The green leaf volatiles (Z)-3-hexenal and (E)-2-hexenal are key components of the characteristic strawberry aroma, an important determinant of consumer preferences. Green leaf volatiles (GLVs) are C6 compounds that impart fresh, green notes and are involved in plant wounding responses. GLV biosynthesis requires several enzymatic steps to convert polyunsaturated fatty acids to C6-aldehydes, alcohols, and esters, respectively. However, the biosynthesis of GLVs in strawberries, such as the isomerization of (Z)-3-hexenal to (E)-2-hexenal, remains poorly understood. In this study, we identified a (Z)-3:(E)-2-hexenal isomerase gene (FvHI) using phylogenetic analysis, characterized its expression in different tissues, and characterized its function using stable transformation. Volatile analysis by gas chromatography-mass spectrometry (GC-MS) of fruits from a Fragaria vesca near-isogenic line (NIL) collection revealed a distinct ratio of (Z)-3-hexenal and (E)-2-hexenal in lines containing Fragaria bucharica introgressions in the distal end of linkage group 5. Consequently, FvHI was located within this genomic region. The coding sequence of FvHI was nearly identical between the recurrent parent and a selected NIL individual containing an introgression in the distal end linkage group 5, indicating that the contrasting ratio of (Z)-3 and (E)-2 GLV isomers may be attributed to transcriptional differences. Accordingly, FvHI expression in ripe fruits was lower in the selected NIL individual than in the recurrent parent. Lastly, FvHI overexpression decreased (Z)-3-hexenal accumulation and increased (E)-2-hexenal accumulation in the recurrent parent and the selected NIL individual. These results suggest that FvHI plays a role in producing the characteristic strawberry aroma by converting (Z)-3-hexenal to (E)-2-hexenal.

Drought stress is a major environmental constraint that severely impacts plant production. However, the genetic basis is primarily misunderstood in chrysanthemum species. The objectives of this study are to examine the genetic variation of drought tolerance in reciprocal F₁ progenies of Chrysanthemum dichrum (drought-tolerant) and Chrysanthemum nankingense (drought-sensitive) and identify candidate genes by integrating linkage mapping, genome-wide association study (GWAS), and RNA-seq analysis. The results revealed extensive variation for the investigated traits in response to drought stress and notable genetic divergence in drought tolerance between the reciprocal crosses. This confirms that the hybridization direction influenced drought tolerance phenotypes. A high-resolution genetic map containing 6677 nonredundant bin markers spanning 1859.31 cM across nine linkage groups (LGs), achieving an average marker density of 0.28 cM, was developed with a genotyping-by-sequencing (GBS) approach. The inclusive composite interval mapping (ICIM) detected 89 significant quantitative trait loci (QTLs), and GWAS identified 1360 significant quantitative trait nucleotides (QTNs) in Single_Env, 394 QTNs, and 114 quantitative epistatic interactions (QEIs) in the Multi_Env algorithm, as well as six pairs of epistatic loci (QEs) related to drought tolerance. Besides the additive effects, we observed considerable adverse dominant and epistatic effects for the significant loci, explaining why drought tolerance exhibits negative heterosis in reciprocal crosses. The integration of QTL mapping and GWAS revealed 38 colocalized loci harboring 10 known and 15 novel candidate genes, eight validated through RNA-seq and qRT-PCR analyses. Moreover, we identified elite haplotypes yielding higher drought tolerance within the candidate gene Cn1062070. The findings help elucidate the genetic architecture of drought tolerance in chrysanthemum species and provide valuable genetic resources for the development of drought-tolerant cultivars.

