Petunia (Petunia hybrida) plants are highly threatened by a diversity of viruses, causing substantial damage to ornamental quality and seed yield. However, the regulatory mechanism of virus resistance in petunia is largely unknown. Here, we revealed that a member of petunia WRKY transcription factors, PhWRKY30, was dramatically up-regulated following Tobacco rattle virus (TRV) infection. Down-regulation of PhWRKY30 through TRV-based virus-induced gene silencing increased green fluorescent protein (GFP)-marked TRV RNA accumulation and exacerbated the symptomatic severity. In comparison with wild-type (WT) plants, PhWRKY30-RNAi transgenic petunia plants exhibited a compromised resistance to TRV infection, whereas an enhanced resistance was observed in PhWRKY30-overexpressing (OE) transgenic plants. PhWRKY30 affected salicylic acid (SA) production and expression of arogenate dehydratase 1 (PhADT1), phenylalanine ammonia-lyase 1 (PhPAL1), PhPAL2b, nonexpressor of pathogenesis-related proteins 1 (PhNPR1), and PhPR1 in SA biosynthesis and signaling pathway. SA treatment restored the reduced TRV resistance to WT levels in PhWRKY30-RNAi plants, and application of SA biosynthesis inhibitor 2-aminoindan-2-phosphonic acid inhibited promoted resistance in PhWRKY30-OE plants. The protein-DNA binding assays showed that PhWRKY30 specifically bound to the promoter of PhPAL2b. RNAi silencing and overexpression of PhPAL2b led to decreased and increased TRV resistance, respectively. The transcription of a number of reactive oxygen species- and RNA silencing-associated genes was changed in PhWRKY30 and PhPAL2b transgenic lines. PhWRKY30 and PhPAL2b were further characterized to be involved in the resistance to Tobacco mosaic virus (TMV) invasion. Our findings demonstrate that PhWRKY30 positively regulates antiviral defense against TRV and TMV infections by modulating SA content.

Satsuma mandarin (Citrus reticulata “Unshiu”) is a global cultivar with superior fruit characteristics and ranking among the top citrus cultivars in terms of production. It is also a key contributor to citrus breeding. However, the lack of high-quality genome makes the origin of Satsuma mandarin has long been a matter of debate. Here, we assembled a gap-free, high-quality genome of Satsuma mandarin. Meanwhile, we collected and sequenced 15 indigenous citrus varieties in Zhejiang Province, 12 Satsuma mandarins, 21 citrus hybrids related to Satsuma mandarin, 10 modern citrus varieties, and 7 other mandarins. Through high-resolution genome analysis, we inferred that Satsuma mandarin originated from a cross between C. reticulata “Ruju” ×  C. reticulata “Bendiguang” and proposed that Satsuma mandarin most probably originated in East area in Zhejiang Province of China, where the two parents-like cultivars are still found in a sympatric region to date. These results provide new insights into the origin model of Satsuma mandarin. The spread of mandarin is also discussed, which probably associated with the culture exchange and trade activities between Japan and China from Tang Dynasty and afterwards.

Cucumber crops face high pressure from pathogens, including various viral species. Mapping quantitative trait loci (QTL) for vegetable resistance to viruses has primarily been conducted after mechanical inoculation in controlled environments, but not in crop field conditions. Moreover, viruses that cannot be mechanically inoculated, e.g. the cucurbit aphid-borne yellows virus (CABYV), have been overlooked in resistance studies. Here, we aimed to identify QTLs reducing epidemics of two prevalent cucumber viruses: CABYV and the cucumber mosaic virus (CMV). We evaluated the resistance of 256 elite cucumber lines and landraces in crop field conditions by screening for the presence of both viruses six-times during the season. We mapped twelve QTLs reducing CABYV epidemics and seven QTLs reducing CMV epidemics by combining multiloci genome-wide association studies and local score approach analyses. We also examined the attractiveness of this cucumber panel for Aphis gossypii, a major cucumber virus vector. We identified five QTLs that reduced the attractiveness, including one co-localizing with a QTL reducing CABYV epidemics. Interestingly, some accessions deemed CMV-resistant after mechanical inoculation in controlled environments showed high infection rates in crop field conditions. Only one QTL for CMV resistance was detected in both conditions, indicating that these phenotypes are regulated by independent QTLs. Local linkage disequilibrium study findings suggested that certain QTLs reducing epidemics were introduced early into elite lines through serendipity or selection. QTLs could be pyramided with other low-effect QTLs through genomic selection to obtain cucumber cultivars with enhanced field resistance to viruses.

