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At least 19 recordsLinked to original sources
PubMed2024

Transcriptional landscape and dynamics involved in sugar and acid accumulation during apple fruit development.

In fleshy fruit, sugars and acids are central components of fruit flavor and quality. To date, the mechanisms underlying transcriptional regulation of sugar and acid during fruit development remain largely unknown. Here, we combined ATAC-seq with RNA-seq to investigate the genome-wide chromatin accessibility and to identify putative transcription factors related to sugar and acid accumulation during apple (Malus domestica) fruit development. By integrating the differentially accessible regions and differentially expressed genes, we generated a global data set of promoter-accessibility and expression-increased genes. Using this strategy, we constructed a transcriptional regulatory network enabling screening for key transcription factors and target genes involved in sugar and acid accumulation. Among these transcription factors, 5 fruit-specific DNA binding with one finger genes were selected to confirm their regulatory effects, and our results showed that they could affect sugar or acid concentration by regulating the expression of sugar or acid metabolism-related genes in apple fruits. Our transcriptional regulatory network provides a suitable platform to identify candidate genes that control sugar and acid accumulation. Meanwhile, our data set will aid in analyzing other characteristics of apple fruit that have not been illuminated previously. Overall, these findings support a better understanding of the regulatory dynamics during apple fruit development and lay a foundation for quality improvement of apple.

Malus↗
PubMed2025

Chromatin accessibility analysis reveals functional cis-regulatory regions related to fruit development and domestication in tomato.

Non-coding DNA sequences harbor vast regulatory programs that ensure the precise spatiotemporal control of gene expression, which is essential for proper plant development and trait formation. Chromatin accessibility analysis could identify functional DNA regions within the extensive non-coding sequences and infer regulatory elements, serving as a crucial approach to unravel the mysteries of non-coding DNA sequences. Tomato fruit, a fleshy organ, provides a special system for studying fruit development and trait formation. However, the role of cis-accessible chromatin regions (cis-ACRs) during tomato fruit development, particularly in comparison with protein-coding DNA sequences, remains poorly understood. Here, we used ATAC-seq to define the landscape of cis-ACRs during fruit development and domestication in tomato. Temporal differential analysis revealed the dynamic opening and closing of cis-ACRs during fruit development. Comparative analysis of cis-ACRs between cultivated and wild tomatoes highlighted their significant contributions to fruit domestication. Combining analysis with genomic structural variations (SVs) suggested that SVs are likely a key factor in the formation of specific accessible cis-ACRs in cultivated tomatoes. Moreover, using gene editing, we identified a functional cis-ACR within the intron of the MBP3 gene that regulates fruit development and size traits. Overall, our findings provide a comprehensive perspective on the roles of cis-ACRs in tomato fruit development and domestication.

Solanum lycopersicum↗
PubMed2026

Cis-regulatory variation in the MdCKX6 promoter is associated with allele-specific expression and fruit size in apple.

Fruit size is a key determinant of apple fruit quality and market value and is strongly influenced by phytohormone-regulated cell proliferation and expansion during early fruit development. Cytokinin oxidase/dehydrogenase (CKX) enzymes regulate cytokinin homeostasis by irreversibly degrading active cytokinins, but the contribution of natural variation in CKX genes to fruit size remains poorly understood. Here, we identified MdCKX6 as a candidate regulator of fruit growth in apple (Malus domestica). MdCKX6 exhibited pronounced allele-specific expression during fruit development in the cultivar 'Royal Gala'. Sequence analysis identified a promoter SNP associated with differential promoter activity and allele-specific expression. Genotyping of diverse apple cultivars and wild Malus accessions revealed a significant association between MdCKX6 promoter genotype and fruit size. Cultivars carrying low-expression alleles produced larger fruits, whereas high-expression alleles were associated with smaller fruits. To investigate gene function, MdCKX6 was overexpressed in tomato, resulting in reduced fruit size. Histological analyses of the transgenic tomato fruit revealed smaller pericarp cells. Transcriptome analysis of transgenic fruits revealed widespread changes in genes associated with cell-cycle regulation, cell wall modification, hormone-related processes, and transcriptional regulation. Together, these results identify MdCKX6 as a potential negative regulator of apple fruit growth and reveal an association between cis-regulatory variants, gene expression, and fruit size. This study provides new insights into the role of cytokinin metabolism in fruit development and highlights regulatory variation in MdCKX6 as a potential target for apple breeding.

