Functional & Integrative Genomics最新文献

Small peptides (SPs) are critical signaling molecules that regulate a wide array of biological processes in plants, including growth, development, and immune responses. However, their specific roles in the interaction between citrus and Candidatus Liberibacter asiaticus (CLas), the causal agent of the devastating huanglongbing (HLB) disease, remain largely unexplored. This study presents a comprehensive genome-wide identification and characterization of SPs in Citrus sinensis. We identified 5,854 transcripts encoding SPs, constituting 11.81% of the total annotated transcripts. Through comparative transcriptome analysis, we identified 422 SPs that were differentially expressed upon CLas infection, with 217 being up-regulated and 205 down-regulated. Bioinformatic analyses revealed that these responsive SPs are involved in key biological processes such as hormone signaling, plant-pathogen interaction, and immune response activation. A focused screen for small secretory peptides (SSPs) among the up-regulated SPs led to the identification of several members of the Phytosulfokine (PSK) family, including CsPSK1, CsPSK2, and CsPSK4, as prominent HLB-responsive candidates. We experimentally validated that these CsPSKs are secreted into the apoplast, a critical interface for plant-pathogen interactions. Functional characterization through virus-induced gene silencing (VIGS) of the PSK homolog in Nicotiana benthamiana resulted in compromised resistance to Pseudomonas syringae. Conversely, transient overexpression of CsPSK1, CsPSK2, and CsPSK4 in C. sinensis significantly enhanced resistance to Xanthomonas citri subsp. citri (Xcc). These findings collectively demonstrate that CsPSKs are positive regulators of plant immunity and play a conserved role in defense against bacterial pathogens. Furthermore, this research provides insights into the molecular functions of SPs in citrus defense and identifies CsPSKs as potential targets for further investigation in HLB management.

One of the most prevalent malignant tumors in the male genitourinary system is prostate cancer (PCa). The health of men is seriously threatened by the lack of appropriate treatment options for advanced prostate cancer. As E3 ubiquitin ligases, the TRIM family is essential for the development and spread of tumors. Of them, TRIM27 plays a crucial role as a fundamental member of the TRIM family. The tumor immune microenvironment was closely linked to high expression of TRIM27, which was found to be an independent risk factor for a poor prognosis in PCa. Additional in vitro tests verified that TRIM27 stimulates the growth of tumors by controlling the expression of CANX by ubiquitination through triggering the PI3K/AKT signaling pathway. In the meantime, we used several transcription factor databases to find the transcription factor MYC, which can bind to the TRIM27 promoter region and increase its expression, in order to investigate the upstream regulators of TRIM27. In conclusion, our results show that MYC-regulated TRIM27 upregulation influences cancer development through CANX, offering new therapeutic targets and avenues for investigation in the detection and management of PCa.

The larvae of Hyphantria cunea are highly polyphagous, infesting a wide range of host plants, including fruit trees, ornamental species, and agroforestry crops. In this study, we evaluated the insect resistance of 10 transgenic poplar lines (B1-B10) co-expressing the Cry1Ac and SCK genes. Results showed that the mortality rate of H. cunea larvae fed on leaves from these transgenic lines was significantly higher than that of larvae fed on wild-type leaves. Notably, the expression levels of the Cry1Ac and SCK genes varied among the different transgenic lines. To further investigate whether the Cry1Ac + SCK transgenic lines alter internal gene expression and metabolic profiles in poplar, we conducted transcriptomic and metabolomic analyses. Transcriptome analysis revealed that the B5 transgenic line, which demonstrated high insect resistance, exhibited the greatest number of differentially expressed genes (DEGs). These DEGs were primarily enriched in pathways related to lipid and membrane metabolism, flavonoid biosynthesis, and plant hormone signal transduction. Metabolome analysis indicated that the differentially accumulated metabolites (DAMs) in the B5 line were largely associated with plant hormone signal transduction and secondary metabolic pathways. Significantly, integrated multi-omics analyses highlighted substantial enrichment in both plant hormone signal transduction and flavonoid biosynthesis pathways. This study systematically identifies key metabolic pathways and defense-related genes in Cry1Ac + SCK transgenic poplars, providing a theoretical foundation for developing next-generation insect-resistant trees through targeted genetic engineering.