Norisoprenoids, which are produced by the cleavage of various carotenoids, are a class of volatile aroma compounds that widely distributed in plants. In wine, they represent a significant source of floral and fruity aromas. β-Damascenone is the most abundant and important norisoprenoid constituent in grape berries (Vitis vinifera L.) and wines. However, the regulatory mechanism of β-damascenone biosynthesis remains poorly understood. The present study has identified a WRKY transcription factor, VviWRKY24, as a key regulator of β-damascenone accumulation in grape berries. The results of overexpression and gene silencing assays in grape leaves, berries, and calli demonstrated that VviWRKY24 altered the flow of norisoprenoid metabolism and influenced the composition ratio of norisoprenoids, particularly enhancing the levels of β-damascenone. The results of the RNA-seq, yeast one-hybrid, electrophoretic mobility shift, and dual-luciferase assays provided confirmation that VviWRKY24 promoted abscisic acid (ABA) biosynthesis by directly upregulating the expression of VviNCED1. The increase in ABA content resulted in further induction of the expression of carotenoid cleavage dioxygenase 4B (VviCCD4b) on β-damascenone metabolic pathway. These findings elucidate the upstream regulation of ABA and the promotion of ABA on the accumulation of β-damascenone in grapes. This study contributes to a novel understanding of the regulatory mechanisms of β-damascenone biosynthesis and provides a strategy for improving the aroma quality of grapes and wine.

Ethylene, a plant hormone, is essential for apple (Malus domestica) ripening. The precise molecular mechanism by which melatonin (MT) influences ethylene biosynthesis during apple fruit ripening remains unclear. This study found that exogenous MT treatment inhibited ethylene production and postponed apple fruit ripening. The endogenous MT content of apple fruits exhibited an inverse correlation with ethylene production during fruit ripening, suggesting that MT functions as a ripening suppressor in apple fruits. MT treatment suppressed the expression of key ethylene biosynthesis genes, MdACS1 and MdACO1, during apple fruit ripening. MT treatment decreased the expression levels of transcription factors MdREM10 and MdZF32. MdREM10 binds to the MdERF3 promoter, enhancing its expression and subsequently promoting MdACS1 transcription. Furthermore, MdREM10 directly bound to the MdZF32 promoter, promoting its transcription. MdZF32 directly bound to the MdACO1 promoter, inducing its expression. The findings suggested that MT suppresses ethylene biosynthesis and fruit ripening by inhibiting MdREM10, which indirectly promotes MdACS1 transcription via MdERF3 upregulation, and MdACO1 transcription via MdZF32 upregulation.

Parthenocarpy can ensure fruit setting without fertilization and generate seedless fruits. PbCYP78A6 has been shown to play a role in gibberellin (GA)-induced parthenocarpy in pears. However, the transcriptional response mechanism of PbCYP78A6 to GA remains unclear. In this study, using a yeast one-hybrid assay combined with co-expression analysis, PbMYB56 was initially identified as a transcription regulator of PbCYP78A6, which was further confirmed by electrophoretic mobility shift assay (EMSA) and dual-luciferase reporter assays. The biofunction of PbMYB56 was further verified using transient transgene tests, stable transgenic pear callus and tomato. PbMYB56 overexpression resulted in reduced cell death and higher fluorescence intensity after fluoresce diacetate (FDA) staining, as well as delayed fruit-drop by increasing PbCYP78A6 expression in unpollinated pear fruitlets and callus. In contrast, silencing PbMYB56 caused cell death and early fruit-drop with decreased PbCYP78A6 expression. Moreover, after emasculation, heterologous overexpression of PbMYB56 induced parthenocarpy and enlarged seed size in pollinated tomato fruits. Silencing SlMYB56, a homolog of PbMYB56 in tomatoes, resulted in smaller fruit and seed size, and these traits were restored by co-overexpression with PbCYP78A6. Furthermore, we investigated the protein interaction between PbMYB56 and PbDELLA, which is crucial component of the GA signaling pathway. This interaction inhibited PbMYB56-induced transcriptional activation of PbCYP78A6. Co-overexpression of PbMYB56 and PbDELLA contributed to reduced seed development and loss of parthenocarpy potential in tomatoes. Collectively, our study identifies PbDELLA-PbMYB56-PbCYP78A6 as a regulatory module of GA_4 + 7-induced pseudo-embryo and parthenocarpy development, offering insights into the mechanism underlying parthenocarpy formation in pears.

Cold damage poses a significant challenge to the cultivation of soft-seeded pomegranate varieties, hindering the growth of the pomegranate industry. The genetic basis of cold tolerance in pomegranates has remained elusive, largely due to the lack of high-quality genome assemblies for cold-tolerant varieties and comprehensive population-scale genomic studies. In this study, we addressed these challenges by assembling a high-quality chromosome-level reference genome for 'Sanbai', a pomegranate variety renowned for its freezing resistance, achieving an impressive contig N50 of 15.93 Mb. This robust assembly, enhanced by long-read sequencing of 38 pomegranate accessions, facilitated the identification of 14 239 polymorphic structural variants, revealing their critical roles in genomic diversity and population differentiation related to cold tolerance. Of particular significance was the discovery of a ~ 5.4-Mb inversion on chromosome 1, which emerged as an important factor affecting cold tolerance in pomegranate. Moreover, through the integration of bulked segregant analysis, differential selection analysis, and genetic transformation techniques, we identified and validated the interaction between the PgNAC12 transcription factor and PgCBF1, disclosing their pivotal roles in response to cold stress. These findings mark a significant advancement in pomegranate genomics, offering novel insights into the genetic mechanisms of cold tolerance and providing valuable resources for the genetic improvement of soft-seeded pomegranate varieties.

