The mechanisms driving rapid plant diversification-often referred to as Darwin's "abominable mystery"-remain a central question in evolutionary biology. Elucidating the genomic basis of rapid speciation and morphological innovation, such as those observed in the Brassicaceae, not only addresses fundamental evolutionary questions but also provides valuable insights for crop improvement. Recent advances in telomere-totelomere genome assembly and graph-based pangenomics have enabled systematic dissection of these processes. Here, we highlight a recent study that uses Brassica rapa-a species that has radiated into a 'kingdom' of subspecies and vegetable crops within millennia-as a model to decode rapid diversification at the genomic level. By integrating 11 complete genomes with resequencing data from 1720 accessions, the study reveals how centromere remodeling driven by young satellite arrays, widespread structural variants (SVs) linked to subspecies-specific traits, and mutation of a single gene (BrLH1), which dominantly controls leafy head formation in Chinese cabbage (B. rapa ssp. pekinensis), collectively contributed to diversification. The work proposes an integrated SV-gene-centromere coevolution model, offering a new framework for understanding rapid radiation in plants. Beyond evolutionary insights, the study provides a high-resolution pangenome that will accelerate precision breeding in B. rapa, demonstrating how cutting-edge genomics can bridge evolutionary research and agricultural innovation.

Transcriptional regulation involves complex and dynamic protein-DNA interactions, which alter chromatin states and, consequently, regulate gene expression. In plants, current technologies face challenges in efficiently capturing dynamically DNA-binding proteins, especially transcription factors. Here, by leveraging the binding ability of dead Cas9 to specific DNA fragments and the labelling capacity of the TurboID protein for adjacent proteins, we have developed a CRISPR-based sequence proximity binding protein labelling system (CSPL) to detect promoter-binding proteins. Using this approach, we identified both known and novel upstream binding proteins on the PIF4 promoter in Arabidopsis, cabbage and rice. This demonstrates the powerful capabilities and broad potential applications of CSPL for detecting promoter-binding proteins in plants.

Background/Objectives: Pepper (Capsicum annuum L.) is a widely grown vegetable and spice crop worldwide. This study aims to reveal the differences of metabolites among pepper accessions from different regions and explore candidate genes related to metabolites of pepper. Methods: The metabolome and transcriptome of 36 pepper accessions were determined by widely targeted metabolomics analysis and RNA sequencing technology, and the differential metabolites and differential genes among C. annuum from four important pepper production and consumption provinces of China, Hunan, Guizhou, Yunnan and Sichuan, were analyzed. Results: Flavonoids are the main characteristic metabolites that distinguish pepper accessions from Yun_Gui_Chuan Group and Hunan Group. The aglycones of characteristic flavonoids in each group are different; in Yun_Gui_Chuan Group mainly are luteolin, quercetin, chrysoeriol and isorhamnetin; in Hunan Group mainly are apigenin. Transcriptome data showed that two genes related to flavonoid 3′-monooxygenase differed significantly between the two groups of chili peppers, and we speculated that they may be the core enzymes regulating their flavonoid profile. And an SNP mutation located in gene Cgla06g001871 showed a strong correlation with pepper accessions from Yun_Gui_Chuan Group, which can be used as a DNA marker to identify pepper accessions from Yun_Gui_Chuan Group, and provide strong support for regional specialty variety conservation. In addition, we also analyzed the metabolites related to the taste and nutrition of pepper accessions in the four provinces, and the results showed that the sugar content of pepper accessions from Guizhou was low and the capsaicinoids content of pepper accessions from Sichuan was low, while no significant difference was found in acid and vitamin contents among pepper accessions from the four provinces. Conclusions: The metabolome and transcriptome of 36 pepper accessions from four important pepper production and consumption provinces of China were determined, and the characteristic metabolites and expressed genes of pepper accessions from each province were analyzed.

With the rapid development of high-throughput sequencing technologies and the accumulation of large-scale multi-omics data, deep learning (DL) has emerged as a powerful tool to solve complex biological problems, with particular promise in plant genomics. This review systematically examines the progress of DL applications in DNA, RNA, and protein sequence analysis, covering key tasks such as gene regulatory element identification, gene function annotation, and protein structure prediction, and highlighting how these DL applications illuminate research of plants, including horticultural plants. We evaluate the advantages of different neural network architectures and their applications in different biology studies, as well as the development of large language models (LLMs) in genomic modelling, such as the plant-specific models PDLLMs and AgroNT. We also briefly introduce the general workflow of the basic DL model for plant genomics study. While DL has significantly improved prediction accuracy in plant genomics, its broader application remains constrained by several challenges, including the limited availability of well-annotated data, computational capacity, innovative model architectures adapted to plant genomes, and model interpretability. Future advances will require interdisciplinary collaborations to develop DL applications for intelligent plant genomic research frameworks with broader applicability.