Climate change, rising global food demand, and shrinking resources require transformative innovations in crop breeding. This review outlines recent advances in new breeding technologies (NBTs), including molecular markers, genome-wide association studies (GWAS), genomic selection (GS), next-generation sequencing (NGS), and gene editing (GE) tools such as the clustered regularly interspaced short palindromic repeat (CRISPR/Cas), base editing, and prime editing. These methods enable the accurate improvement of traits, thereby accelerating the development of crops resistant to both abiotic and biotic stresses. The integration of multi-omics platforms, including genomics, transcriptomics, proteomics, metabolomics, and phenomics, provides a comprehensive framework for deciphering and manipulating complex trait architectures. Artificial intelligence (AI) and machine learning (ML) enhance precision breeding by providing data-driven insights and enabling the forecasting of traits. Emphasis is also placed on combining gene editing with other strategies, such as speed breeding, to accelerate the development of traits. This review underscores the importance of an integrated systems biology approach that combines multi-omics, gene editing, AI, and speed breeding to accelerate the development of climate-resilient, high-yielding, and nutritionally enhanced crops. The integration of these innovative technologies holds great promise for addressing global food security, environmental sustainability, and agricultural resilience in the face of climate change. A strategic framework for the future of plant breeding is outlined, emphasizing the importance of interdisciplinary collaboration in building a sustainable agricultural future.

The global rise of antimicrobial resistance has intensified the demand for novel antimicrobial agents with broad-spectrum efficacy and unique mechanisms of action. Herein, a marine-derived strain, Bacillus velezensis (B. velezensis) AM12, exhibiting clear inhibitory activity against eight major foodborne pathogens, was isolated from coastal seawater near Zhanjiang, China. Whole-genome sequencing revealed a 3,992,266 bp circular chromosome with a GC content of 46%, and functional annotation indicated extensive metabolic potential. Genome mining using the antiSMASH platform identified 14 secondary metabolite biosynthetic gene clusters, including those encoding surfactin, macrolactin H, bacillaene, fengycin, difficidin, bacillibactin, and bacilysin, as well as several additional clusters potentially responsible for the biosynthesis of novel antimicrobial compounds. Analysis using the BAGEL4 database further detected four bacteriocin/RiPP biosynthetic loci, corresponding to Competence/ComX, Amylocyclicin, LCI, and a Lichenicidin-like cluster. These collectively explain the broad-spectrum antibacterial activity of AM12 and suggest potential antifungal capability. Notably, the core genes of ComX and LCI exhibited relatively low similarity (46.67% and 73.91%, respectively) to known references, and B. velezensis AM12-origin lichenicidin component 2 showed no detectable homology, suggesting that AM12 may encode structurally and functionally distinct novel bacteriocins. Comparative genomic analysis with closely related terrestrial B. velezensis strains revealed that AM12-specific genes are predominantly enriched in functions associated with marine environmental adaptation and antimicrobial activity. Furthermore, machine learning-based prediction using the AM12-specific gene set identified seven high-confidence antimicrobial peptide candidates characterized by cationic charge, amphipathicity, and structural stability. This study elucidates the genomic and molecular basis of the broad-spectrum antibacterial activity pertaining to B. velezensis AM12, and establishes a systematic framework for the identification of novel antimicrobial peptides, offering candidate genes for subsequent functional characterization.