The mulberry (Morus notabilis) is a medicinal and edible plant and contains diverse flavonoids and stilbenoids with significant medicinal benefits. The biosynthesis of these compounds has only been partially elucidated. In the present investigation, we identified and characterized two 4-coumarate: coenzyme A ligases (Mn4CL1 and Mn4CL2), two polyketide synthases (MnCHS and MnSTS), three chalcone reductases (MnCHR1-3), and two 2-oxoglutarate-dependent dioxygenases (MnFLS and MnF3H) involved in flavonoids and stilbenoid biosynthesis. MnCHS converts p-coumaroyl-CoA into naringenin and facilitates the novel conversion of 2,4-dihydroxycinnamoyl-CoA to steppogenin, which features hydroxyl groups at the 4′ and 6′ positions on the B ring. MnSTS could convert p-coumaroyl-CoA and 2,4-dihydroxycinnamoyl-CoA into resveratrol and oxyresveratrol, respectively. Furthermore, MnCHR1 was first identified in mulberry and collaborated with MnCHS to produce isoliquiritigenin and 2,4,2′,4′-tetrahydroxychalcone. A co-expression system of Mn4CL1, MnCHS, and MnCHR1 enabled the fermentation production of steppogenin and 2,4,2′,4′-tetrahydroxychalcone in engineered Escherichia coli. The in vitro enzymatic assays confirmed that MnFLS showed both FLS and F3H activities, whereas transgenic experiments revealed its predominant FLS function in vivo; MnF3H was confirmed as a bona fide F3H. These findings provide new insights into the flavonoids and stilbenoids biosynthesis pathway in mulberry and suggest a potential parallel pathway for 4′,6′-dihydroxylated flavonoids biosynthesis.

The ripening of banana fruit at high temperature (HT) exceeding 24°C impedes developing yellow peels, causing green ripening, which considerably lowers its marketability. Our recent study found that HT induces E3 ubiquitin ligase MaNIP1 (NYC1 interacting protein 1)-mediated degradation of MaNYC1 (NON-YELLOW COLORING 1) to inhibit chlorophyll breakdown during banana fruit ripening, but MaNIP1's upstream regulatory mechanism is still unclear. Herein, the ASR transcription factor (TF) MaASR3, which is repressed in green-ripened fruit compared to yellow-ripened fruit, was identified as the potential binding protein for the MaNIP1 promoter. MaASR3 promoted chlorophyll degradation in banana fruit by repressing MaNIP1 expression. More importantly, the histone deacetylase MaHDT1 interacted with MaASR3 and enhanced MaASR3-mediated repression of MaNIP1. Overexpression of MaASR3 in banana fruit reduced the histone acetylation levels in the MaNIP1 promoter and repressed MaNIP1 expression, thereby weakening the HT-inhibited degreening of banana fruit. Our study reveals an innovative regulatory cascade comprising the MaASR3-MaHDT1-MaNIP1 complex, which modulates HT-inhibited chlorophyll degradation. This explains the green ripening in bananas exposed to such conditions and enhances the comprehension of transcriptional and epigenetic regulations of fruit quality deterioration due to temperature stresses.

Drought induces tomato (Solanum lycopersicum) flowers and fruits drop, which causes serious yield and economic losses in agriculture. However, the mechanism of action remains unclear. N6-methyladenosine (m6A) methylation is a prevalent epigenetic change integral to the growth, development, and adaptation of plants to abiotic stress factors. However, whether it participates in drought-induced abscission remains to be further studied. Here, we report that tomato demethylase alpha-ketoglutarate-dependent dioxygenase B (AlkB) homolog 9B (SlALKBH9B) exerts a detrimental influence on the regulation of drought-induced flower drop by mediating ethylene production. We found that drought markedly reduced the expression of SlALKBH9B, and knockout of SlALKBH9B enhanced flower drop, while overexpression of SlALKBH9B delayed the flower drop. Under drought conditions, the ethylene production of Slalkbh9b exhibited a considerably greater yield than that of the wild type (WT), while SlALKBH9B overexpression plants had lower ethylene production. Application of ethylene could abolish the delayed abscission effect of overexpression of SlALKBH9B. Further studies showed that drought downregulated SlALKBH9B expression, which specifically enhanced the methylation level of the 3′ untranslated region (UTR) of tomato ethylene excess producer 1 (SlETO1), leading to a decrease in the stability of SlETO1 mRNA and its protein translation efficiency. The loss of SlETO1 resulted in the accumulation of tomato 1-aminocyclopropane-1-carboxylic acid synthase 3 (SlACS3) and SlACS8 in the abscission zone (AZ) and then boosted ethylene production to accelerate abscission. Our results show that SlALKBH9B is an important inhibitor for drought-induced abscission and reveal a new mechanism through which drought-enhanced ethylene production leads to flower drop.