The Solanaceae family, which includes key crops such as tomato, pepper, eggplant, wolfberry, and groundcherry, is distinguished by its diversity of fruit types. However, the conservation of gene expression regulatory networks across different species remains poorly understood. This study utilizes comparative transcriptomics to analyze 293 transcriptome samples from 22 Solanaceae species, focusing on the expression profiles of reproductive organ (flower and fruit)-specific genes. Our results reveal evolutionary conservation in the expression patterns of these genes, particularly within regulatory pathways essential for plant reproduction. A detailed comparative analysis of gene expression patterns between tomato and pepper reveals common regulatory networks governing fruit development. Furthermore, through co-expression network analysis, we identified functional partners of YABBY in flower/fruit development and found that YABBY genes coordinate fruit development through spatiotemporal dynamic expression, shaping its regulatory role. These findings provide valuable insights that can guide future research on fruit development genes in Solanaceae species.

Pepper (Capsicum spp.) is a widely consumed vegetable with exceptionally large genomes in Solanaceae, yet its genomic evolutionary history remains largely unknown. Here we present 11 high-quality Capsicum genome assemblies, including two gap-free genomes, covering four wild and all five domesticated pepper species. We reconstructed the ancestral karyotype and inferred the evolutionary trajectory of peppers. The expanded and variable genome sizes were attributed to differential transposable element accumulations, which shaped 3D chromatin architecture and introduced mutations associated with traits such as fruit orientation and colour. Using a chromatin accessibility atlas of Capsicum, we highlight the influence of transposable elements on regulatory element evolution. Furthermore, by constructing a haploblock map of 124 pepper core germplasms, we uncover frequent introgressions that facilitate the formation of sweet blocky pepper and the acquisition of important traits such as resistance to pepper mild mottle virus. These findings on the genomic and functional evolution of Capsicum will benefit pepper breeding. This study presents 11 telomere-to-telomere genomes of wild and domesticated pepper, highlights how transposable elements have shaped the evolution of genome structure and regulatory elements and identifies structural variations and introgressions associated with key traits in cultivated pepper.

Pepper (Capsicum spp.), one of the world's most important vegetable and spice crops, has attracted considerable attention due to its phenotypic diversity, abundant secondary metabolites (particularly capsaicinoids), and substantial economic value. However, current research on the genetic basis and key regulatory genes underlying most traits in pepper is limited. Therefore, in this study, we used two parental lines that presented multiple phenotypic differences-namely, BVRC1 and BVRC25-to generate a recombinant inbred line (RIL) population (F10 generation, 216 lines), after which we performed whole-genome re-sequencing on all lines. Based on a high-resolution bin map, 19 significant loci were identified in association with 13 traits, explaining an average of 26% of the phenotypic variance in the RILs. On the basis of uncovering the major effect locus FL-3.2 (FS-3.1) for fruit shape/fruit length, we constructed new genetic populations to finely map and clone a novel minor-effect regulatory locus FL-10.1 for fruit length. Candidate gene CaSUN29 encoded an IQD protein that was specifically expressed in the early stage of fruit development, affected cell expansion in the pepper pericarp, and subsequently impacted fruit elongation. Virus-induced gene silencing of CaSUN29 in pepper resulted in shorter fruit, while heterologous CaSUN29 overexpression in tomato led to longer fruit. In contrast to the pleiotropic locus FL-3.2, which regulated fruit length, width, and shape simultaneously, FL-10.1 only regulated fruit length. Based on the identified loci, a trait-locus network was constructed to understand the correlations among traits based on the degree of locus linkage. These findings are helpful for our exploration of new genes regulating important traits, providing better understanding of the linkage relationships among complex traits.

