Solanum commersonii (2 n = 2 x = 24, 1EBN, Endosperm Balance Number), native to the southern regions of Brazil, Uruguay, and northeastern Argentina, is the first wild potato germplasm collected by botanists and exhibits a remarkable array of traits related to disease resistance and stress tolerance. In this study, we present a high-quality haplotype-resolved genome of S. commersonii. The two identified haplotypes demonstrate chromosome sizes of 706.48 and 711.55 Mb, respectively, with corresponding chromosome anchoring rates of 94.2 and 96.9%. Additionally, the contig N50 lengths are documented at 50.87 and 45.16 Mb. The gene annotation outcomes indicate that the haplotypes encompasses a gene count of 39 799 and 40 078, respectively. The genome contiguity, completeness, and accuracy assessments collectively indicate that the current assembly has produced a high-quality genome of S. commersonii. Evolutionary analysis revealed significant positive selection acting on certain disease resistance genes, stress response genes, and environmentally adaptive genes during the evolutionary process of S. commersonii. These genes may be related to the formation of diverse and superior germplasm resources in the wild potato species S. commersonii. Furthermore, we utilized a hybrid population of S. commersonii and S. verrucosum to conduct the mapping of potato freezing tolerance genes. By combining BSA-seq analysis with traditional QTL mapping, we successfully mapped the potato freezing tolerance genes to a specific region on Chr07, spanning 1.25 Mb, with a phenotypic contribution rate of 18.81%. In short, current research provides a haplotype-resolved reference genome of the diploid wild potato species S. commersonii and establishes a foundation for further cloning and unraveling the mechanisms underlying cold tolerance in potatoes.

Grapevine ( Vitis vinifera L.,) is among the world’s leading fruit crops. The production of grapes is severely affected by many diseases including gray mold, caused by the necrotrophic fungus Botrytis cinerea. Although all Vitis species can be hosts for B. cinerea, V. vinifera are particularly susceptible. Accordingly, this disease poses a significant threat to the grape industry and causes substantial economic losses. Development of resistant V. vinifera cultivars has progressed from incidental selection by farmers, to targeted selection through the use of statistics and experimental design, to the employment of genetic and genomic data. Emerging technologies such as marker-assisted selection and genetic engineering have facilitated the development of cultivars that possess resistance to B. cinerea. A promising method involves using the CRISPR/Cas9 system to induce targeted mutagenesis and develop genetically modified non-transgenic crops. Hence, scientists are now engaged in the active pursuit of identifying genes associated with susceptibility and resistance. This review focuses on the known mechanisms of interaction between the B. cinerea pathogen and its grapevine host. It also explores innate immune systems that have evolved in V. vinifera, with the objective of facilitating the rapid development of resistant grapevine cultivars.

Fruit set is a key stage in determining yield potential and guaranteeing quality formation and regulation. N-(2-chloro-4-pyridyl)-N′-phenylurea (CPPU) has been widely applied in grape production, the most iconic of which is the promotion of grape fruit set. However, current studies still lack the molecular mechanism of CPPU-induced grape fruit set. Here, the dynamic, high-resolution stage-specific transcriptome profiles were generated based on two different treatments and five developmental periods during fruit set in ‘Kyoho’ grape (Vitis vinifera L. × V. labrusca L.). Pairwise comparison and functional category analysis showed that phytohormone action cytokinin was significantly enriched during the CPPU-induced grape fruit set, but not the natural one. Value differentially expressed gene (VDEG) was a newly proposed analysis strategy for mining genes related to the grape fruit set. Notably, the cytokinin metabolic process was significantly enriched among up-regulated VDEGs. Of importance, a key VDEG VlCKX4 related to the cytokinin metabolic process was identified as related to the grape fruit set. Overexpression of VlCKX4 gene promoted the Arabidopsis plants that produce more and heavier siliques. The transcription factor VlMYB59 directly bound to the promoter of VlCKX4 and activated its expression. Moreover, overexpression of VlMYB59 gene also promoted the Arabidopsis fruit set. Overall, VlMYB59 responded to CPPU treatment and directly activated the expression of VlCKX4, thus promoting the fruit set. A regulatory pathway of the VlMYB59-VlCKX4 module in the fruit set was uncovered, which provides important insights into the molecular mechanisms of the fruit set and good genetic resources for high fruit set rate breeding.