The sexual reproduction of triploids induces chromosomal karyotype variations, which are significant for germplasm resource innovation. Most triploid plants are with low fertility. Therefore, triploid offspring karyotypes’ variation pattern and phenotypic response remain poorly understood. Here, we employed three diploids with diverse genetic distances as male parents to cross-pollinate the female fertile triploid loquat Q24 to construct three experimental populations. The chromosome numbers of 93.82% of hybrid plants were 34~46 in three hybrid populations. All 168 aneuploids with 160 karyotypes and a small percentage of euploids were detected among 178 hybrids by the improved molecular karyotype analysis method. Further analysis revealed that when being transmitted to offspring, chromosome 5 of Q24 as disomy had the highest frequency (>50%), while chromosome 12 had the lowest frequency (≤30%). The frequency of Q24’s chromosomes being transmitted to offspring as disomy was influenced by the gene function on the chromosomes and the number of interchromosome collinear gene links. Whole-genome resequencing showed that the Q24 alleles exhibited segregation distortions in the offspring aneuploid population. Transgenic experiments demonstrated that the EjRUN1 gene, which was on one segregation distortion region of Q24, promoted the seed viability of triploid Arabidopsis. Furthermore, chromosome number, dosage, and male parent genotype affected the aneuploid phenotype. These findings advance the understanding of genome genetic characteristics of triploid loquat, and provide a reference for germplasm innovation of loquat rapidly through triploid sexual reproduction.

Plant factories (PFs), also known as vertical farms, are advanced agricultural production systems that operate independently of geographical and environmental conditions. They utilize artificial light and controlled environments to produce horticultural plants year-round. This approach offers a promising solution for the stable and efficient supply of high-quality horticultural produce in urban areas, enhancing resilient urban food systems. This review explores the economic and environmental impacts and potential of PFs. Breakthroughs in PF research and development are highlighted, including increased product yields and quality, reduced energy input and CO₂ emissions through optimized growing conditions and automation systems, transitioning to clean energy, improved resource use efficiency, and reduced food transport distances. Moreover, innovations and applications of PFs have been proposed to address challenges from both economic and environmental perspectives. The proposed development of PF technologies for economic and environmental benefits represents a comprehensive and promising approach to urban horticulture, significantly enhancing the impact and benefits of fundamental research and industrial applications.

Light is essential for rose (Rosa spp.) growth and development. Different light qualities play differing roles in the rose floral transition, but the molecular mechanisms underlying their effects are not fully understood. Here, we observed that red light suppresses rose flowering and increases the expression of sensitivity to red light reduced 1 (RcSRR1) compared with white light. Virus-induced gene silencing (VIGS) of RcSRR1 led to early flowering under white light and especially under red light, suggesting that this gene is a flowering repressor with a predominant function under red light. We determined that RcSRR1 interacts with the COP9 signalosome subunit 5B (RcCSN5B), while RcCSN5B, RcCOP1, and RcCO physically interact with each other. Furthermore, the RcCSN5B-induced deneddylation of Cullin4-RING E3 ubiquitin ligase (RcCRL4) in rose was reduced by the addition of RcSRR1, suggesting that the interaction between RcSRR1 and RcCSN5B relieves the deneddylation of the RcCRL4-COP1/SPA complex to enhance RcCO proteolysis, which subsequently suppresses the transcriptional activation of RcFT and ultimately flowering. Far-red light-related sequence like 1 (RcFRSL3) was shown to specifically bind to the G-box motif of the RcSRR1 promoter to repress its transcription, removing its inhibition of RcFT expression and inducing flowering. Red light inhibited RcFRSL3 expression, thereby promoting the expression of RcSRR1 to inhibit flowering. Taken together, these results provide a previously uncharacterized mechanism by which the RcFRSL3-RcSRR1-RcCSN5B module targets RcCO stability to regulate flowering under different light conditions in rose plants.

Natural antimicrobial compounds (NACs) in the plant stem are crucial for replacing conventional synthetic pesticides in the control of soil-borne diseases, and microbial fermentation can enhance their concentration and bioactivity. In this study, the stems of 10 plant species were collected for fermentation by probiotic bacteria Bacillus amyloliquefaciens T-5 to identify the most effective plant resource for controlling tomato bacterial wilt disease and discover key NACs. Chrysanthemum stem was identified as an optimal fermentation substrate, as its water-soluble extracts (WSEs) significantly inhibited the growth of pathogenic Ralstonia solanacearum and effectively alleviated tomato wilt under greenhouse conditions. Key metabolites, primarily phenolic acids including 2-hydroxy-3-phenylpropanoic acid (PLA), 3-(4-hydroxyphenyl)-propionic acid (HPPA), and mandelic acid (MA), were determined by metabolomics, all of which significantly inhibited the growth of R. solanacearum at a concentration of 0.2 mM, with only HPPA effectively controlling tomato wilt. Thus, fermented chrysanthemum stem contains NACs that are effective against bacterial wilt, providing a green option for controlling soil-borne diseases.