Jasmonates (JAs) play essential roles in plant development and defense. JA perception and responses remain elusive in citrus. Here, we identified core components for JA perception in citrus and elucidated transcriptional changes associated with JA signaling in growth and defense. We showed the F-box protein CORONATINE INSENSITIVE1 (COI1) in citrus is a JA receptor, as Cscoi1 mutants are insensitive to methyl jasmonate and CsCOI1 interacts with CsJAZs in the presence of JA-Ile. CsCOI1-mediated JA signaling represses shoot growth while enhancing resistance to insects. Consistently, CsCOI1 represses the expression of growth promoting genes such as PIF7, while upregulating genes related to defense metabolites in terpene and flavonoid pathways. Additionally, JA signaling antagonizes salicylic acid (SA) signaling at the transcriptional level and promotes susceptibility to citrus canker disease. This study highlights the role of JA signaling in balancing growth and resistance to biotic stress in citrus, revealing critical trade-offs for consideration in precision citrus breeding.

Sugar content serves as a crucial determinant of fruit flavor quality and nutritional value. Calcium plays extensive regulatory roles in fruit development and quality formation, yet the molecular mechanisms underlying calcium-mediated sugar accumulation remain poorly understood. In this study, we demonstrate that calcium treatment enhances sugar accumulation in both citrus fruits and calli, concomitant with upregulated expression of the sucrose transporter gene CsSWEET17. Functional characterization revealed that the membrane-localized CsSWEET17 protein exhibits sucrose transport activity. Transgenic overexpression of CsSWEET17 in citrus juice sacs, calli and heterologous tomato systems consistently elevated sucrose levels. Conversely, suppression of CsSWEET17 expression through either virus-induced gene silencing or RNA interference significantly reduced sucrose content in citrus. Further investigation identified CsMYB36 as a calcium-responsive transcription factor that directly activates CsSWEET17 expression. Transgenic validation demonstrated that both calcium signaling and CsMYB36-mediated sucrose accumulation strictly depend on CsSWEET17 transcriptional regulation. Our findings elucidate a novel calcium-MYB36-SWEET17 regulatory module controlling sucrose accumulation, providing molecular insights into calcium-based strategies in citrus quality improvement and informing fundamental mechanisms of sugar transporter regulation in fruit crops.

Rising temperatures cause advanced phenology of grapevines and increased sugar concentration in berries, which ultimately modify variety suitability in a given region. Here, four bioclimatic indices and a refined grapevine sugar ripeness (GSR) model were employed to assess the suitability of six winegrape varieties across six winegrape-growing regions of China under historical climate conditions (1961-2020). First, four indices were compared between two periods, one before (P1) and one after (P2) an abrupt climate change events identified during 1988-2002 in these regions. Results showed three temperature-related indices increased in six regions, while the first fall frost day was delayed by 0-16 days in five out of the six regions during P2 compared with P1. Second, GSR model was applied to simulate target sugar concentrations as a proxy for grape harvest dates (GHDs). Direct utilization of original GSR model yielded unsatisfactory predictions with clear bias. Consequently, GSR model was recalibrated with local data to obtain an acceptable performance with R² and NRMSE values of 0.83 and 2.8% as well as 0.83 and 3.1% for the calibration and validation datasets, respectively, and further simulated GHDs of six varieties with advanced values of 6-30 days in six regions for P2 in comparison with P1. To provide a holistic view of freezing injury risk before harvest, comprehensive freezing injury index (CFI) was developed by integrating the frequency, duration and severity of the freezing risk. CFI decreased (2-60%) during P2 in all regions and the magnitude of decrease was elevation dependent. These findings provide valuable insights into the selection of varieties that can more reliably achieve fully mature fruit, producing more balanced wines with greater typicity under warming climate.