Nitric oxide (NO) is a redox-dependent signaling molecule that plays a crucial role in regulating a wide range of biological processes in plants. It functions by post-translationally modifying proteins, primarily through S-nitrosation. Thioredoxin (Trx), a small and ubiquitous protein with multifunctional properties, plays a pivotal role in the antioxidant defense system. However, the regulatory mechanism governing the response of tomato Trxh (SlTrxh) to excessive nitrate stress remains unknown. In this study, overexpression or silencing of SlTrxh in tomato led to increased or decreased nitrate stress tolerance, respectively. The overexpression of SlTrxh resulted in a reduction in levels of reactive oxygen species (ROS) and an increase in S-nitrosothiol (SNO) contents; conversely, silencing SlTrxh exhibited the opposite trend. The level of S-nitrosated SlTrxh was increased and decreased in SlTrxh overexpression and RNAi plants after nitrate treatment, respectively. SlTrxh was found to be susceptible to S-nitrosation both in vivo and in vitro, with Cysteine 54 potentially being the key site for S-nitrosation. Protein interaction assays revealed that SlTrxh physically interacts with SlGrx9, and this interaction is strengthened by S-nitrosation. Moreover, a combination of yeast one-hybrid (Y1H), electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR), and transient expression assays confirmed the direct binding of SlMYB86 to the SlTrxh promoter, thereby enhancing its expression. SlMYB86 is located in the nucleus and SlMYB86 overexpressed and knockout tomato lines showed enhanced and decreased nitrate stress tolerance, respectively. Our findings indicate that SlTrxh functions downstream of SlMYB86 and highlight the potential significance of S-nitrosation of SlTrxh in modulating its function under nitrate stress.

Forsythia suspensa, commonly known as weeping forsythia, holds significance in traditional medicine and horticulture. Despite its ecological and cultural importance, the existing reference genome presents challenges with duplications and gaps, hindering in-depth genomic analyses. Here, we present a Telomere-to-Telomere (T2T) assembly of the F. suspensa genome, integrating Oxford Nanopore Technologies (ONT) ultra-long, Hi-C datasets, and high-fidelity (HiFi) sequencing data. The T2T reference genome (Fsus-CHAU) consists of 14 chromosomes, totaling 688.79 Mb, and encompasses 33 932 predicted protein-coding genes. Additionally, we characterize functional centromeres in the F. suspensa genome by developing a specific CENH3 antibody. We demonstrate that centromeric regions in F. suspensa exhibit a diverse array of satellites, showcasing distinctive types with unconventional lengths across various chromosomes. This discovery offers implications for the adaptability of CENH3 and the potential influence on centromere dynamics. Furthermore, after assessing the insertion time of full-length LTRs within centromeric regions, we found that they are older compared to those across the entire genome, contrasting with observations in other species where centromeric retrotransposons are typically young. We hypothesize that asexual reproduction may impact retrotransposon dynamics, influencing centromere evolution. In conclusion, our T2T assembly of the F. suspensa genome, accompanied by detailed genomic annotations and centromere analysis, significantly enhances F. suspensa potential as a subject of study in fields ranging from ecology and horticulture to traditional medicine.

The soil-borne bacterial pathogen Ralstonia solanacearum causes significant losses in Solanaceae crop production worldwide, including tomato, potato, and eggplant. To efficiently prevent outbreaks, it is essential to understand the complex interactions between pathogens and the microbiome. One promising mechanism for enhancing microbiome functionality is siderophore-mediated competition, which is shaped by the low iron availability in the rhizosphere. This study explores the critical role of iron competition in determining microbiome functionality and its potential for designing high-performance microbiome engineering strategies. We investigated the impact of siderophore-mediated interactions on the efficacy of Pseudomonas spp. consortia in suppressing R. solanacearum, both in vitro and in vivo. Our findings show that siderophore production significantly enhances the inhibitory effects of Pseudomonas strains on pathogen growth, while other metabolites are less effective under iron-limited conditions. Moreover, siderophores play a crucial role in shaping interactions within the consortia, ultimately determining the level of protection against bacterial wilt disease. This study highlights the key role of siderophores in mediating consortium interactions and their impact on tomato health. Our results also emphasize the limited efficacy of other secondary metabolites in iron-limited environments, underscoring the importance of siderophore-mediated competition in maintaining tomato health and suppressing disease.