Malus↗
PubMed2025

CRISPR/Cas9-directed disruption of wc-2 leads to the absence of fruiting body development in Pleurotus ostreatus.

Light, particularly blue light, is a key environmental factor that induces fruiting in certain agaricomycetes. In this study, we characterized mutant strains of Pleurotus ostreatus with disrupted wc-2, which encodes one of the white-collar proteins, Wc-2, to investigate the role of light in fruiting in P. ostreatus. We introduced two different plasmids containing expression cassettes for Cas9 and two different gRNAs targeting wc-2 separately into the dikaryotic P. ostreatus strain PC9×#64. Among the 11 dikaryotic hygromycin-resistant transformants, six strains did not form fruiting bodies. Genomic PCR followed by sequencing analysis suggested that all six fruitless strains were dikaryotic wc-2 disruptants. Small aggregate structures were not observed in the dikaryotic wc-2 disruptants grown under light conditions, as in PC9×#64 grown in a red box. These results suggest that Wc-2 is essential for the initiation of blue light-induced fruiting in P. ostreatus.

Pleurotus↗
PubMed2026

GA4+7 alleviates pear fruit semi-russeting partly by suppressing PRX-mediated lignin deposition.

Pear fruit semi-russeting is a surface disorder that frequently occurs during fruit development and significantly diminishes fruit appearance quality and commercial value. Although Gibberellin 4 + 7 (GA4+7) has been used to reduce fruit surface defects in horticultural crops, the physiological and molecular mechanisms underlying its inhibitory effect on pear fruit semi-russeting remain poorly understood. In this study, preharvest GA4+7 treatment of 'Cuiguan' pear significantly reduced russet coverage and lignin accumulation in mature fruit skin without adversely affecting fruit size, fruit shape index, or total soluble solids content. Integrated metabolomic and transcriptomic analyses revealed that GA4+7 treatment was associated with the repression of phenylpropanoid and lignin biosynthesis at both metabolic and transcriptional levels. Among the lignin-related differentially expressed genes, two class III peroxidase genes, PpyPRX22 and PpyPRX65, were strongly downregulated by both GA4+7 and bagging treatments. Both proteins localized to the cell wall, and transient expression assays in pear fruit skin supported positive roles for PpyPRX22 and PpyPRX65 in lignin deposition. Furthermore, dual-luciferase reporter assays combined with transient overexpression experiments suggested that several PpyMYB transcription factors may regulate PpyPRX expression and lignin accumulation, with PpyMYB138 and PpyMYB139 significantly activating PpyPRX22 and/or PpyPRX65 promoter activity. Taken together, these results suggest that GA4+7 alleviates pear fruit semi-russeting at least partly by reducing lignin deposition in the fruit skin, with PpyPRX22 and PpyPRX65 potentially contributing to this process.

Class III peroxidase↗
PubMed2026

Genome-wide identification of the superoxide dismutase gene family in Lycium barbarum and their expression profiles under abiotic stress and phytohormone treatment.

BACKGROUND: Superoxide dismutases (SODs) are crucial metalloenzymes that constitute the first line of defense against reactive oxygen species in plants under abiotic stress. Wolfberry (Lycium barbarum) is an economically important medicinal plant with notable stress tolerance, however, a comprehensive genome-wide analysis of its SOD gene family has not yet been performed. RESULTS: We identified ten wolfberry SOD genes (LbaSODs) and classified them into three subfamilies: iron-SODs (Fe-SODs), manganese-SODs (Mn-SODs), and copper/zinc-SODs (Cu/Zn-SODs). Members within each subfamily shared conserved gene structures and motifs. Segmental duplication was the primary driver of LbaSOD expansion, with three paralogous pairs identified. Analysis of cis-regulatory elements in the promoter region revealed a predominance of stress- and hormone-responsive cis-elements, particularly ABA-responsive elements (ABREs) (22 copies) and LTR (17 copies) motifs. Tissue-specific expression profiling revealed that LbaSOD2 and LbaSOD5 expression peaked during early fruit development, whereas LbaSOD6, LbaSOD9, and LbaSOD10 were progressively upregulated through fruit maturation. Under abiotic conditions, Fe-SOD members were markedly suppressed during prolonged drought, whereas LbaSOD9 and LbaSOD10 were rapidly induced in response to salt stress. Among the phytohormone treatments, methyl jasmonate (MeJA) elicited the most pronounced response, with LbaSOD5 expression increasing by approximately 60-fold after 24 hours. Notably, abscisic acid (ABA) triggered an exceptionally strong transcriptional induction of LbaSOD5 (2.5 × 105-fold), LbaSOD10 (6 × 105-fold), and LbaSOD6 (70-fold). In addition, LbaSOD3 and LbaSOD7 transcripts were undetectable in any of the tested conditions. CONCLUSIONS: This study provides the first comprehensive characterization of the LbaSOD gene family and elucidates its hormone- and stress-responsive regulatory landscape, providing a valuable foundation for future functional investigations of LbaSOD genes in abiotic stress adaptation. The extraordinarily strong ABA-mediated induction of specific LbaSOD members, together with their tissue- and stress-specific expression patterns, highlights their potential as targets for genetic improvement of stress tolerance in wolfberry.