Guangdong Citri Reticulatae Pericarpium from the dry and mature peel of Citrus reticulata ‘Chachi’ (CRC) is a well-known medicinal and food material in Asia. The main propagation methods of CRC are layerage and grafting. It is generally considered that the quality of CRC from layerage is superior to that obtained from plants propagated by grafting. Nevertheless, the effects of layerage and grafting on the biosynthesis of flavonoid (main bioactive ingredients) in the peel of CRC remain unknown. Here, metabolomic analyses revealed the effects of layerage, self-grafting, and heterografting (Citrus limonia as rootstock) on flavonoid biosynthesis in CRC from two main harvesting periods, CRCV (Citri Reticulatae Chachiensis Viride) and CRCR (Citri Reticulatae Chachiensis Reddish). Compared with CRCR, CRCV exhibited a higher content of flavonoids. Grafting CRC onto C. limonia exhibited a higher content of hesperidin, nobiletin, tangeretin, narirutin, demethylnobiletin, and sinensetin than layerage and self-grafting. This increase can be attributed to the upregulation of genes involved in flavonoid synthesis. Further, the transcription factor CrcMYBF1 was identified within the gene coexpression network and is confirmed to be significantly induced by methyl jasmonate (MeJA) and upregulate the expression of Crc1,6RhaT through interacting with its promoter region, thereby boosting the biosynthesis and accumulation of hesperidin. In summary, our findings provide mechanistic insights into the coordinated regulation of hesperidin biosynthesis via MeJA-inducing CrcMYBF1 in CRC. Our study is expected to provide a theoretical basis for CRC propagation and cultivation.

Steroidal glycoalkaloids (SGAs) and steroidal saponins (STSs) play significant role in the plant defence against pests and offer various pharmaceuticals applications. SGAs and STSs generally share common biosynthetic pathways in Solanum, originating from a furostanol scaffold. Despite the discovery of multiple GLYCOALKALOID METABOLISM (GAME) genes involved in the biosynthesis of these compounds, previous attempts for the metabolic engineering of these pathways have remained unsuccessful. The GAME15 protein, with its dual enzymatic roles, has unlocked a mystery surrounding the intricate process of metabolizing cholesterol. This protein not only acts as a glucuronosyltransferase but also serves as a metabolic scaffold, organizing several proteins for the proper functioning. This mini review briefly describes the molecular mechanisms and functional dynamics of GAME genes, particularly focusing on GAME15 as a key game changer gene and its role in metabolite channelling, regulation of pathway, and ecological importance. We highlighted the potential of this discovery for advancing metabolic engineering in crop improvement and the pharmaceutical industry. This finding opens doors for designing crops that are resistant to pests. Additionally, we identify important future research directions, including the regulatory mechanisms of these pathways and uncovering structural aspects of pivotal enzymes.

Post-polyploid karyotype evolution represents a crucial cytological mechanism contributing to angiosperm diversification and speciation. Many polyploids show extensive karyotypic reshuffling relative to their pre-ancestors. However, karyotypic stasis is gaining popularity as an alternative evolutionary pathway following polyploidization, whose underlying cytological mechanisms remain poorly understood. Here, we successfully developed a set of enhanced oligo-painting (EOP) probes specific to 20 chromosomes of Cucurbita (2n = 40), a paleo-polyploid with very small chromosomes and rich genetic diversity. The probes generated robust fluorescence in situ hybridization (FISH) signals across six Cucurbita and one sister outgroup species. Cross-species EOP results confirmed that Cucurbita genomes originated from a paleo-allotetraploid and maintained remarkably conserved chromosomal synteny without chromosome reshuffling, indicating karyotypic structural stasis during post-polyploid diploidization. Repositioning and amplification/elimination of rDNA loci (45S and 5S) across species caused significant morphological variations on seven out of 20 chromosomes. Six predicted centromeric monomers showed dramatic variations in localization and copy number along the phylogenetic relationships, highlighting the rapid turnover of centromere-associated sequences. In conclusion, our results suggest that Cucurbita genomes maintain karyotypic structural stasis during post-polyploid diploidization, with karyotype evolution instead being driven by rDNA repositioning and centromere turnover events, which constitute the cytogenetic basis for species divergence in Cucurbita. This finding highlights the more refined cytological evolutionary mechanisms underlying karyotypic stasis, providing new insights into post-polyploid karyotype evolution.