White lupin exhibits remarkable adaptability to phosphorus (P)-deficient soil through the development of cluster roots (CR), thereby enhancing P use sufficiency. Despite its crucial role, the underlying mechanism governing CR formation remains elusive. Here, we reveal an elevated DNA methylation level through whole-genome bisulfite sequencing in CR in response to P deficiency, particularly in gene and flanking regions, suggesting a responsive epigenetic mechanism. To further investigate the potential involvement of epigenetic remodelling, we treated lupin plants with the DNA methyltransferase (DNMT) inhibitor 5-azacytidine, which led to a disruption of total DNMT activity and impaired CR formation under phosphorus-deficient conditions. Integrated analysis of methylome and RNA-Seq highlights the methylation of CAFFEIC ACID O-METHYLTRANSFERASE 1 (COMT1), a key enzyme in melatonin synthesis, as pivotal for promoting CR formation in white lupin. Functional validation through overexpression or gene silencing of LaCOMT1 in transgenic lupin roots confirms the positive impact of LaCOMT1 on CR formation. Furthermore, melatonin application directly increases CR numbers, indicating the role of methylation-activated LaCOMT1 in promoting CR formation via melatonin synthesis. Those findings provide insights into the epigenomic landscape of white lupin, establishing a direct genetic link between epigenetic mechanisms and P-deficiency-induced CR formation.

BACKGROUND:Acute gouty arthritis is a metabolic disease characterized by hyperuricemia, with acute attacks involving neutrophil-released NETs activating immune responses through their major component, DNA, as danger-associated molecular patterns (DAMPs). OBJECTIVE:To investigate whether DNA from NETs activates the AIM2 inflammasome in synovial fibroblasts during acute gouty arthritis attacks, inducing pyroptosis and exacerbating inflammation. METHODS:The AIM2 gene knockdown mouse model of acute gouty arthritis was constructed, the joint pathological changes were observed by H&E staining, the synovium fibroblasts and neutrophils were sorted by flow cytometry, and the expressions of AIM2, Caspase-1 and GSDMD related proteins were detected by Western blot. The levels of TNF-α, IL-6, IL-1β and IL-18 in serum and cell supernatant were detected by ELISA. Neutrophils were induced to release NETs by urate, and NETs markers (dsDNA, MPO-DNA, NE-DNA) were detected by immunofluorescence (Cit-H3, PAD4) and ELISA. NETs media were co-cultured with synovial fibroblasts, cell activity and migration were evaluated by CCK8 and scrape assay, markers of synovitis (Thy1, VCAM-1, PDPN) were detected by immunofluorescence, and pyroptosis was evaluated by TUNEL and LDH release. By silencing or overexpression of AIM2 gene, Western blot and ELISA, the role of AIM2 in NETs induced pyrodeath and inflammatory response was investigated. RESULTS:AIM2 gene knockdown significantly alleviated the symptoms of MSU-induced acute gouty arthritis in mice, reducing joint swelling and pathological damage. Expression levels of inflammatory factors (TNF-α, IL-6, IL-1β, IL-18) and cleaved Caspase-1/Caspase-1, GSDMD-NT/GSDMD) were decreased. It was found that neutrophils released NETs in response to sodium urate stimulation, manifested by significant upregulation of Cit-H3 and PAD4, as well as increased dsDNA, MPO-DNA, and NE-DNA complexes. NETs can induce inflammatory response in synovial fibroblasts, which is manifested as decreased cell activity and migration ability, increased release of inflammatory factors, and significantly increased markers of synovitis (Thy1, VCAM-1, PDPN). In addition, NETs induce scorch death of synovium fibroblasts by activating AIM2 inflammatories, which aggravates the inflammatory response, and AIM2 gene knockdown can effectively inhibit the scorch death and inflammatory response induced by NETs, indicating that NETs play a key role in the occurrence and development of gout arthritis through AIM2-mediated scorch death of synovium fibroblasts. CONCLUSION:NETs-activated AIM2-mediated synovial fibroblast pyroptosis plays a crucial role in acute gouty arthritis, providing a new therapeutic target.

Cytosine DNA methylation (5mCs) is an important epigenetic modification in genomic research. However, the methylation states of some cytosine sites are not available due to the limitations of different studies, and there are few tools developed to deal with this problem, especially in plants, which have more methylation types than animals. Here, we report PlantDeepMeth, a novel deep learning model that utilizes deep learning to predict DNA methylation states in plants. The evaluation of PlantDeepMeth on known cytosine sites in both the Brassica rapa and Arabidopsis thaliana genomes shows good performance in predicting methylation states, indicating that the tool is good at learning patterns for methylation imputation. Motif analysis of the model’s predictions identified specific motifs associated with hypo- or hyper-methylation states in B. rapa and A. thaliana, further revealing key regulatory patterns captured by the model. Moreover, cross-species validation between B. rapa and A. thaliana demonstrated the generalizability of PlantDeepMeth, with the model maintaining high performance across different plant species. These results highlight the effectiveness of PlantDeepMeth and demonstrate the potential of deep learning to advance plant genomics research.