Agrobacterium-mediated transformation remains a cornerstone of plant biology, fueling advancements in molecular genetics, new genomic techniques (NGTs), and the biotech industry. However, recalcitrant crops and technical hurdles persist as bottlenecks. The goal was to develop super-infective ternary vector systems that integrate a novel salicylic acid-degrading enzyme, GABA, and ethylene-degrading enzymes, targeting the transformation of crops by neutralizing plant defense system on Agrobacterium. Firstly, both the effect and activity of introducing enzymes were validated in EHA105, an important Agrobacterium strain. Our study demonstrates that all ternary vector (Tv) system variants significantly enhance reporter expression in transient assays with Nicotiana benthamiana and Cannabis sativa. Specifically, incorporating a constitutive virG mutation with novel enzyme combinations increased GFP and RUBY expression in C. sativa by > 5-fold and 13-fold, respectively. The Tv system, combined with a geminivirus replicon, markedly boosted GUS gene expression in tomato, enhancing genome editing efficiency. Notably, compared to controls, Tv-VS demonstrated up to 18-fold and 4.5-fold increases in genome editing efficiency in C. sativa and tomato, respectively. Additionally, stable transformation rates in tomato and Arabidopsis improved significantly, with Tv-VS showing a remarkable 2.5-fold increase in transformation efficiency compared to control strains. The research marks notable progress in Agrobacterium-mediated plant transformation. The innovative ternary vectors overcome plant defense mechanisms, enabling genetic manipulation in previously challenging plant species. This development is anticipated to broaden the applications of plant genetic engineering, contributing to advancements in crop genome editing.

Nuclear-mitochondrial communication is crucial for plant growth, particularly in the context of cytoplasmic male sterility (CMS) repair mechanisms linked to mitochondrial genome mutations. The restorer of fertility-like ( RFL ) genes, known for their role in CMS restoration, remain largely unexplored in plant development. In this study, we focused on the evolutionary relationship of RFL family genes in poplar specifically within the dioecious Salicaceae plants. PtoRFL30 was identified to be preferentially expressed in stem vasculature, suggesting a distinct correlation with vascular cambium development. Transgenic poplar plants overexpressing PtoRFL30 exhibited a profound inhibition of vascular cambial activity and xylem development. Conversely, RNA interference-mediated knockdown of PtoRFL30 led to increased wood formation. Importantly, we revealed that PtoRFL30 plays a crucial role in maintaining mitochondrial functional homeostasis. Treatment with mitochondrial activity inhibitors delayed wood development in PtoRFL30 -RNAi transgenic plants. Further investigations unveiled significant variations in auxin accumulation levels within vascular tissues of PtoRFL30- transgenic plants. Wood development anomalies resulting from PtoRFL30 overexpression and knockdown were rectified by NAA and NPA treatments, respectively. Our findings underscore the essential role of the PtoRFL30-mediated mitochondrion-auxin signaling module in wood formation, shedding light on the intricate nucleus-organelle communication during secondary vascular development.

Prunus mume (mei), a traditional ornamental plant in China, is renowned for its fragrant flowers, primarily emitted by its petals. However, the cell types of mei petals and where floral volatile synthesis occurs are rarely reported. The study used single-cell RNA sequencing to characterize the gene expression landscape in petals of P. mume ‘Fenhong Zhusha’ at budding stage (BS) and full-blooming stage (FS). Six major cell types of petals were identified: epidermal cells (ECs), parenchyma cells (PCs), xylem parenchyma cells, phloem parenchyma cells, xylem vessels and fibers, and sieve elements and companion cells complex. Cell-specific marker genes in each cell type were provided. Floral volatiles from mei petals were measured at four flowering development stages, and their emissions increased from BS to FS, and decreased at the withering stage. Fifty-eight differentially expressed genes (DEGs) in benzenoid/phenylpropanoid pathway were screened using bulk RNA-seq data. Twenty-eight DEGs expression increased from BS to FS, indicating that they might play roles in floral volatile synthesis in P. mume, among which PmBAHD3 would participate in benzyl acetate synthesis. ScRNA-seq data showed that 27 DEGs mentioned above were expressed variously in different cell types. In situ hybridization confirmed that PmPAL2, PmCAD1, PmBAHD3, 5, and PmEGS1 involved in floral volatile synthesis in mei petals are mainly expressed in EC, PC, and most vascular tissues, consistent with scRNA-seq data. The result indicates that benzyl acetate and eugenol, the characteristic volatiles in mei, are mostly synthesized in these cell types. The first petal single-cell atlas was constructed, offering new insights into the molecular mechanism of floral volatile synthesis.