Tomato (Solanum lycopersicum L.) is a species of high economic value, an essential food source, and a model organism for both applied and basic research in crop science. Tomato plants also produce and emit a wide variety of volatile organic compounds (VOCs), which are thought to play a prominent role in multitrophic interactions. This review aims to provide a comprehensive overview of the extensive literature about tomato VOCs emitted by leaves. We explored the role of VOCs in the interactions of tomato plants with the environment, focusing on VOCs that provide plant protection against herbivores, pathogen vectors, pathogens, and abiotic stresses. VOC functions in plant-plant communication and defence are less known, but new evidence is now being collected showing that VOCs sent by plants can inform neighbour plants about impending stresses. Overall, improved knowledge on VOC biochemistry and functions may soon allow their use for sustainable protection practices of tomato crops. Remaining gaps and promising areas for future research are also examined.

This work presents the first eight-way multi-parental advanced generation inter-cross (MAGIC) population in pepper. This interspecific MAGIC population was built with six Capsicum annuum accessions and two C. chinense accessions, selected for encompassing a representative and wide genetic diversity, and being complementary for morphological, agronomic, and fruit quality traits. The population in its third selfing generation has been phenotyped with reliable descriptors and genotyped using genotyping-by-sequencing to assess its overall diversity, homozygosity, parental contributions, and genetic structure. A great variability was found in the phenotyping study, showing many forms of recombination of all the founder lines. Moreover, new phenotypic combinations were found, as well as transgressive inheritance in quantitative traits. The S3 generation contained a balanced distribution of the parental genomes and each S3 individual seemed to contain a unique genomic combination of the founder lines, reaching high homozygosity. In this regard, a preliminary genome-wide association study (GWAS) was performed for highly heritable traits to evaluate the potential of this population for future breeding prospects. Strong associations were found for most traits analysed, like stem pubescence and fruit colour at maturity stage, with associated genes related to response to stress and defence functions; or fruit wall consistency, with associated genes related to lipid metabolism. Our results show that this first Capsicum MAGIC population is a valuable genetic resource for research and breeding purposes in peppers, by identifying genomic regions associated with traits of interest and its potential for future GWAS in more complex agronomical and fruit quality traits.

Actinidia arguta has become popular with consumers recently because of its edible and colorful fruit skin. The 3D spatial organization of its genome plays a key role in the formation of various biological traits. However, the function of 3D genome reorganization during fruit skin color formation is poorly understood in A. arguta. In this study we constructed the 3D genome of the red-skinned A. arguta cultivar ‘Zhonghongbei’ (ZHB) and the green-skinned cultivar ‘Zhonglvbei’ (ZLB), and performed chromatin structure comparisons between them at compartment, topologically associating domain (TAD), and loop levels. Global compartment comparisons at whole 3D genome level between red-skinned and green-skinned A. arguta showed that A-B compartment transition specifically occurred in chromosome 7 and chromosome 16, based on which all genes within 3 Mb upstream and downstream of A-B compartment transition were retrieved to construct a four-way Venn diagram, which showed that AaCBP60B-like, encoding calmodulin-binding protein 60 B-like, is the key candidate gene negatively correlating with fruit color. Exogenous calcium chloride treatments enhancing AaCBP60B-like expression to repress anthocyanin biosynthesis proved a negative role of AaCBP60B-like in anthocyanin biosynthesis. Overexpression and virus-induced gene silencing assays of AaCBP60B-like revealed the inhibition of anthocyanin biosynthesis derived from differential expression of AaCBP60B-like resulting from a 346-bp InDel variation located at the AaCBP60B-like promoter resulting in activity differences in red-and green-skinned A. arguta. ATAC-seq results proved that the 346-bp InDel variation affects 3D genome organization. Our study provides the first 3D chromosome organization in red-and green-skinned A. arguta, based on which a candidate gene, AaCBP60B-like, involved in anthocyanin regulation is identified.

This study comprehensively reveals the origin and evolution mechanisms of ascorbic acid (AsA) synthesis and breakdown pathways during plants’ transition from water to land. By analyzing genomic data from 21 key plant species and transcriptomic data from the One Thousand Plants transcription project, we found that the L-galactose pathway emerged in green algae, with variations in the HIT domain of the rate-limiting enzyme GGP driving adaptive divergence between lower and higher plants. The galacturonic acid pathway integrated with the L-galactose pathway through the emergence of GalUR in bryophytes. The myo-inositol pathway became complete in bryophytes, and its refinement likely promoted dehydration adaptation via oxidative protection. The AsA recycling pathway (APX/MDHAR/DHAR) originated in red algae, while the appearance of AO enzymes is significantly related to rising oxygen levels during land colonization. Statistical analysis of 218 plant species shows that AsA content increases significantly with evolution, in line with heightened light and oxygen stress. This study explains the dynamic evolution of the AsA metabolic network during plant terrestrialization, highlighting how key gene families (e.g. GGP, GalUR, GLOase) undergo functional and structural domain divergence to boost antioxidant capacity and thus facilitate adaptation to terrestrial life. These findings offer a theoretical basis for improving crop stress resistance.

