
Methods
We reconstructed a chromosome-level genome assembly for H. incana (Nijmegen, v2.0) using nanopore and chromosome conformation capture (Hi-C) technologies, with 409Mb in size and an N50 of 52Mb (a 10× improvement over the previously published scaffold-level v1.0 assembly). The updated assembly and annotation was subsequently employed to investigate the WGT history of H. incana in a comparative phylogenomic framework from the Brassiceae ancestral genomic blocks and related diploidized crops.
Key Results
Hirschfeldia incana (x=7) shares extensive genome collinearity with Raphanus sativus (x=9). These two species share some commonalities with Brassica rapa and B. oleracea (A genome, x=10 and C genome, x=9, respectively) and other similarities with B. nigra (B genome, x=8). Phylogenetic analysis revealed that H. incana and R. sativus form a monophyletic clade in between the Brassica A/C and B genomes. We postulate that H. incana and R. sativus genomes are results of hybridization or introgression of the Brassica A/C and B genome types. Our results might explain the discrepancy observed in published studies regarding phylogenetic placement of H. incana and R. sativus in relation to the “Triangle of U” species. Expression analysis of WGT retained gene copies revealed sub-genome expression divergence, likely due to neo- or sub-functionalization. Finally, we highlighted genes associated with physio-biochemical-anatomical adaptive changes observed in H. incana which likely facilitate its high-photosynthesis traits under high light.
Conclusions
The improved H. incana genome assembly, annotation and results presented in this work will be a valuable resource for future research to unravel the genetic basis of its ability to maintain a high photosynthetic efficiency in high-light conditions and thereby improve photosynthesis for enhanced agricultural production.
... Previous attempts to engineer a single-cell C 4 pathway into O. sativa resulted in increased photoinhibition of photosynthesis, leaf chlorophyll bleaching, and severe stunting without proper CO 2 concentration in chloroplasts (Taniguchi et al. 2008). Most C 4 plants utilize a 2-cell C 4 pathway, with strict compartmentation of photosynthetic enzymes in mesophyll cells (MCs) and bundle sheath cells (BSCs) (Wang et al. 2009). Engineering a functional C 4 pathway into O. sativa necessitates the construction of a biochemical pump for CO 2 concentration in modified BSCs (Lin et al. 2020). ...
... Notably, SsPEPCK was an exception. Eight genes in S. spontaneum,SsPEPC1,SsPPDK1,SsCA1,and SsCA2, are clustered together with their putatively orthologous C 4 genes from S. bicolor and Z. mays (Wang et al. 2009). ...
In agronomically important C4 grasses, efficient CO2 delivery to Rubisco is facilitated by NADP-malic enzyme (C4NADP-ME), which decarboxylates malate in bundle sheath cells. However, understanding the molecular regulation of the C4NADP-ME gene in sugarcane (Saccharum spp.) is hindered by its complex genetic background. Enzymatic activity assays demonstrated that decarboxylation in sugarcane Saccharum spontaneum predominantly relies on the NADP-ME pathway, similar to sorghum (Sorghum bicolor) and maize (Zea mays). Comparative genomics analysis revealed the recruitment of eight core C4 shuttle genes, including C4NADP-ME (SsC4NADP-ME2), in the C4 pathway of sugarcane. Contrasting to sorghum and maize, the expression of SsC4NADP-ME2 in sugarcane is regulated by different transcription factors (TFs). We propose a gene regulatory network for SsC4NADP-ME2, involving candidate TFs identified through gene co-expression analysis and yeast one-hybrid experiment. Among these, ABA INSENSITIVE5 (ABI5) was validated as the predominant regulator of SsC4NADP-ME2 expression, binding to a G-box within its promoter region. Interestingly, the core element ACGT within the regulatory G-box was conserved in sugarcane, sorghum, maize, and rice (Oryza sativa), suggesting an ancient regulatory code utilized in C4 photosynthesis. This study offers insights into SsC4NADP-ME2 regulation, crucial for optimizing sugarcane as a bioenergy crop.
... Interestingly, these tend to come from the same gene families as the previously identified C 4 leaf anatomy regulators in other species. This parallel recruitment appears to mirror the pattern observed in the core metabolic enzymes, with the paralog recruited for the C 4 function depending on its ancestral expression pattern and catalytic properties (Wang et al., 2009;Hibberd & Covshoff, 2010;Christin et al., 2013Christin et al., , 2015Aubry et al., 2014;Emms et al., 2016;Moreno-Villena et al., 2018). Thus, the easiest path to C 4 leaf anatomy would be context-dependent, which likely has implications for engineering C 4 anatomy in C 3 species. ...