Biotrophic phytopathogenic fungi such as Podosphaera xanthii have evolved sophisticated mechanisms to adapt to various environments causing powdery mildews leading to substantial yield losses. Today, due to known adverse effects of pesticides, development of alternative control means is crucial and can be achieved by combining plant protection products with resistant genotypes. Using plant defense inducers, natural molecules that stimulate plant immune system mimicking pathogen attack is sustainable, but information about their mode of action in different hosts or host genotypes is extremely limited. Reynoutria sachalinensis extract, a known plant defense inducer, especially through the Salicylic acid pathway in Cucurbitaceae crops against P. xanthii, was employed to analyze the signaling cascade of defense activation. Here, we demonstrate that R. sachalinensis extract enhances phospholipid production and signaling in a Susceptible to P. xanthii courgette genotype, while limited response is observed in an Intermediate Resistance genotype due to genetic resistance. Functional enrichment and cluster analysis of the upregulated expressed genes revealed that inducer application promoted mainly lipid- and membrane-related pathways in the Susceptible genotype. On the contrary, the Intermediate Resistance genotype exhibited elevated broad spectrum defense pathways at control conditions, while inducer application did not promote any significant changes. This outcome was obvious and at the metabolite level. Main factor distinguishing the Intermediate Resistance form the Susceptible genotype was the epigenetic regulated increased expression of a G3P acyltransferase catalyzing phospholipid production. Our study provides evidence on phospholipid-based signaling after plant defense inducer treatment, and the selective role of plant’s genetic background.

Purple tea, rich in anthocyanins, has a variety of health benefits and is attracting global interest. However, the regulation mechanism of anthocyanin in purple tea populations has not been extensively studied. In this experiment, RNA-seq, BSA-seq, and BSR-seq were performed using 30 individuals with extreme colors (dark-purple and green) in an F₁ population of ‘Zijuan’ and ‘Jinxuan’. The results show that 459 genes were differentially expressed in purple and green leaves, among which genes involved in the anthocyanin synthesis and transport pathway, such as CHS, F3H, ANS, MYB75, GST, MATE, and ABCC, were highly expressed in purple leaves. Moreover, there were multiple SNP/InDel variation sites on chromosomes 2 and 14 of the tea plant, as identified by BSA-seq. The integrated analysis identified two highly expressed genes (CsANS and CsMYB75) with SNP/InDel site variations in the purple tea plants. By silencing leaves, we proved that CsMYB75 could positively regulate anthocyanin accumulation and expression of related structural genes in tea plants. A 181-bp InDel in the CsMYB75 promoter was also found to be co-segregating with leaf color. The results of this study provide a theoretical reference for the molecular mechanism of anthocyanin accumulation in purple tea plants and contribute to the creation of new tea cultivars with high anthocyanin content.

Lateral branching is a crucial agronomic trait that impacts crop yield. In tomato (Solanum lycopersicum), excessive lateral branching is unfavorable and results in substantial labor and management costs. Therefore, optimizing lateral branching is a primary objective in tomato breeding. Although many genes related to lateral branching have been reported in tomato, the molecular mechanism underlying their network remains elusive. In this study, we found that the expression profile of a WRKY gene, WRKY-B (for WRKY-BRANCING), was associated with the auxin-dependent axillary bud development process. Wrky-b mutants generated by the CRISPR/Cas9 editing system presented fewer lateral branches, while WRKY-B overexpression lines presented more lateral branches than did wild-type plants. Furthermore, WRKY-B can directly target the well-known branching gene BLIND (BL) and the auxin efflux carrier gene PIN4 to activate their expression. Both the bl and pin4 mutants exhibited reduced lateral branching, similar to the wrky-b mutant. The IAA contents in the axillary buds of the wrky-b, bl, and pin4 mutant plants were significantly higher than those in the wild-type plants. In addition, WRKY-B can also directly target the AUX/IAA gene IAA15 and repress its expression. In summary, WRKY-B works upstream of BL, PIN4, and IAA15 to regulate the development of lateral branches in tomato.