Nitrogen-fixing bacteria establish symbiotic relationships with their host plants via two different entry systems: root hair-mediated (intracellular) entry and intercellular entry. However, the molecular mechanisms underlying the intercellular entry system have received relatively little research attention. In this study, we compared the transcriptomes of the nodules and roots of Myrica rubra, which forms an ancient type of symbiosis with Frankia via intercellular entry. We found that cysteine-rich receptor-like secreted protein 1 (CRRSP1) was highly upregulated in M. rubra nodules. We then investigated the function of MrCRRSP1 in Aeschynomene indica, which establishes symbiosis with Bradyrhizobium sp. ORS285 through an intercellular entry system. The overexpression of MrCRRSP1 and AiCRRSP1 in A. indica enhanced the nodule number and plant growth. Exogenous application of glutathione S-transferase (GST)-tagged MrCRRSP1 and AiCRRSP1 in A. indica promoted rhizobial attachment at cracks in the lateral root base, as well as rhizobial motility and biofilm formation. These results suggest that CRRSP1 promotes nodulation by enhancing rhizobial attachment to lateral root cracks. In addition to providing new insights into the molecular mechanisms underlying nodule formation through intercellular entry, this research enhances our understanding of actinorhizal plant-Frankia symbiosis.

Apomixis, a reproductive mechanism that enables clonal seed production, generates progeny genetically identical to the maternal parent. In plant breeding, sexual reproduction can enhance traits through genetic recombination and hybrid vigor, yet trait segregation significantly raises breeding costs and complexity. Although apomixis occurs naturally across various plant species, it remains notably absent in major crops like rice and maize. Significant progress has been made in identifying the genes that govern this process. Recent breakthroughs in synthetic apomixis provide promising pathways for crop improvement. This review offers a comprehensive analysis of natural apomixis and its genetic regulators, with a focus on recent advances in synthetic apomictic systems. We also explore the current state and potential of apomixis in forage breeding, especially in addressing challenges related to self-incompatibility, polyploidy, and genomic complexity in forage species. Finally, we discuss the challenges in applying apomixis to forage breeding and future directions for this research.

Walnut (Juglans regia L.) is an economically valuable tree species globally, renowned for its nutritious nuts and quality timber. However, walnut breeding is significantly constrained by inherent biological factors, and an efficient and reliable genome-editing system has yet to be established. In this study, we developed an optimized walnut genome-editing platform by systematically selecting superior receptor from 30 walnut cultivars using genotype-dependent direct somatic embryogenesis and regeneration systems. Walnut cultivar HT-14 exhibited the highest embryogenic induction (53.33%) and regeneration efficiency (85.33%), and 35S: RUBY was effectively expressed in somatic embryos of the HT-14 genotype, proving it ideal receptor material for genetic transformation. Additionally, 12 walnut-specific endogenous Pol III promoters (JrU3 and JrU6) were cloned and validated for their ability to significantly enhance CRISPR/Cas9-editing efficiency by targeting the walnut phytoene desaturase gene (JrPDS). Compared to commonly used exogenous promoters (AtU6-26 and BpU6-6), these native promoters, the JrU3-chr3 promoter achieving an editing efficiency of 58.82%, significantly increased mutation efficiencies in walnut. Furthermore, endogenous promoters promoted higher frequencies of homozygous and biallelic mutations and greater mutation diversity. Collectively, this study establishes a robust and efficient genome-editing platform for walnut, providing essential technical support for functional genomics research and accelerating the precision breeding walnut varieties. These findings also offer valuable methodologies and insights into genome-editing applications in other perennial woody plants.