Polyploids are widespread in plants and are important drivers for evolution and biodiversity. Allopolyploidy activates transposable elements (TEs) and causes genomic shock. Plant genomes can regulate gene expression by changing the epigenetic modification of TEs, but the mechanism for TEs to capture genes remains to be explored. Helitron TEs used the ‘peel-and-paste’ mechanism to achieve gene capture. We identified 3156 capture events and 326 donor genes of Helitron TEs in Brassica napus (A_nA_nC_nC_n). The donor genes captured by TEs were related to the number, length, and location of their exons. The gene-capturing TEs carrying donor gene fragments were evenly distributed on the genome, and more than half of them were involved in the construction of pseudogenes, becoming the reserve force for polyploid evolution. Gene fragment copies enhanced information storage, providing opportunities for gene mutation and the formation of new genes. Simultaneously, the siRNAs targeting TEs may act on the donor genes due to siRNA crosstalk, and the gene methylation levels increased and the expression levels decreased. The genome sought a balance between sacrificing donor gene expression and silencing TEs, allowing TEs to hide in the genome. In addition, epigenetic modifications may temporarily relax the control of gene capture during allopolyploidization. Our study identified and characterized gene capture events in B. napus, analyzed the effects of DNA methylation and siRNA on gene capture events, and explored the regulation mechanism of gene expression by TE epigenetic modification during allopolyploidization, which will contribute to understanding the formation and evolution mechanism of allopolyploidy.

The spatiotemporal transcriptome dataset reported here provides the peach flower bud’s gene expression atlas at spatiotemporal resolution level using the 10x Genomics Visium platform. This dataset can be used to define transcript accumulation for any interesting genes across several flower bud cells. It was generated using three peach flower bud samples during the activity-dormancy period, providing valuable insight into gene expression profiling and developmental stages under different environmental contexts or conditions. Importantly, we found that different cell types are related to specific regulatory programs, including signal transduction, environment and stress responses, and flower development. Our research provides insight into the transcriptomic landscape of the key cell types for flower buds and opens new avenues to study cell-type specification, function, and differentiation in Rosaceae fruit trees. A series of pivotal genes (e.g. AMS, MS188, MS1) for flower bud development were identified. These results provide a valuable reference for the activity-dormancy transition in perennial deciduous fruit trees.

Platycodon grandiflorus has been widely used in Asia as a medicinal herb and food because of its anti-inflammatory and hepatoprotective properties. P. grandiflorus has important clinical value because of the active triterpenoid saponins in its roots. However, the biosynthetic pathway of triterpenoid saponins in P. grandiflorus remains unclear, and the related genes remain unknown. Therefore, in this study, we assembled a high-quality and integrated telomere-to-telomere P. grandiflorus reference genome and combined time-specific transcriptome and metabolome profiling to identify the cytochrome P450s (CYPs) responsible for the hydroxylation processes involved in triterpenoid saponin biosynthesis. Nine chromosomes were assembled without gaps or mismatches, and nine centromeres and 18 telomere regions were identified. This genome eliminated redundant sequences from previous genome versions and incorporated structural variation information. Comparative analysis of the P. grandiflorus genome revealed that P. grandiflorus underwent a core eudicot γ-WGT event. We screened 211 CYPs and found that tandem and proximal duplications may be crucial for the expansion of CYP families. We outlined the proposed hydroxylation steps, likely catalyzed by the CYP716A/72A/749A families, in platycodin biosynthesis and identified three PgCYP716A, seven PgCYP72A, and seven PgCYP749A genes that showed a positive correlation with platycodin biosynthesis. By establishing a T2T assembly genome, transcriptome, and metabolome resource for P. grandiflorus, we provide a foundation for the complete elucidation of the platycodins biosynthetic pathway, which consequently leads to heterologous bioproduction, and serves as a fundamental genetic resource for molecular-assisted breeding and genetic improvement of P. grandiflorus.

Volatile compounds serve physiological, signaling, and defensive purposes in plants and have beneficial effects on the growth, reproduction, resistance, and yield of horticultural plants. They are released through fragrance glands and become gasses by passing through the plasma membrane, cell walls that contain water, and cuticle. Transporter proteins facilitate their transport and reduce the resistance of these barriers. They also regulate the rate of release and concentration of volatiles inside and outside of the membrane. However, there has been no summary of the structure and function of the fragrance glands of horticultural plants, as well as an introduction to the latest research progress on the mechanism of the transport of volatiles. This review focuses on the structure and function of the release of aromas in horticultural plants and explores the mechanism of the release of volatiles through a transporter model. Additionally, it considers the factors that affect their release and ecological functions and suggests directions for future research.