Lycium barbarum↗
PubMed2026

Phytochrome-interacting factor 1b (SlPIF1b) affects the fruit quality of tomato by regulating chloroplast development.

The increased abundance and functionality of fruit chloroplasts could promote the accumulation of nutrients and flavor in the fruit. Tomato fruit has fully developed fruit chloroplasts, whose abundance and functionality have much untapped potential in improving fruit quality by controlling fruit chloroplast development. Previous studies have identified many regulatory factors that specifically regulate fruit chloroplast development in tomatoes, but there are fewer reports on tomato phytochrome-interacting factors (SlPIFs). Arabidopsis AtPIFs have been implicated in chloroplast development and chlorophyll biosynthesis. In this study, we identified and characterized an SlPIF1b mutant in tomato, named GS, which exhibited a dark green fruit shoulder with enhanced chloroplast development. RNA-seq and genotyping analysis identified a - 21 bp (A → T) mutation in the promoter of SlPIF1b, resulting in the absence of the TATA-box core transcriptional element and inhibiting SlPIF1b transcription. The overexpression of SlPIF1b in GS inhibited chloroplast development of fruits, leading to a lighter green shoulder color, decreased chlorophyll content, reduced photosynthetic activity, diminished starch accumulation, and compromised fruit quality upon ripening. Conversely, the down expression of SlPIF1b significantly enhanced fruit chloroplast development and functionality in fruits, resulting in increased chlorophyll and carotenoid accumulation. Further analysis of expression profile and transcriptional activity indicated that SlPIF1b could bind to G/PBE-box elements present in SlGLK2, SlTKN4, SlCAO1a, SlPOR1, SlPOR3, SlCAB1 and SlCAB1b promoters, thereby inhibiting their expression. This study revealed the specific regulatory mechanism by which SlPIF1b modulates chloroplast development and chlorophyll synthesis in tomato fruit and provided valuable genetic resources and a theoretical basis for tomato quality improvement.

Solanum lycopersicum↗
PubMed2026

Temporal DIA-MS proteomics reveals coordinated metabolic reprogramming associated with oil accumulation in oil palm mesocarp.

Oil palm (Elaeis guineensis Jacq.) is the most productive oil-bearing crop globally, yet the molecular basis of mesocarp development and lipid accumulation remains poorly understood. Ultra-deep data-independent acquisition mass spectrometry (DIA-MS) was applied to characterize proteome dynamics in two contrasting genotypes, seedless (KS) and thin-shelled (TS), across five developmental stages (P1-P5) spanning fruit development to mature oil accumulation. Phenotypic analysis revealed higher mesocarp proportion and oil content in KS during late maturation. A total of 137,615 peptides corresponding to 12,163 protein groups were identified, providing a temporal proteomic landscape of mesocarp development. Multivariate analysis indicated that developmental progression was the primary contributor to proteomic variation, whereas genotype-associated differences increased during lipid accumulation. Differentially abundant proteins were mainly associated with carbohydrate metabolism, photosynthesis, proteolysis, antioxidant responses, and lipid biosynthesis. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and KOG analyses suggested extensive remodeling of metabolic networks, including developmental changes in photosynthesis-associated proteins and increased representation of lipid-associated pathways during maturation. Weighted protein co-expression network analysis identified 17 modules associated with developmental progression and lipid accumulation, highlighting candidate proteins involved in carbon metabolism, energy production, and cellular protection. Genes encoding selected hub protein candidates were further examined by RT-qPCR. Biochemical analyses supported these proteomic patterns, showing increased acetyl-CoA availability, enhanced antioxidant enzyme activities (SOD, CAT, APX, and GR), improved GSH/GSSG balance, and reduced oxidative damage in KS. Together, these findings provide a temporal proteomic and biochemical framework for understanding genotype-associated differences in oil accumulation and identify candidate metabolic networks for functional studies.