Background: Pepper (Capsicum annuum L.) is a widely cultivated vegetable crop worldwide, with its rich fruit colors providing unique visual traits and economic value. This study investigated the genetic basis of the immature green fruit color by constructing a F2 segregating population derived from a cross between yellow fruit C20 and green fruit C62 parent lines. Methods: Bulked segregant analysis sequencing (BSA-seq) was performed to identify genomic regions associated with fruit color. Candidate genes were pinpointed through functional annotation and genetic variation analysis, supported by SNP markers, genotype analysis, and transcriptome profiling. Results: Two genomic regions associated with fruit color were identified on chromosomes 1 (14.55-20.85 Mb) and 10 (10.15-22.85 Mb), corresponding to previously reported loci pc1 and pc10.1. Two chlorophyll synthesis-related genes, CaAPRR2 and CaGLK2, were identified as candidate regulators of fruit color. Mutations in these genes include a premature stop codon in both CaGLK2 and CaAPRR2. The mutation of CaAPRR2 and CaGLK2 jointly regulate the yellow fruit trait in pepper, with CaGLK2 being the major gene and CaAPRR2 being the minor gene. Transcriptome analysis showed that the expression levels of the two genes increased during the green ripening stage of the parent fruits, with higher expression levels of CaGLK2. Conclusions: This study identifies CaGLK2 and CaAPRR2 as key regulators of immature green fruit color in pepper, with CaGLK2 playing a predominant role. These findings provide a theoretical foundation and data support for elucidating the molecular regulatory mechanisms of fruit color and advancing marker-assisted breeding in pepper.

Genetic degeneration is a striking feature of Y chromosomes, often involving losses of many genes carried on the X chromosome. However, the time course of gene losses remains unclear. Sex chromosomes of plants evolved more recently than animals' highly degenerated ones, making them ideal for studying degeneration timing. To investigate Spinacia sex chromosome evolution and the time course of degeneration, we compared genome sequences of cultivated Spinacia oleracea, with a small Y-linked region on Chr4, with its two wild relatives. In spinach and its closest relative Spinacia turkestanica, the Y duplication region (YDR) introduced a male-determining factor into Chr4's low-recombining pericentromeric region. In other words, a turnover event occurred in these species' recent common ancestor. The homologous Chr4 of the more distantly related S. tetrandra has a c. 133 Mb completely sex-linked and partially degenerated region, possibly reflecting the ancestral state. Sequence divergence analysis suggests that two 'evolutionary strata' evolved shortly before the two Spinacia lineages split. Consistent with the turnover hypothesis, the YDR of the other two Spinacia species is not within the S. tetrandra older stratum. We discuss the unexpected findings in S. tetrandra that genetic degeneration, genomic rearrangements, and repetitive sequence density are all greatest in the younger stratum.

Quercetin glucosides are important phytopharmaceutical metabolites in Descurainia sophia seeds, which are widely used in traditional herbal medicine. However, the key genes involved in quercetin glucoside biosynthesis in D. sophia have not been characterized. Herein, we present the telomere-to-telomere genomes of a tetraploid D. sophia, which accumulates high levels of quercetin glucoside, and a diploid D. sophia, which accumulates only trace amounts. Multi-omics analyses and uridine diphosphate glucosyltransferase (UGT) enzyme assays revealed that the gene duplication and functional evolution of Dscd6AG01520, a UGT gene, led to high quercetin-3-O-β-D-glucoside and quercetin-3,7-O-β-D-diglucoside accumulation in tetraploid D. sophia seeds. Further UGT enzyme assays with the point mutations of Dscd6AG01520 showed that S213 was a critical amino acid for the enzymatic activity of Dscd6AG01520. In addition, we found that diploid D. sophia evolved from an ancestral crucifer karyotype through chromosome fusion and rearrangement. Collectively, our findings illuminate the mechanism of high quercetin glucoside accumulation in tetraploid D. sophia, clarify the origin of the diploid D. sophia genome, and provide valuable genomic resources for comparative genomics and research into polyploid evolution.

Cultivated spinach (Spinacia oleracea) is a dioecious species. We report high-quality genome sequences for its two closest wild relatives, Spinacia turkestanica and Spinacia tetrandra, which are also dioecious, and are used to study the genetics of spinach domestication. Using a combination of genomic approaches, we assembled genomes of both these species and analyzed them in comparison with the previously assembled S. oleracea genome. These species diverged c. 6.3 million years ago (Ma), while cultivated spinach split from S. turkestanica 0.8 Ma. In all three species, all six chromosomes include very large gene-poor, repeat-rich regions, which, in S. oleracea, are pericentromeric regions with very low recombination rates in both male and female genetic maps. We describe population genomic evidence that the similar regions in the wild species also recombine rarely. We characterized 282 structural variants (SVs) that have been selected during domestication. These regions include genes associated with leaf margin type and flowering time. We also describe evidence that the downy mildew resistance loci of cultivated spinach are derived from introgression from both wild spinach species. Collectively, this study reveals the genome architecture of spinach assemblies and highlights the importance of SVs during the domestication of cultivated spinach.