C4 photosynthesis is a complex trait requiring multiple developmental and metabolic alterations. Despite this complexity, it has independently evolved over 60 times. However, our understanding of the transition to C4 is complicated by the fact that variation in photosynthetic type is usually segregated between species that diverged a long time ago.
Here, we perform a genome‐wide association study (GWAS) using the grass Alloteropsis semialata, the only known species to have C3, intermediate, and C4 accessions that recently diverged. We aimed to identify genomic regions associated with the strength of the C4 cycle (measured using δ¹³C), and the development of C4 leaf anatomy.
Genomic regions correlated with δ¹³C include regulators of C4 decarboxylation enzymes (RIPK), nonphotochemical quenching (SOQ1), and the development of Kranz anatomy (SCARECROW‐LIKE). Regions associated with the development of C4 leaf anatomy in the intermediate individuals contain additional leaf anatomy regulators, including those responsible for vein patterning (GSL8) and meristem determinacy (GIF1).
The parallel recruitment of paralogous leaf anatomy regulators between A. semialata and other C4 lineages implies the co‐option of these genes is context‐dependent, which likely has implications for the engineering of the C4 trait into C3 species.
... Sorghum (Sorghum bicolor L.) represents the fifth most grown crop worldwide after maize, wheat, and rice [1][2][3] and is a C4 crop with high nitrogen and water use efficiency [4]. It has a strong environmental adaptability and wide distribution and is extensively grown in arid and semi-arid regions worldwide, thus playing a vital role in the world's agroecosystems [4].The sorghum aphid (Melanaphis sacchari (Zehntner) (Homoptera: Aphididae) is a major pest of sorghum that seriously harms the yield and quality of sorghum under field conditions [5]. ...
... Sorghum (Sorghum bicolor L.) represents the fifth most grown crop worldwide after maize, wheat, and rice [1][2][3] and is a C4 crop with high nitrogen and water use efficiency [4]. It has a strong environmental adaptability and wide distribution and is extensively grown in arid and semi-arid regions worldwide, thus playing a vital role in the world's agroecosystems [4].The sorghum aphid (Melanaphis sacchari (Zehntner) (Homoptera: Aphididae) is a major pest of sorghum that seriously harms the yield and quality of sorghum under field conditions [5]. Sorghum aphids occurr on sugarcane and sorghum in India, China, South Africa, Japan, and the United States, mainly during late sorghum growth [6][7][8]. ...
Background
The sorghum aphid Melanaphis sacchari (Zehntner) (Homoptera: Aphididae) is an important insect in the late growth phase of sorghum (Sorghum bicolor L.). However, the mechanisms of sorghum response to aphid infestation are unclear.
Results
In this paper, the mechanisms of aphid resistance in different types of sorghum varieties were revealed by studying the epidermal cell structure and performing a transcriptome and metabolome association analysis of aphid-resistant and aphid-susceptible varieties. The epidermal cell results showed that the resistance of sorghum to aphids was positively correlated with epidermal cell regularity and negatively correlated with the intercellular space and leaf thickness. Transcriptome and metabolomic analyses showed that differentially expressed genes in the resistant variety HN16 and susceptible variety BTX623 were mainly enriched in the flavonoid biosynthesis pathway and differentially expressed metabolites were mainly related to isoflavonoid biosynthesis and flavonoid biosynthesis. The q-PCR results of key genes were consistent with the transcriptome expression results. Meanwhile, the metabolome test results showed that after aphidinfestation, naringenin and genistein were significantly upregulated in the aphid-resistant variety HN16 and aphid-susceptible variety BTX623 while luteolin was only significantly upregulated in BTX623. These results show that naringenin, genistein, and luteolin play important roles in plant resistance to aphid infestation. The results of exogenous spraying tests showed that a 1‰ concentration of naringenin and genistein is optimal for improving sorghum resistance to aphid feeding.
Conclusions
In summary, the physical properties of the sorghum leaf structure related to aphid resistance were studied to provide a reference for the breeding of aphid-resistant varieties. The flavonoid biosynthesis pathway plays an important role in the response of sorghum aphids and represents an important basis for the biological control of these pests. The results of the spraying experiment provide insights for developing anti-aphid substances in the future.
... For instance, segmental duplication accounted for the rapid expansion and large size of PHB gene expansion in Arabidopsis [42], IQM genes in rice [43], CPK and RBL gene families in wheat [44,45], and the R2R3-MYB gene family in land plants [46]. Moreover, WGD is often followed by the loss of most duplicated genes over a few million years [47], whereas various types of SSD occur more or less continuously and are essential in plant development and adaptation to the environment [48,49]. Many studies found that the expansion of genes related to signal transduction, transcriptional regulation, and ribosome structures were mainly driven by WGD events [50,51], while those related to environmental stress responses were mainly driven by SSD events [52,53]. ...