Carbon metabolism↗
PubMed2026

Genome-wide identification and functional analysis of the BES1-like (VfBES1) gene family in Vernicia fordii reveals its role in floral development.

BACKGROUND: Vernicia fordii Hemsl (also known as Tung tree), an significant commercial oil-producing tree species, is a monoecious and diclinous species with male and female flowers on the same inflorescence; however, the molecular mechanisms governing its floral sex determination remain elusive, particularly the genetic basis underlying the skewed female-to-male flower ratio and the evolutionary dynamics of sex-related gene families, which severely restrict targeted breeding for yield enhancement. In the model plant Arabidopsis, the BRI1 EMS SUPPRESSOR 1 (BES1) transcription factor family plays a crucial role in Brassinosteroid (BR) signaling and reproductive development. However, its function remains largely unexplored in woody perennials. RESULTS: In this study, we introduce the genome-wide identification and functional characterization of the BES1-like (VfBES1) gene family in the Tung tree for the first time. Integrative multi-omics approaches reveal seven VfBES1 genes that are clustered into three phylogenetically distinct clades, each characterized by clade-specific motifs and structural simplicity. Segmental duplication events (VfBES1-1/VfBES1-5 and VfBES1-4/VfBES1-7) and promoter cis-element enrichment (hormone-responsive and abiotic stress-related motifs) highlight evolutionary innovation and functional diversification. Spatiotemporal expression profiling reveals VfBES1 genes' tissue- and stage-specific roles. VfBES1-1 predominantly expresses in female flowers and fruits, suggesting its possible roles in late-stage sex maintenance or ovule and fruit development. VfBES1-2 and VfBES1-6 exhibit male flower-specific and early floral developmental activation, respectively. Nuclear-localized VfBES1-6 displays co-expression with VfMYB35-1 gene, which is a regulator of male structure degeneration. CONCLUSIONS: Findings in this study shed light on the regulatory roles of VfBES1 genes in the floral development of the Tung tree, providing a reference for its precision breeding to enhance flowering synchrony and seed productivity. This study also provides a comparative framework for understanding the functional diversity of BES1-like genes in non-model woody plants.

Flowers↗
PubMed2026

Genome-wide identification and characterization of 1-amino-cyclopropane-1- carboxylate synthase (ACS) gene family in Carica papaya and expression insights in response to hormone stress.

ACC-synthase (1-aminocyclopropane-1-carboxylate synthase), also known as the ACS gene, plays a pivotal role in ethylene production, which is of great importance in the fruit ripening process for producing saleable yield (marketable fruit). The ACS gene family presumably controls stress responses, plant growth and development, and particularly fruit ripening. Computational biology was used as an essential tool to identify seven ACS genes in Carica papaya (red hermaphrodite) using an RNA-seq database (NCBI GEO). Further, the phylogenetic relationships of ACS genes determined gene family resemblance in the genomes of Hordeum vulgare, Musa acuminata, C. papaya, and Arabidopsis thaliana; therefore, the identified gene families were further classified into four distinct clades (Type-I, Type-II, Type-III, and Type-IV) in alignment with the well-established Arabidopsis classification. Moreover, encompassing gene structure, domain motifs, cis-element phylogenetic profiling, synteny, and transcriptomic profiling unveiled latent structural and functional attributes within CpACS genes. Through segmental duplication of CpACS, insights into evolutionary duplication events were predicted. The paralogous behavior of ACS genes in C. papaya and a comprehensive transcriptomic analysis demonstrated both up- and down-regulation patterns in response to ethylene treatment at different time points during the fruit ripening process, using the papaya manual handbook V2 (2021). Gene expression showed upregulation of two essential CpACS genes, CpACS5 and CpACS6. RT-qPCR validates the expression of these important genes during fruit ripening. However, one gene, CpACS7, is expressed in the later stages of fruit development. Our results demonstrated novel avenues for understanding the expression pathways of the ACS gene family in red hermaphrodite papaya, and most of these genes were linked to regulating various abiotic stresses, plant growth, and fruit development.

Carica↗
PubMed1979

Myxococcus xanthus mutants with temperature-sensitive, stage-specific defects: evidence for independent pathways in development.