Amorphophallus konjac, as a significant representative of the Araceae family, demonstrates considerable potential for applications in medicine, healthcare, food, industry, and bioenergy due to its rich content of konjac glucomannan (KGM). However, the synthetic pathway of KGM remains largely unclear. Although genomic sequencing has been completed for various representative Araceae plants, including Amorphophallus konjac, a comprehensive data platform for deep analysis and exploration of the functions of these genes is lacking. In the current work, genomic and transcriptomic data from multiple Araceae species were integrated, and a database, AraceaeDB (http://www.araceaedb.com/), was constructed specifically for analyzing and comparing gene functions in Araceae plants. The gene functions in the database were annotated in detail, and their ortholog groups were identified and classified into different functional modules based on their expression patterns across various transcriptomic datasets. Multiple functional genomics analysis tools were developed, including OrthoGroup analysis, BLAST search, co-expression analysis, KEGG/GO enrichment analysis, and the JBrowse visualization tool. Moreover, the database incorporates several medicinally significant bioactive compounds traditionally important in the Araceae family, providing target prediction capabilities for these compounds. Furthermore, the major biosynthetic pathway of KGM has been successfully elucidated through these database resources, and a key gene AkCSL3 has been identified. It has been further confirmed that overexpression of AkCSL3 can significantly increase the content of KGM, suggesting its potential crucial role in the polymerization process of glucomannan in konjac corms.

Hydrogen sulfide (H₂S) is a newly identified gasotransmitter that plays an irreplaceable physiological role in plant growth, development, and environmental responses through persulfidation of cysteine (Cys) residues (RSSH). However, reports on the direct RSSH targets of H₂S in plants remain limited. The flowering regulation mechanisms of Brassica rapa ssp. pekinensis are a significant scientific issue in the crop production industry; however, they remain poorly understood. BraATO2 is an important splicing factor in genetic alternative splicing (AS). Our study demonstrated that H₂S regulated BraATO2 function by persulfidating the Cys residue at position 416. In turn, this influenced the AS patterns of multiple genes in B. rapa, specifically the flowering regulator BraAGL31/MAF2 within the FLOWERING LOCUS C-like (FLC-like) gene family, causing accelerated flowering. This study identified a new direct target of H₂S and uncovered a novel pathway influencing flowering in B. rapa. Furthermore, the study findings provide fresh insights into the development of innovative flowering regulators for plants.

Sacred lotus is widely used in the agricultural, nutraceutical, and pharmaceutical industries. Terpenes are not only crucial components of sacred lotus essential oil, but also serve as signaling molecules involved in plant-environment interactions. However, the biosynthesis of terpenes in sacred lotus has not yet been reported. Thus, gene-directed heterologous mining and combinatorial biosynthesis methods were used in this study to systematically characterize the function of terpene synthase genes in the sacred lotus. As a result, two monoterpene, 11 sesquiterpene, and three diterpene products were synthesized, and a highly efficient γ-eudesmol synthase was discovered. In addition, a mechanistic study revealed that N314 is the key amino acid responsible for the secondary cyclization that produces γ-eudesmol. In vitro assays demonstrated that γ-eudesmol exhibited substantial insecticidal and antimicrobial activities. Furthermore, de novo biosynthesis of γ-eudesmol was achieved in a yeast chassis through a series of metabolic engineering strategies, reaching a titer of 801.66 mg/L in a shake flask, the highest yield reported to date. The present study uncovered the biosynthesis of terpenes in sacred lotus, as well as successfully synthesized the bioactive compound γ-eudesmol by synthetic biology. This comprehensive strategy can be readily adapted for investigation and the production of other valuable plant-derived natural products.

The flower color has drawn extensive attention in rapeseed breeding for its ornamental value. However, the color formation and precise design are still elusive. Here, we successfully introduced betalain biosynthesis pathway into rapeseed and achieved constitutive betalain production by overexpressing RUBY. The varying expression levels of RUBY and the flower colors of the receptor materials jointly determined the final color presentation. When RUBY was expressed in yellow-flowered rapeseed (cultivar R10), the flower color turned into different shades of orange. In white-flowered background (cultivar R2), RUBY created red flowers. However, RUBY overexpression led to dark-red leaves and decreased photosynthesis. To recover normal photosynthesis, we created orange flowers with green leaves using petal-specific XY355 promoter in yellow-flowered R10. We further verified that white flower is dominant to yellow and created green leaves with shining red flowers by crossing orange flower (XY355:RUBY expressed in yellow background) with white flower (R2). Given that the widespread carotenoid, betalain, and anthocyanin can produce the three major colors of yellow, red, and blue, respectively, we provide a promising approach for creating derivative colors in Brassica napus by employing bioengineering approaches to precisely regulate the pigment biosynthesis.