Background: Phosphorus (P) is an essential macronutrient for Brassica napus L. growth and development, and is mainly acquired from the soil as phosphate (Pi). However, there is no research on the system analysis of Pi utilization related genes (PURs) in B. napus yet.
Results: In this study, 285 PURs were identified in B. napus genome, including 4 transcription factor (TF) families (83 genes) and 17 structural gene families (202 genes). Subcellular localization analysis showed that the proteins encoded by PURs were mainly located in the nucleus (~46.0%) and cell membrane (~36.5%). Chromosome localization analysis suggested that PURs were unequally distributed on the 19 chromosomes of B. napus, and tended to distribute on the Cn-subgenome (An:131, Cn:149). Collinearity analysis revealed that allopolyploidization and small-scale duplication events resulted in the large expansion of PURs. Expression and functional divergence of PURs may initially occur in the promoter region during evolution due to the lower sequence identity in the promoter than in CDS regions. A total of 362 genes were identified as PURs regulators, belonging to 32 TF families and 56 types of miRNAs. Spatiotemporal expression analysis demonstrated that PURs were widely expressed during the whole developmental stages, and most synteny-gene pairs (76.42%) shared conserved expression patterns. RNA-seq analyses revealed that most PURs were induced by LP stress, and the hub genes were generally the Pi transporter (PHT) family members. qRT-PCR analysis proved that the expression levels of four PURs were positively correlated with the root system architecture of three B. napus varieties under LP supply at the seedling stage.
Conclusion: The 285 PURs were identified from B. napus with strong LP inducible expression profile. Our findings regarding the evolution, transcriptional regulation, and expression of PURs provide valuable information for further functional research.
... Furthermor e, man y components of the C4 metabolic pathway were brought by these WGD events and single duplication e v ents . T his is an interesting case of convergence throughout the evolution of differ ent plant linea ges [ 7 ]. These c hanges ar e influenced by the synergistic effect of WGDs, transposed duplication, and dispersed gene duplication, evidenced by overlapping peaks in the rates of synonymous substitutions [ 6 ]. ...
Background
Structural variants (SVs) are genomic polymorphisms defined by their length (>50 bp). The usual types of SVs are deletions, insertions, translocations, inversions, and copy number variants. SV detection and genotyping is fundamental given the role of SVs in phenomena such as phenotypic variation and evolutionary events. Thus, methods to identify SVs using long-read sequencing data have been recently developed.
Findings
We present an accurate and efficient algorithm to predict germline SVs from long-read sequencing data. The algorithm starts collecting evidence (signatures) of SVs from read alignments. Then, signatures are clustered based on a Euclidean graph with coordinates calculated from lengths and genomic positions. Clustering is performed by the DBSCAN algorithm, which provides the advantage of delimiting clusters with high resolution. Clusters are transformed into SVs and a Bayesian model allows to precisely genotype SVs based on their supporting evidence. This algorithm is integrated into the single sample variants detector of the Next Generation Sequencing Experience Platform, which facilitates the integration with other functionalities for genomics analysis. We performed multiple benchmark experiments, including simulation and real data, representing different genome profiles, sequencing technologies (PacBio HiFi, ONT), and read depths.
Conclusion
The results show that our approach outperformed state-of-the-art tools on germline SV calling and genotyping, especially at low depths, and in error-prone repetitive regions. We believe this work significantly contributes to the development of bioinformatic strategies to maximize the use of long-read sequencing technologies.
... On the contrary, a PEPCk-deficient Kalanchoë fedtschenkoi RNAi line showed perturbations of CAM photosynthesis, carbohydrate metabolism, and circadian rhythms [14]. Sorghum bicolor SbPPCK gene family includes three genes (SbPPCK1-3; Sb04g036570, Sb04g026490, and Sb06g022690) [15]. ZmPPCK1 expression is triggered by light in mesophyll cells from maize, and its transcript is more abundant in mesophyll than bundle sheath cells [16]. ...