Over the decades, evolutionists and ecologists have shown intense interest in the role of polyploidization in plant evolution. Without clear knowledge of the diploid ancestor(s) of polyploids, we would not be able to answer fundamental ecological questions such as the evolution of niche differences between them or its underlying genetic basis. Here, we explored the evolutionary history of two Fragaria tetraploids, Fragaria corymbosa and Fragaria moupinensis. We de novo assembled five genomes including these two tetraploids and three diploid relatives. Based on multiple lines of evidence, we found no evidence of subgenomes in either of the two tetraploids, suggesting autopolyploid origins. We determined that Fragaria chinensis was the diploid ancestor of F. corymbosa while either an extinct species affinitive to F. chinensis or an unsampled population of F. chinensis could be the progenitor of F. moupinensis. Meanwhile, we found introgression signals between F. chinensis and Fragaria pentaphylla, leading to the genomic similarity between these two diploids. Compared to F. chinensis, gene families related to high ultraviolet (UV)-B and DNA repair were expanded, while those that responded towards abiotic and biotic stresses (such as salt stress, wounding, and various pathogens) were contracted in both tetraploids. Furthermore, the two tetraploids tended to down-regulate defense response genes but up-regulate UV-B response, DNA repairing, and cell division gene expression compared to F. chinensis. These findings may reflect adaptions toward high-altitude habitats. In summary, our work provides insights into the genome evolution of wild Fragaria tetraploids and opens up an avenue for future works to answer deeper evolutionary and ecological questions regarding the strawberry genus.

Arbuscular mycorrhizal symbiosis (AMS), a complex and delicate process, is precisely regulated by a multitude of transcription factors. PHYTOCHROME-INTERACTING FACTORS (PIFs) are critical in plant growth and stress responses. However, the involvement of PIFs in AMS and the molecular mechanisms underlying their regulator functions have not been well elucidated. Here, we show that SlPIF4 negatively regulates the arbuscular mycorrhizal fungi (AMF) colonization and AMS-induced phosphate uptake in tomato. Protein- protein interaction studies suggest that SlDELLA interacts with SlPIF4, reducing its protein stability and inhibiting its transcriptional activity towards downstream target genes. This interaction promotes the accumulation of strigolactones (SLs), facilitating AMS development and phosphate uptake. As a transcription factor, SlPIF4 directly transcriptionally regulates genes involved in SLs biosynthesis, including SlCCD7, SlCDD8, and SlMAX1, as well as the AMS-specific phosphate transporter genes PT4 and PT5. Collectively, our findings uncover a molecular mechanism by which the SlDELLA-SlPIF4 module regulates AMS and phosphate uptake in tomato. We clarify a molecular basis for how SlPIF4 interacts with SLs to regulate the AMS and propose a potential strategy to improve phosphate utilization efficiency by targeting the AMS-specific phosphate transporter genes PTs.

Sterols are secondary metabolites commonly found in rapeseed that play crucial physiological roles in plants and also benefit human health. Consequently, unraveling the genetic basis of sterol synthesis in rapeseed is highly important. In this study, 21 individual sterols as well as total sterol (TS) content were detected in a double haploid (DH) population of Brassica napus, and a total of 24 quantitative trait loci (QTL) and 157 mQTL were identified that were associated with TS and different individual sterols. Time-series transcriptomic analysis showed that the differentially expressed genes (DEGs) involved in sterol and lipid biosynthesis pathways were enriched. Additionally, a regulatory network between sterol-related DEGs and transcription factors (TFs) was established using coexpression analysis. Some candidate genes were identified with the integration of transcriptomic analysis and QTL mapping, and the key candidate gene BnSQS1. C03 was selected for further functional analysis. BnSQS1.C03 demonstrated squalene synthase activity in vitro and increased the TS by 3.8% when overexpressed in Arabidopsis. The present results provide new insights into sterol regulatory pathways and a valuable genetic basis for breeding rapeseed varieties with high sterol content in the future.