Leaf color is a crucial determinant of photosynthetic efficiency and crop yield, but the molecular mechanisms regulating chloroplast development in tomato remain incompletely understood. Here, we identified a novel tomato mutant, gret1, that exhibits yellow cotyledons and young leaves that gradually turn green upon maturation. The gret1 mutant displays significantly reduced chlorophyll content and defective chloroplast development at early leaf stages, accompanied by changes in expression of genes involved in photosynthesis and chloroplast biogenesis. Genetic analysis revealed that the gret1 phenotype is controlled by a single recessive nuclear gene. Using map-based cloning, we identified SlPPR138, encoding a DYW-type pentatricopeptide repeat (PPR) protein, as the causal gene. A T-to-C point mutation in SlPPR138 causes a Cys-to-Arg substitution, which disrupts its function. Both genetic complementation and CRISPR/Cas9 knockout experiments validated that the gret1 phenotype is caused by the loss of SlPPR138. Mechanistically, we found that SlPPR138 mediates chloroplast RNA editing, particularly affecting the C-to-U editing efficiency of rpoC1, which encodes a core subunit of plastid-encoded RNA polymerase (PEP) complex. These findings demonstrate SlPPR138 is essential for early chloroplast development through RNA editing, providing new insights into the post-transcriptional regulation of photosynthesis in plants.

The mottled rind is an important fruit external appearance trait that influences consumer preferences. Previous studies reported that CmMt1 and CmMt2 regulate rind mottling in melon, yet CmMt2 has not been cloned. In this study, we developed near-isogenic lines (NILs) using the nonmottled rind ‘13C’ as the recurrent parent and mottled ‘P114’ as the donor parent, and screened a mottled rind mutant ‘S249’ by ethyl methanesulfonate mutagenesis of ‘13C’. Combined with these genetic materials, CmMt2 was delimited to a 44-kb region on chromosome 2. Within this genetic interval, a CACTA-type TIR transposon insertion was detected in all nonmottled rind lines, and this insertion may lead to impaired nuclear localization and dimerization capability of CmKNAT2-like2 encoding a homeobox protein through the loss of conserved ELK and Homeodomain. Further, CRISPR/Cas9-mediated knockout of CmKNAT2-like2 confirmed its pivotal role in regulating mottled rind phenotype. In addition, transcriptome analysis suggested that the transposon insertion in CmKNAT2-like2 results in nonmottled rind by disrupting chloroplast development and altering the expression of chlorophyll biosynthesis-related genes, and population analysis revealed that the transposon associated with CmKNAT2-like2 has undergone selection in cultivated melons. Collectively, these results demonstrate that CmKNAT2-like2 is the causal gene underlying CmMt2, which regulates mottled rind in melon.

Panax quinquefolius L., commonly known as American ginseng, is a valuable beneficial medicinal herb renowned for its health-promoting properties and rich phytochemical profile. Despite significant progress in understanding ginsenoside biosynthesis, the genetic basis for flavonoid diversity in American ginseng remains unclear. This study reports the first telomere-to-telomere (T2T) genome assembly for yellow-fruited American ginseng cultivar ‘Zhongnongyangshen No. 2’. The genome assembly, achieved using PacBio HiFi and Oxford Nanopore Technology ultra-long read technologies, offers a high-quality reference for genomic research, addressing previous gaps in structural accuracy. Combining transcriptomic and metabolomic analyses, we investigated flavonoid biosynthesis and the regulatory mechanisms underlying fruit color variation during different developmental stages of American ginseng. Our findings highlight the phylogenetic evolution of the American ginseng genome and offer new insights into the biosynthetic pathways of anthocyanins and flavonols. This comprehensive genomic resource facilitates deeper exploration of flavonoid diversity, supports genetic improvement efforts, and enhances the potential for future applications in medicinal plant research.