Plant trichomes serve as a protective barrier against various stresses. Although the molecular mechanisms governing the initiation of trichomes have been extensively studied, the regulatory pathways underlying the trichome branching in tomato remain elusive. Here, we found that Woolly (Wo) mutant and its overexpression transgenic plants displayed branched type I trichomes. The expression level of SlTCP25, a transcription factor of type TB1 of the TCP subfamily, was obviously decreased in Wo mutant and Wo overexpressing lines. Knockout of SlTCP25 resulted in the formation of type I trichome branches on the hypocotyls. Genetic evidence showed that SlTCP25 is epistatic to Wo in the branched trichome formation. Biochemical data further indicated that Wo can directly bind to the L1-box cis-element in the SlTCP25 promoter and repress its transcription. We further determined that SlTCP25 interacts with Wo to weaken Wo-regulated the expression of SlCycB2, a trichome branching inhibitor. In addition, the number of trichome branches was significantly increased in Sltcp25Slcycb2 double mutant, suggesting that SlTCP25 and SlCycB2 coordinately repress trichome branching in wild type. In conclusion, we elucidate a molecular network governing the morphogenesis of multicellular trichomes in tomato.

Over the past decade, genome sequencing and assembly approaches have been greatly improved, resulting in the assembly of many genomes for citrus, including wild, domesticated, and citrus-related genomes. Improvements in technologies have led to assembled genomes with higher completeness, contiguity, quality, and accuracy that have greatly facilitated annotation and analysis. This review summarizes the evolution of the sequencing, assembly, and annotation technologies leading to citrus genomes over the past 11 years, a comprehensive evaluation of their quality, contiguity, and completeness, and the major findings and applications. Of the 50 genomes now available, 35 have been assembled to chromosome level and 15 to draft level, and 14 were haplotype-resolved assemblies. To date there have been four pangenome-wide studies for citrus. The very recent genomes assembled with long-read sequencing have achieved >99% and >98% assembly and annotation completeness (BUSCO), respectively. However, some early genomes are not of the same high quality as more recently sequenced genomes and would benefit from re-sequencing. A more comprehensive pangenome based upon a larger set of species and genotypes assembled at the haplotype level would allow genomics to deliver the maximum benefits for citrus improvement and research.

Monoterpenoids are small volatile molecules produced by many plants that have applications in consumer products and healthcare. Plants from the mint family (Lamiaceae) are prodigious producers of monoterpenoids, including a chemotype of Agastache rugosa (Huo Xiang), which produces pulegone and isomenthone. We sequenced, assembled and annotated a haplotype-resolved chromosome-scale genome assembly of A. rugosa with a monoterpene chemotype. This genome assembly revealed that pulegone biosynthesis genes are in a biosynthetic gene cluster, which shares a common origin with the pulegone gene cluster in Schizonepeta tenuifolia. Using phylogenetics and synteny analysis, we describe how the clusters in these two species diverged through inversions and duplications. Using Hi-C analysis, we identified tentative evidence of contact between the pulegone gene cluster and an array of pulegone reductases, with both regions also enriched in retrotransposons. This genome and its analysis add valuable and novel insights to the organization and evolution of terpenoid biosynthesis in Lamiaceae.

Sour cherry (Prunus cerasus L.) is an economically significant species in the Rosaceae family. Hitherto, there had been limited genetic and genomic resources to elucidate important horticultural traits in this species mainly because of the complex polyploid nature of its genome, a hybrid between Prunus avium and Prunus fruticosa. An important trait that has not been well studied in sour cherry is resistance to cherry leaf spot (CLS), caused by the fungus Blumeriella jaapii. This work took advantage of the RosBREED 6 + 9 K SNP array to study the genetic basis of CLS resistance and inheritance in sour cherry. We established an F₁ segregating population by crossing two cultivars, ‘Schattenmorelle’ and ‘Pc 2’ and genotyped both parents and the progeny with the cherry 6 + 9 K SNP array and SSR markers. We evaluated both parents and progeny for resistance and susceptibility to CLS under field conditions. The applied marker systems facilitated the development of parental genetic maps, and the identification of two stable QTLs associated with CLS resistance, CLSR_1f in ‘Pc 2’ and susceptibility, CLSS_1f, in ‘Schattenmorelle’ explaining 40.9% and 21.5%, respectively, of the phenotypic variation within the population. The mechanism of resistance in sour cherry appears to be independent of the CLS resistance QTL, CLSR_G4, previously identified in P. canescens, as the CLSR_G4-QTL and associated allele were not identified. Based on our findings, we propose a two-gene model for CLS resistance in sour cherry involving a susceptibility QTL, which might explain why some CLSR_G4-resistant plants in previous studies were susceptible.