The Agrobacterium -mediated transient expression system has been developed and applied to various plants as an alternative to stable transformation. However, its application in tomatoes is still limited due to low expression efficiency. In this study, we describe an improved vacuum-infiltration system that can be used in both tomato fruits and leaves. Notably, this study is the first report of vacuum infiltration in attached tomato fruits. The feasibility of the improved vacuum-infiltration system in Micro-Tom tomato was confirmed by various assays, including multiple fluorescent protein expression analysis, β -glucuronidase activity analysis, and RUBY reporter visualization. Subsequently, the improved vacuum-infiltration system was successfully applied to tomato biotechnology research. Herein, a trichome-specific promoter in tomato was identified that can drive the directional synthesis of specific plant natural products (PNPs). Additionally, based on the assessment results of the improved vacuum-infiltration system, we obtained a flavonoid-rich tomato variety through the stable transformation of AmRosea and AmDelila. In a significant practical application, we successfully synthesized the high-value scutellarin in tomato, which provides an alternative route for the production of PNPs from plants. In addition, the improved vacuum-infiltration system has been demonstrated to be suitable for commercial tomato varieties (‘Emerald’ and ‘Provence’) as well. The improved vacuum-infiltration system not only speeds up fundamental and applied research in tomato but also offers an additional powerful tool for advancing tomato synthetic biology research.

Chili pepper is an important spice and a model plant for fruit development studies. Large-scale omics information on chili pepper plant development continues to be gathered for understanding development as well as capsaicin biosynthesis. In this study, a full-spectrum transcriptome data of eight chili pepper tissues at five growth stages using the Oxford Nanopore long-read sequencing approach was generated. Of the 485 351 transcripts, 35 336 were recorded as reference transcripts (genes), while 450 015 were novel including coding, lnc, and other non-coding RNAs. These novel transcripts belonged to unknown/intergenic (347703), those retained introns (26336), and had multi-exons with at least one junction match (20333). In terms of alternative splicing, retained intron had the highest proportion (14795). The number of tissue-specific expressed transcripts ranged from 22 925 (stem) to 40 289 (flower). The expression changes during fruit and placenta development are discussed in detail. Integration of gene expression and capsaicin content quantification throughout the placental development clarifies that capsaicin biosynthesis in pepper is mainly derived from valine, leucin, and isoleucine degradation as well as citrate cycle and/or pyrimidine metabolism pathways. Most importantly, a user-friendly Pepper Full-Length Transcriptome Variation Database (PFTVD 1.0) ( http://pepper-database.cn/ ) has been developed. PFTVD 1.0 provides transcriptomics and genomics information and allows users to analyse the data using various tools implemented. This work highlights the potential of long-read sequencing to discover novel genes and transcripts and their diversity in plant developmental biology.

It is well known that if a fruit is harvested extremely early its development and function are interrupted, and it may never attain full maturity and optimal quality. Reports revealing insights regarding the alterations of maturation, ripening and postharvest quality in very early picked fruits are rare. We examined the effects of early harvesting on tomatoes by characterizing different accessions at the molecular, physiological, and biochemical levels. We found that even very early-harvested fruits could achieve postharvest maturation and ripening though with some defects in pigment and cuticle formation, and seeds from very early-harvested fruits could still germinate and develop as normal and healthy plants. One critical regulator of tomato cuticle integrity, SlCER1-2, was shown to contribute to cuticle defects in very early-harvested fruits. Very early fruit harvest still allowing ripening and seed development indicate that the genetic and physiological programs of later maturation and ripening are set into motion early in fruit development and are not dependent on complete fruit expansion nor attachment to the plant.