The meat production traits of pigs are influenced by the expression regulation of multiple gene types, including mRNAs, miRNAs, and lncRNAs. To study the differences in meat production traits at the transcriptional level among individuals with different growth rates, the longissimus dorsi samples from eight Duroc × Bama Xiang F2 crossbred pigs with a fast growth rate (high gTroup) or a slow growth rate (low group) were selected to perform whole transcriptome sequencing and ceRNA regulatory network construction. This study first analyzed the differences in physiological and biochemical indicators, muscle histological characteristics, and muscle fiber types. A total of 248 mRNAs, 25 miRNAs, and 432 lncRNAs were identified as differentially expressed by whole transcriptome sequencing. Key genes that may influence meat production traits include MTMR14, PPP1R3A, PYGM, PGAM2, MYH1, and MYH7. The ceRNA regulatory network map showed that ENSSSCG00000042061-ssc-mir-208b-MYH7, ENSSSCG00000042223-ssc-mir-146a-MTMR14, ENSSSCG00000045539-ssc-mir-9-3-MYH1, and ENSSSCG00000047852-ssc-mir-103-1-PPP1R3A may be the key factors affecting meat production traits through their regulatory relationships. This study provides valuable insights into the molecular mechanisms underlying porcine muscle development and can aid in improving meat production traits.

Polyploidization plays a crucial role in plant evolution and is becoming increasingly important in breeding. Structural variations and epigenomic repatterning have been observed in synthetic polyploidizations. However, the mechanisms underlying the occurrence and their effects on gene expression and phenotype remain unknown. Here, we investigated genome-wide large deletion/duplication regions (DelDups) and genomic methylation dynamics in leaf organs of progeny from the first eight generations of synthetic tetraploids derived from Chinese cabbage (Brassica rapa L. ssp. pekinensis) and cabbage (Brassica oleracea L. var. capitata). One- or two-copy DelDups, with a mean size of 5.70 Mb (400 kb to 65.85 Mb), occurred from the first generation of selfing and thereafter. The duplication of a fragment in one subgenome consistently coincided with the deletion of its syntenic fragment in the other subgenome, and vice versa, indicating that these DelDups were generated by homoeologous exchanges (HEs). Interestingly, the larger the genomic syntenic region, the higher the frequency of DelDups, further suggesting that the pairing of large homoeologous fragments is crucial for HEs. Moreover, we found that the active transcription of continuously distributed genes in local regions is positively associated with the occurrence of HE breakpoints. In addition, the expression of genes within DelDups exhibited a dosage effect, and plants with extra parental genomic fragments generally displayed phenotypes biased toward the corresponding parent. Genome-wide methylation fluctuated remarkably, which did not clearly affect gene expression on a large scale. Our findings provide insights into the early evolution of polyploid genomes, offering valuable knowledge for polyploidization-based breeding. A comprehensive multi-omics landscape across synthetic Brassica napus tetraploids reveals active transcription of homoeologous exchange-related genes.

Summary Structural variations (SVs) are major genetic variants that can be involved in the origin, adaptation and domestication of species. However, the identification and characterization of SVs in Spinacia species are rare due to the lack of a pan‐genome. Here, we report eight chromosome‐scale assemblies of cultivated spinach and its two wild species. After integration with five existing assemblies, we constructed a comprehensive Spinacia pan‐genome and identified 193 661 pan‐SVs, which were genotyped in 452 Spinacia accessions. Our pan‐SVs enabled genome‐wide association study identified signals associated with sex and clarified the evolutionary direction of spinach. Most sex‐linked SVs (86%) were biased to occur on the Y chromosome during the evolution of the sex‐linked region, resulting in reduced Y‐linked gene expression. The frequency of pan‐SVs among Spinacia accessions further illustrated the contribution of these SVs to domestication, such as bolting time and seed dormancy. Furthermore, compared with SNPs, pan‐SVs act as efficient variants in genomic selection (GS) because of their ability to capture missing heritability information and higher prediction accuracy. Overall, this study provides a valuable resource for spinach genomics and highlights the potential utility of pan‐SV in crop improvement and breeding programmes.