The China National GeneBank Sequence Archive (CNSA) is an open and freely accessible curated data repository built for archiving, sharing, and reutilizing of multiomics data. The remarkable advancement in sequencing technologies has triggered a paradigm shift in life science research. However, it also poses tremendous challenges for the research community in data management and reusability. With the dramatic advance of sequencing technologies like spatial transcriptome sequencing, it brings an unprecedented explosion in sequence data and new requirements for data archiving. CNSA was established in 2017 as one of the fundamental infrastructures to offer multiomics data archiving for the worldwide research community. Here, we present the state-of-the-art enhancements of CNSA encompassing the dramatical increase of varied types of data, the latest features and services implemented in CNSA as well as consistent efforts supporting global cooperation in biodiversity preservation and utilization. CNSA provides public archiving and open-sharing services for sequencing data and relevant metadata including genome, transcriptome, metabolism, and proteome from single-cell (also spatial resolved) level to individual and population level, as well as further analyzed results. As of 2024, CNSA has archived >16.3 petabytes of data and provided the data curation, preservation, and open-share service for >1581 publications from >560 institutions. It plays a pivotal role in supporting global scientific projects such as the 10 000 Plant Genomes Project. So far, CNSA has been recommended by various academic publishers such as Cell, Elsevier, and Oxford University Press. CNSA is accessible at https://db.cngb.org/cnsa/.

Centella asiatica is renowned for its medicinal properties, particularly due to its triterpenoid saponins, such as asiaticoside and madecassoside, which are in excess demand for the cosmetic industry. However, comprehensive genomic resources for this species are lacking, which impedes the understanding of its biosynthetic pathways. Here, we report a telomere-to-telomere (T2T) C. asiatica genome. The genome size is 438.12 Mb with a contig N50 length of 54.12 Mb. The genome comprises 258.87 Mb of repetitive sequences and 25 200 protein-coding genes. Comparative genomic analyses revealed C. asiatica as an early-diverging genus within the Apiaceae family with a single whole-genome duplication (WGD, Apiaceae-ω) event following the ancient γ-triplication, contrasting with Apiaceae species that exhibit two WGD events (Apiaceae-α and Apiaceae-ω). We further constructed 3D chromatin structures, A/B compartments, and topologically associated domains (TADs) in C. asiatica leaves, elucidating the influence of chromatin organization on expression WGD-derived genes. Additionally, gene family and functional characterization analysis highlight the key role of CasiOSC03 in α-amyrin production while also revealing significant expansion and high expression of CYP716, CYP714, and UGT73 families involved in asiaticoside biosynthesis compared to other Apiaceae species. Notably, a unique and large UGT73 gene cluster, located within the same TAD, is potentially pivotal for enhancing triterpenoid saponin. Weighted gene coexpression network analysis (WGCNA) further highlighted the pathways modulated in response to methyl jasmonate (MeJA), offering insights into the regulatory networks governing saponin biosynthesis. This work not only provides a valuable genomic resource for C. asiatica but also sheds light on the molecular mechanisms driving the biosynthesis of pharmacologically important metabolites.

Genetic breeding and molecular identification in varieties depend on high-performance genotyping tools. The high heterozygosity of the litchi genome contributes to increased resequencing costs and elevated error rates in hybridization-based genotyping methods. In this study, a liquid chip named Litchi40K v1.0 was developed with high-depth resequencing data from 875 litchi samples, and its efficacy was validated across three different populations. In the L. chinensis var. fulvosus population, three subpopulations characterized by spatial distribution, and a total of 1110 genes were identified in the genomic regions with subpopulation differentiation. Additionally, a total of 30 significant signals associated with diverse agronomic traits were identified. The H002 haplotype of LITCHI02696, dominant in the Sub2 subgroup, significantly increased the soluble solid content in the L. chinensis var. fulvosus population. In a hybrid F₁ population, a high-density genetic map was constructed and 79 dwarfing-related QTLs were identified with the liquid chip. An NAC transcription factor was identified as a candidate gene with a heterozygous frameshift variant in the male parent. To facilitate the digitization of germplasm resources, 384 SNPs were selected, and the DNA fingerprint map revealed clear genetic relationships and a total of 10 potential synonym groups or instances of bud mutations were identified in 164 main cultivated litchi varieties. This study provides cost-effective, flexible, and versatile liquid chip for genetic analysis and digitalization of germplasm resources in litchi.

Epiphyllum oxypetalum, a renowned ornamental species in Cactaceae, releases attractive fragrance during its infrequent, transient, and nocturnal blooms. However, the floral fragrance composition and biosynthesis remain largely unexplored. Employing volatilomics, transcriptomics, and biochemistry, we systematically characterized the composition, emission dynamics, and biosynthesis of the floral scent of E. oxypetalum. The floral scent composition of E. oxypetalum was highly dynamic. Starting after 8 p.m. local time, volatile emission increased 200-fold within 6 h. At full bloom, geraniol accounted for 72.54% of the total emission, followed by benzyl alcohol (12.96%) and methyl salicylate (3.75%). These scents predominantly originated from petals and sepals. Transcriptomic analysis and inhibition assays using pathway-specific inhibitors revealed that the mevalonate pathway was the precursor source for geraniol biosynthesis. Functionally characterized cytosol-localized geraniol synthase EoTPSa1 was the key enzyme responsible for geraniol biosynthesis. Together, these findings pinpoint a cytosolic biosynthetic route for the major scent volatile geraniol in E. oxypetalum. Our study provides new insights into the emission dynamics and biosynthesis of E. oxypetalum floral scents. In particular, we demonstrate a distinctive mevalonate pathway-based geraniol biosynthetic pathway, which may hold potential for the development of novel perfume products.