The overload of Cl⁻ typically causes cell damage and death in plants, especially in Cl⁻-sensitive crops. Abscisic acid (ABA) is a stress-induced phytohormone that can alleviate chloride stress by reducing Cl⁻ accumulation; however, the mechanism is not clear. Here, we found that the application of ABA elevated Cl⁻ efflux from roots and reduced membrane damage and cell death in chloride-stressed Malus hupehensis. MhSLAH3, a homolog of the slow anion channel from M. hupehensis, encoded a channel controlling Cl⁻ efflux and was induced by both chloride and ABA. MhSLAH3 overexpression accelerated Cl⁻ efflux, which enhanced the tolerance of M. hupehensis to chloride stress, and retarded chloride-induced cell death. However, the suppression of MhSLAH3 partially offset the acceleration effect of ABA on Cl⁻ efflux. MhZAT10L was then identified as a C2H2-type transcription factor upstream of MhSLAH3, repressing MhSLAH3 transcription under chloride stress. The suppression of MhZAT10L accelerated Cl⁻ efflux by releasing suppressed MhSLAH3, but MhZAT10L overexpression counteracted the effects of ABA on Cl⁻ efflux. MhABI5 promoted Cl⁻ efflux mediated by MhSLAH3 due to induction by ABA and transcriptional repression of MhZAT10L, but this function of MhABI5 was reversed by MhZAT10L overexpression. The suppression of MhABI5 diminished the positive effects of ABA on Cl⁻ efflux and retarding cell death. Thus, ABA repressed MhZAT10L transcription by activating MhABI5, further releasing MhSLAH3 to accelerate Cl⁻ efflux. These findings provide a new evidence of ABA regulation of Cl⁻ efflux.

Pigeonpea (Cajanus cajan) is a nutrient-rich and versatile food legume crop of tropical and subtropical regions. In this study, we describe the de novo assembly of a high-quality genome for the ancient pigeonpea landrace ‘D30’, achieved through a combination of Pacific Biosciences high-fidelity (PacBio HiFi) and high-throughput chromatin conformation capture (Hi-C) sequencing technologies. The assembled ‘D30’ genome has a size of 813.54 Mb, with a contig N50 of 10.74 Mb, a scaffold N50 of 73.07 Mb, and a GC content of 35.67%. Genomic evaluation revealed that the ‘D30’ genome contains 99.2% of Benchmarking Universal Single-Copy Orthologs (BUSCO) and achieves a 29.06 long terminal repeat (LTR) assembly index (LAI). Genome annotation indicated that ‘D30’ encompasses 431.37 Mb of repeat elements (53.02% of the genome) and 37 977 protein-coding genes. Identification of single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variations between ‘D30’ and the published genome of pigeonpea cultivar ‘Asha’ suggests that genes affected by these variations may play important roles in biotic and abiotic stress responses. Further investigation of genomic regions under selection highlights genes enriched in starch and sucrose metabolism, with 42.11% of these genes highly expressed in seeds. Finally, we conducted genome-wide association studies (GWAS) to facilitate the identification of 28 marker-trait associations for six agronomic traits of pigeonpea. Notably, we discovered a calmodulin-like protein (CcCML) that harbors a dominant haplotype associated with the 100-seed weight of pigeonpea. Our study provides a foundational resource for developing genomics-assisted breeding programs in pigeonpea.

Tomato fruit colors are directly associated with their appearance quality and nutritional value. However, tomato fruit color formation is an intricate biological process that remains elusive. In this work we characterized a tomato yellow fruited tomato 3 (yft3, e9292, Solanum lycopersicum) mutant with yellow fruits. By the map-based cloning approach, we identified a transversion mutation (A2117C) in the YFT3 gene encoding a putative isopentenyl diphosphate isomerase (SlIDI1) enzyme, which may function in the isoprenoid biosynthetic pathway by catalyzing conversion between isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The mutated YFT3 (A2117C) (designated YFT3 allele) and the YFT3 genes did not show expression difference at protein level, and their encoded YFT3 allelic (S126R) and YFT3 proteins were both localized in plastids. However, the transcript levels of eight genes (DXR, DXS, HDR, PSY1, CRTISO, CYCB, CYP97A, and NCED) associated with carotenoid synthesis were upregulated in fruits of both yft3 and YFT3 knockout (YFT3-KO) lines at 35 and 47 days post-anthesis compared with the red-fruit tomato cultivar (M82). In vitro and in vivo biochemical analyses indicated that YFT3 (S126R) possessed much lower enzymatic activities than the YFT3 protein, indicating that the S126R mutation can impair YFT3 activity. Molecular docking analysis showed that the YFT3 allele has higher ability to recruit isopentenyl pyrophosphate (IPP), but abolishes attachment of the Mg²⁺ cofactor to IPP, suggesting that Ser126 is a critical residue for YTF3 biochemical and physiological functions. As a result, the yft3 mutant tomato line has low carotenoid accumulation and abnormal chromoplast development, which results in yellow ripe fruits. This study provides new insights into molecular mechanisms of tomato fruit color formation and development.