Fruiting-body formation in the bacterium Myxococcus xanthus consists of a temporal sequence of cellular aggregation and sporulation. To examine the developmental stages more closely, we established synchronous and reproducible conditions for fruiting-body formation. Mutants that are temperature sensitive for fruiting-body formation were isolated and analyzed under these conditions. The terminal morphologies of the mutant strains at the nonpermissive temperature were found to resemble intermediate stages of fruiting-body formation and therefore were grouped in the following phenotypic classes: (i) rough mutants, which show no aggregation; (ii) swirl mutants, which show defective aggregation; (iii) flat-mound mutants and translucent-mound mutants, mutants which aggregate but show very low levels of sporulation. The mutants were characterized by temperature-shift experiments and found to exhibit discrete and reproducible temperature-sensitive periods. The ends of the temperature-sensitive periods in the various mutants covered a broad range of the developmental cycle. No correlation was found between the terminal morphologies at the restrictive temperature and the timing of the temperature-sensitive periods. However, the terminal morphologies correlated well with sporulation. The rough and swirl mutants produced normal numbers of myxospores at 34 degrees C even though they failed to aggregate. In contrast, the flat-mound and translucent-mound mutants, which aggregate normally, produced very few spores. The translucent-mound mutants were also temperature sensitive for induction of glycerol spores. The results indicate that both aggregation and sporulation are initiated early in the developmental cycle and that these processes are largely independent of each other.

Glycerol↗
PubMed2025

The NmpRSTU multi-component signaling system of Myxococcus xanthus regulates expression of an oxygen utilization regulon.

UNLABELLED: Myxococcus xanthus has numerous two-component signaling systems (TCSs), many of which regulate the complex social behaviors of this soil bacterium. A subset of TCSs consists of NtrC-like response regulators (RRs) and their cognate histidine sensor kinases (SKs). We have previously demonstrated that a multi-component, phosphorelay TCS named NmpRSTU plays a role in M. xanthus social motility. NmpRSTU was discovered through a screen that identified mutations in nmp genes that restored Type-IV pili-dependent motility to a nonmotile strain. The Nmp pathway begins with the SK NmpU, which is predicted to be active in the presence of oxygen. NmpU phosphorylates another SK, NmpS, a hybrid kinase containing an RR domain and a HisKA-CA domain. These two kinases work in a reciprocal fashion: when NmpU is active, NmpS is inactive, and vice versa. Finally, the phosphorelay culminates in NmpS phosphorylating the NtrC-like RR NmpR. To better understand the role of NmpRSTU in M. xanthus physiology, we determined the NmpR regulon by combining in silico predictions of the NmpR consensus binding sequence with in vitro electromobility shift assays (EMSAs) and in vivo transcriptional reporters. We identified several NmpR-dependent, upregulated genes likely to be important in oxygen utilization. Additionally, we demonstrate NmpRSTU plays a role in fruiting body development, suggesting a role for oxygen sensing in this behavior. We propose that NmpRSTU senses oxygen-limiting conditions, and NmpR upregulates genes associated with optimal utilization of that oxygen. This may be necessary for M. xanthus physiology and behaviors in the highly dynamic soil where oxygen concentrations vary dramatically. IMPORTANCE: Bacteria use two-component signaling systems (TCSs) to respond to a multitude of environmental signals and subsequently regulate complex cellular physiology and behaviors. Myxococcus xanthus is a ubiquitous soil bacterium that encodes numerous two-component systems to respond to the conditions of its soil environment and coordinate multicellular behaviors such as coordinated motility, microbial predation, fruiting body development, and sporulation. To better understand how this bacterium uses a two-component system that has been linked to the sensing of oxygen concentrations, NmpRSTU, we determined the gene regulatory network of this system. We identified several genes regulated by NmpR that are likely important in oxygen utilization and for the M. xanthus response to varied oxygen concentrations in the dynamic soil environment.

Myxococcus xanthus↗
PubMed2026

The TANG cluster comprising ten nitrate transporter genes controls fruit sweetness and size in tomato.