The shikimate pathway is crucial for the production of aromatic amino acids and various secondary plant products, including anthocyanins. Phosphoenolpyruvate (PEP) is an important source for shikimate production. The pre-chorismate part of the shikimate pathway is confined to plastids. There are three sources of PEP in plastids. PEP can be imported into the plastids from cytoplasm via the PEP/phosphate translocator (PPT), and it can also be generated in plastids via enolase (ENO) and pyruvate orthophosphate dikinase (PPDK) catalysis. A large number of anthocyanins are synthesized in the flowers of most ornamental plants in the coloring stage. However, the source of PEP, the precursor of anthocyanin synthesis, is still unknown. Herein, Petunia hybrida PhENO1, PhPPT and PhPPDK genes were identified and their expression patterns and subcellular localization of encoded proteins were analyzed. Silencing of PhENO1, PhPPT, and PhPPDK alone and co-silencing of PhENO1 and PhPPDK or PhPPT and PhPPDK did not exhibit any visible phenotypic change compared with the control, while co-silencing of PhENO1 and PhPPT resulted in the flower color change from purple to light purple. The content of PEP, shikimate, flavonoids, anthocyanins, and aromatic amino acids were all significantly decreased in PhENO1 and PhPPT co-silenced plants. Co-silencing of PhENO1 and PhPPT did not affect the expression level of key genes in anthocyanin synthesis and shikimate pathways. Furthermore, co-silencing of PhENO1, PhPPT, and PhPPDK resulted in a phenotype similar to the co-silencing of PhENO1 and PhPPT. Altogether, our study suggested that PEP used for anthocyanin synthesis is mainly provided by PhENO1 and PhPPT, rather than PhPPDK.

Blueberry is promoted as a super food with several health properties derived from chlorogenic acid and anthocyanin. Previous studies indicated that anthocyanin acylation and the content of chlorogenic acid could affect their level of absorption and biological activity. In this study, a genome-wide association study was performed to identify loci associated with anthocyanin and chlorogenic acid and characterize the candidate genes controlling anthocyanin acylation. Two stable loci controlling anthocyanin acylation and glucose specific glycosylation were confirmed on chromosomes 2 and 4, respectively, while no stable loci associated with chlorogenic acid were identified. Two acyl-CoA acyltransferases named VcBAHD-AT1 and VcBAHD-AT4 were identified as best candidate genes controlling anthocyanin acylation. Interestingly, the two genes clustered in acyl-CoA acyltransferases clade III, a clade that is not commonly associated with anthocyanin acylation. A virus-induced gene silencing approach optimized for silencing VcBAHD-AT1 and VcBAHD-AT4 in the whole blueberry fruits, confirmed the role of these two genes in anthocyanin acylation. Overall, this study establishes the foundation to develop a molecular marker to select for higher acylated anthocyanin and delivered a method for rapid functional characterization of genes associated with other fruit related traits in blueberry. Also, the study adds evidence that during the evolution of acyl-CoA acyltransferases multiple routes led to the emergence and/or fixation of the anthocyanin acyltransferase activity. These outcomes advance knowledge about the genes controlling anthocyanin acylation in blueberries and that extend to other plants. Selecting new blueberry cultivars with higher acylated anthocyanin levels could potentially increase absorption of this health-related bioactive.

Highbush blueberry (Vaccinium corymbosum) is an economically important fruit-bearing woody perennial. Despite the importance of microbial communities to plant health, the aboveground (phyllosphere) microbiome of blueberry is understudied. The phyllosphere is exposed to varying conditions throughout a growing season. The fruit undergoes extensive physiological change across a season from bud to fruit. This study aimed to provide a temporal characterization of the blueberry phyllosphere across a growing season and a characterization of specific tissues and phenological stages. Blueberry branches were harvested every other week across 2 years and two locations during the development process of the blueberry fruits. The internal transcribed spacer regions were amplified from DNA extracts and sequenced to perform amplicon-based characterization of the fungal microbiome across time and plant tissue. Fungal communities showed changes in α-diversity depending on the week of harvest and tissue type. Early in the season, α-diversity was high, but it decreased in midseason when flowers developed into fruit. Later in the season, as the fruit ripened, α-diversity increased again. The β-diversity of the community changed across time and tissue types during plant development. Notable members of the identified core microbiome were members of the genus Alternaria, Peltaster, and Taphrina, as well as the pathogenic taxa Aureobasidium pullulans and Botrytis cinerea. This research provides background for future experimentation of understanding the microbial composition in the blueberry phyllosphere in relation to the infection court of pathogens (e.g. Colletotrichum fioriniae and B. cinerea) and the temporal components of blueberry plant health and management.