Phosphoenolpyruvate carboxylase (PEPC) plays central roles in photosynthesis, respiration, amino acid synthesis, and seed development. PEPC is regulated by different post-translational modifications. Between them, the phosphorylation by PEPC-kinase (PEPCk) is widely documented. In this work, we simultaneously silenced the three sorghum genes encoding PEPCk (SbPPCK1-3) by RNAi interference, obtaining 12 independent transgenic lines (Ppck1-12 lines), showing different degrees of SbPPCK1-3 silencing. Among them, two T2 homozygous lines (Ppck-2 and Ppck-4) were selected for further evaluation. Expression of SbPPCK1 was reduced by 65% and 83% in Ppck-2 and Ppck-4 illuminated leaves, respectively. Expression of SbPPCK2 was higher in roots and decreased by 50% in Ppck-2 and Ppck-4 in this tissue. Expression of SbPPCK3 was low and highly variable. Despite the incomplete gene silencing, it decreased the degree of phosphorylation of PEPC in illuminated leaves, P-deficient plants, and NaCl-treated plants. Both leaves and seeds of Ppck lines had altered metabolic profiles and a general decrease in amino acid content. In addition, Ppck lines showed delayed flowering, and 20% of Ppck-4 plants did not produce flowers at all. The total amount of seeds was lowered by 50% and 36% in Ppck-2 and Ppck-4 lines, respectively. The quality of seeds was lower in Ppck lines: lower amino acid content, including Lys, and higher phytate content. These data confirm the relevance of the phosphorylation of PEPC in sorghum development, stress responses, yield, and quality of seeds.
... The evolution of plant C 4 photosynthesis represents a unique example of convergent evolution [4,37,38]. With the availability of the annotated genomes for G. gynandra and T. hassleriana, direct comparison between these C 4 and C 3 species presents an excellent model to unravel why C 4 photosynthesis evolved in only one of the two plants. ...
The carbon concentrating mechanism—C4 photosynthesis—represents a classic example of convergent evolution. While how this important trait originated and evolved remains largely enigmatic. The spider-flower Gynandropsis gynandra is a valuable leafy vegetable crop and medicinal plant that has also been recognized as a C4 model species. Here we present a high-quality chromosome-scale annotated genome assembly of G. gynandra through a combination of ONT, HiFi and Hi-C technology. The seventeen super scaffolds cover 98.66% of the estimated genome (997.61 Mb), with a contig N50 of 11.43 Mb and a scaffold N50 of 51.02 Mb. Repetitive elements occupy up to 71.91% of its genome, and over half are LTR-RTs derived from recent bursts, contributing to genome size expansion. Strikingly, LTR-RT explosion also played a critical role in C4 evolution by altering expression features of photosynthesis-associated genes via preferential insertion in promoters. Integrated multi-omics analyses of G. gynandra and the ornamental horticulture C3 relative Tarenaya hassleriana reveal that species-specific whole-genome duplication, gene family expansion, recent LTR-RT amplification and more recent tandem duplication events have all facilitated evolution of C4 photosynthesis, revealing uniqueness of C4 evolution in the Cleome genus. Moreover, high leaf vein density and heat stress resilience are associated with shifted gene expression patterns. The mode of C3-to-C4 transition found here yields new insights into evolutionary convergence of a complex plant trait. The availability of this reference-grade genomic resource makes G. gynandra an ideal model system facilitating efforts toward C4-aimed crop engineering.
... Genes generate functional innovation through multiple duplication mechanisms and contribute to the adaptive evolution of species [55][56][57][58]. Nevertheless, plants often do not need very many copies of genes, as more copies may complicate the regulatory pathways and more homologues, mutated or intact, can induce conflicts and lead to plant death [37]. ...
... Our study showed that the optimal codon numbers of the seven grass TLP gene families ranged from 12 to 18, and these small numbers reflected the effects of purifying selection and mutational pressure [64]. Moreover, previous research findings have shown that GC content elevation results in codon usage bias [56,65]. The majority of the optimal codons of the grass TLP family contain GC bases, which may be evidence that codon usage bias is related to GC content. ...
... Single-copy clustered genes were used to construct the ML phylogenetic tree via FastTree [93], and the trees were then used to perform further maximum likelihood analysis using the Codeml program in PAML [94]. To detect whether a specific TLP gene had been positively selected, we compared two types of competing models, a free ratio model and a ratio-restriction model [95], following our previous steps [36,56]. ...
Background
In the evolutionary study of gene families, exploring the duplication mechanisms of gene families helps researchers understand their evolutionary history. The tubby-like protein (TLP) family is essential for growth and development in plants and animals. Much research has been done on its function; however, limited information is available with regard to the evolution of the TLP gene family. Herein, we systematically investigated the evolution of TLP genes in seven representative Poaceae lineages.
Results
Our research showed that the evolution of TLP genes was influenced not only by whole-genome duplication (WGD) and dispersed duplication (DSD) but also by transposed duplication (TRD), which has been neglected in previous research. For TLP family size, we found an evolutionary pattern of progressive shrinking in the grass family. Furthermore, the evolution of the TLP gene family was at least affected by evolutionary driving forces such as duplication, purifying selection, and base mutations.
Conclusions
This study presents the first comprehensive evolutionary analysis of the TLP gene family in grasses. We demonstrated that the TLP gene family is also influenced by a transposed duplication mechanism. Several new insights into the evolution of the TLP gene family are presented. This work provides a good reference for studying gene evolution and the origin of duplication.