Sucrose is a major transport form of photoassimilated carbon in tomato, Arabidopsis, and many other plant species, and plays a critical regulatory role in plant growth, development, and fruit quality. Plant vacuoles function as storage organelles, accumulating substantial quantities of metabolically inactive nitrates as a nitrogen reserve and soluble sugars as a carbon reserve. Consequently, the balance between nitrate and sucrose accumulation determines plant growth dynamics and fruit taste. In this study, we identified a gene cluster designated TANG (Total soluble solidsAccumulation viaNitrate transporterGene cluster), comprising ten nitrate transporter genes that are significantly associated with sucrose accumulation in tomato. This gene cluster mediates the transport of nitrate between the cytoplasm and vacuole, thereby influencing its storage. Functional disruption of TANG8, a member of the gene cluster, results in either enhanced sugar accumulation or increased fruit size. Selective disruption of multiple TANG cluster members yields fruits with elevated sweetness and increased fruit size in S. pimpinellifolium. The interaction between the TANG members and a tonoplast localized Sucrose Transporter 4 provides insight into the competitive accumulation of nitrate and sugar. The multiplex editing of a gene cluster provides a successful example of engineering crops with high quality and yield.

Gene cluster↗
PubMed1978

Light-stimulated morphogenesis in the fruiting myxobacterium Stigmatella aurantiaca.

When the fruiting myxobacterium Stigmatella aurantiaca, a gliding prokaryote, is starved on an agar surface, the cells form multicellular aggregates resulting from morphogenetic movements. In the presence of incandescent light, each aggregate develops into a structurally complex fruiting body, possessing a stalk and several sporangia. In contrast, this pattern of development is not seen when cultures are incubated in the dark. The cells form irregular interconnecting aggregates, which rarely develop into fruits. However, aggregates formed in the light will develop into fruits even if placed in the dark, suggesting that the light produced a relatively stable alteration in the phenotype of the cells.

Light↗
PubMed2025

N-glycan remodeling by α-D-mannosidase and β-D-N-acetylhexosaminidase regulates fruit softening, redox balance, and post-harvest pathogen resistance.

Post-harvest loss of fruits and vegetables poses significant challenges to food security and economic sustainability, primarily due to ripening-associated excessive softening that shortens shelf life and increases susceptibility to pathogens. N-glycans, N-glycoproteins, and their processing enzymes are integral to various plant processes, including fruit ripening. Among these, α-D-mannosidase (α-Man) and β-D-N-acetylhexosaminidase (β-Hex) are key ripening-specific enzymes that modulate fruit softening. Previously, we have shown that RNAi-mediated suppression of α-Man or β-Hex improves fruit shelf life and firmness in both climacteric and non-climacteric fruits. However, the underlying molecular and biochemical basis of fruit softening regulation by α-Man and β-Hex was not well understood. In this study, we developed transgenic tomato (Solanum lycopersicum) plants by silencing α-Man and β-Hex simultaneously using RNAi. Suppression of these enzymes reduces N-glycoprotein degradation, downregulates pectin dissolution, and inhibits ripening-related gene expression. RNAi fruits exhibited enhanced shelf life, greater firmness, reduced reactive oxygen species (ROS) accumulation and increased resistance against post-harvest pathogens without affecting plant growth, fruit development, yield, or nutritional quality. To further explore the molecular mechanism of α-Man and β-Hex function, we purified and quantified N-glycans in RNAi fruits and other ripening-impaired mutants, identifying key N-glycan species. We also carried out iTRAQ-based quantitative proteome profiling to investigate the abundance of proteins in ripened fruit affected by silencing of α-Man and β-Hex. Molecular insights revealed that N-glycan processing and degradation are key events during ripening, influencing cell wall softening, fruit redox state, and post-harvest quality attributes. This study highlights the potential of co-silencing α-Man and β-Hex as a novel approach to extending the shelf life of fruits, regardless of their climacteric behavior, without compromising quality or yield.

Fruit↗
PubMed2026

Efficient genome editing in tomato using Cas12i3 variants.

Systematic comparison of Cas12i gene-editing tools in tomato identifies Cas-SF01 as the most efficient variant, achieving editing efficiencies comparable to conventional Cas9 at some genomic sites and providing a compact, highly specific, and versatile tool for studying gene function, engineering fruit metabolism, and developing improved tomato varieties through precision breeding.

Journal Article↗
PubMed2025

Charting the development and engineering of CRISPR base editors: lessons and inspirations.

CRISPR base editors (BEs) have introduced a new chapter in precise genome editing. The brief but fruitful history of BE development documents many case studies that not only lay the foundation of base-editing technology but are also instrumental to future protein engineering efforts. In this review, we summarize the development and engineering of various BEs with a focus on recent progress. These include traditional cytosine and adenine base editors (CBEs and ABEs), novel TadA-derived CBEs, transversion BEs, dual BEs, and CRISPR-free BEs. We discuss each aspect of the workflow and highlight the successes and challenges encountered in the engineering process.

Gene Editing↗