Bud dormancy, which serves as a survival mechanism during winter, is crucial for determining the timing and quality of flowering in many perennial woody plants, including tree peony. The gibberellin (GA) signaling pathway participates in breaking bud dormancy in tree peony. Specifically, PsRGL1, a key DELLA protein, is a negative regulator in this process. MADS-box family members participate in plant growth and development regulation. In this study, a MADS-domain transcription factor, AGAMOUS-LIKE 9 (PsAGL9), was identified as a candidate interaction protein of PsRGL1 using a pull-down assay coupled with liquid chromatography-tandem mass spectrometry. PsAGL9 expression was induced by chilling and exogenous GA₃. Yeast two-hybrid (Y2H), pull-down, and luciferase complementation assays (LCAs) confirmed that PsAGL9 interacted with PsRGL1. PsAGL9 overexpression significantly promoted dormancy break and upregulated the expression of marker genes such as PsBG6, PsBG9, PsEBB1, PsEBB3, and PsCYCD, suggesting a potential regulatory function of PsAGL9. Classical and nonclassical CArG motifs were identified in the promoter regions of PsCYCD and PsEBB3, respectively. Yeast one-hybrid (Y1H), electrophoretic mobility shift (EMSA), and dual-luciferase assays confirmed that PsAGL9 directly bound to and activated PsCYCD and PsEBB3 expression, and PsRGL1 abolished the DNA-binding activity of PsAGL9. Furthermore, interaction proteins of PsAGL9 were screened, and MADS-box members PsAGL9, PsAGL6, and PsPI were identified. Y2H, LCA, and pull-down assays confirmed that PsAGL9 formed both homodimers and heterodimers, and heterodimers further promoted target gene expression. This study provides an in-depth exploration of the GA pathway and elucidates a novel pathway, PsRGL1-PsAGL9-PsCYCD, involved in regulating dormancy break in tree peony.

Bananas (Musa spp.) are among the top-produced food crops, serving as a primary source of food for millions of people. Cultivated bananas originated primarily from the wild diploid species Musa acuminata (A genome) and Musa balbisiana (B genome) through intra- and interspecific hybridization and selections via somatic variation. Following the publication of complete A- and B-genome sequences, prospects for complementary studies on S- and T-genome traits, key gene identification for yield, ripening, quality, and stress resistance, and advances in molecular breeding have significantly expanded. In this review, latest research progress on banana A, B, S, and T genomes is briefly summarized, highlighting key advances in banana cytoplasmic inheritance, flower and fruit development, sterility, and parthenocarpy, postharvest ripening and quality regulation, and biotic and abiotic stress resistance associated with desirable economic traits. We provide updates on transgenic, gene editing, and molecular breeding. We also explore future directions for banana breeding and genetic improvement.

Papaya (Carica papaya L.) is an important tropical and subtropical fruit crop, and understanding its genome is essential for breeding. In this study, we assembled a high-quality genome of 344.17 Mb for the newly cultivated papaya ‘Zihui’, which contains 22 250 protein-coding genes. By integrating 201 resequenced papaya genomes, we identified four distinct papaya groups and a 34 Mb genomic region with strong domestication selection signals. Within these regions, two key genes associated with papaya yield were discovered: Cp_zihui06549, encoding a leucine-rich receptor-like protein kinase, and Cp_zihui06768, encoding the accumulation of photosystem one 1 (APO1) protein. Heterologous expression of Cp_zihui06549 in tomato confirmed that the total number of fruits in transgenic lines more than doubled compared to wild-type plants, resulting in a significant yield increase. Furthermore, we constructed a pan-genome of papaya and obtained a 77.41 Mb nonreference sequence containing 1543 genes. Within this pan-genome, 2483 variable genes, we detected, including four genes annotated as the ‘terpene synthase activity’ Gene Ontology term, which were lost in cultivars during domestication. Finally, gene retention analyses were performed using gene presence and absence variation data and differentially expressed genes across various tissues and organs. This study provides valuable insights into the genes and loci associated with phenotypes and domestication processes, laying a solid foundation for future papaya breeding efforts.

Lobed leaves are advantageous for gas exchange, canopy architecture, and high-density planting; however, the genetic mechanisms of leaf lobe formation in Brassica crops remains poorly understood. Here, lob10.1, our previously identified major QTL controlling the presence/absence of leaf lobes in B. rapa (AA), was fine mapped to a confidence interval of 69.8 kb. REDUCED COMPLEXITY ORGAN (BrRCO, BraA10g032440.3c), a homeodomain leucine zipper class I (HD ZIP I) transcription factor, was predicted to be the most likely candidate gene underlying lob10.1. Null mutations of BrRCO by CRISPR/Cas9 in the lobed-leaf parent RcBr and over-expression in the counter-part near isogenic lines (NIL^RcBr) lead to entire and lobed leaves, respectively. Analysis of the gene evolution revealed that A10. RCO functions as a core gene and was generally negatively selected in B. rapa. Moreover, BrRCO function as a negative regulator by directly binding to promoters of BrACP5 and repressing its expression. The function of ACID PHOSPHATASE TYPE 5 (BrACP5) was subsequently confirmed as VIGS-BrACP5 produced entire leaves in RcBr. This study identified the core gene BrRCO to be involved in the development of leaf lobes in B. rapa and elucidated a new pathway for leaf lobe formation by the BrRCO-BrACP5 module. These findings provide a theoretical basis for the formation of leaf lobes in Brassica crops.