Houttuynia cordata Thunb., commonly known as yuxingcao in China, is known for its characteristic fishy smell and is widely recognized as an important herb and vegetable in many parts of Asia. However, the lack of genomic information on H. cordata limits the understanding of its population structure, genetic diversity, and biosynthesis of medicinal compounds. Here we used single-molecule sequencing, Illumina paired-end sequencing, and chromosome conformation capture technology to construct the first chromosome-scale decaploid H. cordata reference genome. The genome assembly was 2.63 Gb in size, with 1348 contigs and a contig N50 of 21.94 Mb further clustered and ordered into 88 pseudochromosomes based on Hi-C analysis. The results of genome evolution analysis showed that H. cordata underwent a whole-genome duplication (WGD) event ∼17 million years ago, and an additional WGD event occurred 3.3 million years ago, which may be the main factor leading to the high abundance of multiple copies of orthologous genes. Here, transcriptome sequencing across five different tissues revealed significant expansion and distinct expression patterns of key gene families, such as l-amino acid/l-tryptophan decarboxylase and strictosidine synthase, which are essential for the biosynthesis of isoquinoline and indole alkaloids, along with the identification of genes such as TTM3, which is critical for root development. This study constructed the first decaploid medicinal plant genome and revealed the genome evolution and polyploidization events of H. cordata.

Low-temperature storage is used to extend the shelf life of fruits, but prolonged storage at temperatures below tolerable levels may cause postharvest chilling injury (PCI) in sensitive commodities. This review aims to highlight adenosine triphosphate (ATP) activation and the interplay of extracellular ATP (eATP) and intracellular ATP (iATP) in fruits and to find out its significance in mitigating PCI. Various pathways, such as the Embden-Meyerhof-Parnas pathway, the tricarboxylic acid cycle, the pentose phosphate pathway, the γ-aminobutyric acid shunt pathway, and the cytochrome pathway, are studied critically to elucidate their role in continuous ATP supply and maintaining the membrane fluidity and integrity. This review summarizes the treatments helpful in modulating energy metabolism in fruit. Additionally, this work provides insights into the energy status in attenuating chilling tolerance. Moreover, it states the potential of nicotinamide adenine dinucleotide in mitigating PCI. Furthermore, it discusses the role of eATP and its receptor DORN1 in mitigating chilling stress.

Our knowledge of crop domestication, genomics, and of the plant virosphere unevenly represents the taxonomic distribution of the global biodiversity, and, as we show here, is significantly enriched for the Solanaceae. Within the family, potato, tomato, eggplant, pepper, and over 100 lesser-known edible species play important nutrition and cultural roles in global and local food systems. Technologies using engineered viruses are transitioning from proof-of-concept applications in model plants to the precise trait breeding of Solanaceae crops. Leveraging this accumulated knowledge, we highlight the potential of virus-based biotechnologies for fast-track improvement of Solanaceae crop production systems, contributing to enhanced global and local human nutrition and food security.

Root-knot nematodes (Meloidogyne spp.) are widely spread root parasites that infect thousands of vascular plant species. These highly polyphagous nematodes engage in sophisticated interactions with host plants that results in the formation of knot-like structures known as galls whose ontogeny remains largely unknown. Here, we determined transcriptome changes and alternative splicing variants induced by Meloidogyne incognita in galls and neighboring root cells at two distinct infective stages. M. incognita induced substantial transcriptome changes in tomato roots both locally in galls and systemically in neighboring cells. A considerable parallel regulation of gene expression in galls and neighboring cells were detected, indicative of effective intercellular communications exemplified by suppression of basal defense responses particularly during the early stage of infection. The transcriptome analysis also revealed that M. incognita exerts a tight control over the cell cycle process as a whole that results in an increase of ploidy levels in the feeding sites and accelerated mitotic activity of the gall cells. Alternative splicing analysis indicated that M. incognita significantly modulates pre-mRNA splicing as a total of 9064 differentially spliced events from 2898 genes were identified where intron retention and exon skipping events were largely suppressed. Furthermore, a number of differentially spliced events were functionally validated using transgenic hairy root system and found to impact gall formation and nematode egg mass production. Together, our data provide unprecedented insights into the transcriptome and spliceome reprogramming induced by M. incognita in tomato with respect to gall ontogeny and nematode parasitism.