Arrhythmogenic right ventricular cardiomyopathy (ARVC; OMIM #609040) is an inherited cardiomyopathy characterized by juvenile sudden cardiac death (SCD), with > 40% of familial cases driven by PLAKOPHILIN 2 (PKP2; OMIM #602861) mutations. This study reports a Chinese ARVC family with neonatal severe early-onset phenotype caused by novel compound heterozygous PKP2 mutations that exhibiting cosegregation with biallelic mutations (while heterozygous carriers remained asymptomatic), and aims to elucidate the synergistic pathogenic mechanisms and clinical implications. Mutations were identified via whole-genome sequencing and familial cosegregation analysis. Pathogenicity was predicted using SpliceAI and MutationTaster. MiniGene splicing assays and RT-PCR validated aberrant splicing. We analyzed subcellular protein localization by immunofluorescence microscopy and assessed protein stability via cycloheximide chase (CHX). The proband carried a maternally inherited novel splice-site variant (PKP2: c.224–3 C > G) and a paternally inherited frameshift deletion (PKP2: c.1125_1132del). Functional validation demonstrated: (a) c.224–3 C > G caused exon 2 skipping (deletion rate > 90%), generating a truncated protein (p.Asn76Trpfs*7); (b) c.1125_1132del induced frameshift (p.Phe376Alafs*8) without altering splicing. The mutant protein exhibited unchanged half-life but aberrant nuclear aggregation (immunofluorescence-confirmed). This study first confirms that compound heterozygous PKP2 mutations cause severe early-onset ARVC through biallelic inactivation: the maternal splice variant (c.224–3 C > G) truncates the protein, ablating all functional domains, while the paternal frameshift mutation (c.1125_1132del) mislocalizes the protein to the nucleus. Both defects synergistically disrupt desmosomal integrity in cardiomyocytes. These findings expand the PKP2-associated genotype-phenotype spectrum and provide molecular basis for prenatal diagnosis and genetic counseling in high-risk families.

Over the last couple of decades, tremendous progress has been made in legume genomics. Genomics information generated for legume crops is being explored through molecular breeding and transgenic approaches. However, the gap between knowledge generation and its utilization is increasing. In this regard, recent developments in genome editing techniques provide an excellent opportunity to utilize the available knowledge for the improvement of legume crops. This review highlights recent developments with Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-based genome-editing approaches, including Cas variants/orthologs and Protospacer adjacent motif-less (PAMless) Genome Editing, multiplex genome editing, base editing, prime editing, transcriptional regulation, methylome editing, and DNA-free editing methods. Furthermore, the applications of non-homologous end joining (NHEJ) and homology-directed repair (HDR)- based editing, are addressed which enable targeted and precise genomic modifications. Moreover, virus-mediated genome editing, in planta transformation, and mobile guide RNAs are increasingly being leveraged to enhance the efficiency and heritability of genome editing. Additionally, the role of artificial intelligence in guide RNA design, off-target prediction, and the development of novel Cas variants is also discussed, which can speed up the legume improvement. This article highlights the successful examples of efforts utilizing CRISPR/Cas9 for the development of legume crops with biotic and abiotic stress tolerance, desirable plant architecture, improved nutrient uptake, and enhanced yield and quality. The biggest limitation in the genome editing of legume crops is their recalcitrance to both transformation and tissue culture. This article discusses how this particular limitation can be addressed in the context of genome editing of legume crops. Finally, the possibilities of integrating these recently developed tools with translational breeding have also been discussed, which will facilitate the legume production for sustainable agriculture and food security.

Climate change poses more challenges to the productivity of cotton because of the increasing influence of Abiotic stresses like drought, salinity, heat, cold, and heavy metal toxicity. Complex, polygenic, and linkage drag challenge the conventional breeding of stress tolerance. The development of molecular biology and biotechnology has helped to explain the regulatory and signaling network in abiotic stress responses in cotton. It is a review of the existing information on the perception of stress, signal transduction and adaptive responses in cotton with the primary emphasis on the main pathways such as calcium signaling, reactive oxygen species (ROS) dynamics, abscisic acid (ABA)-mediated responses, mitogen-activated protein kinase (MAPK), and hormone-regulated networks that facilitate cellular homeostasis to stress. Gene regulation under stress by the crucial functions of transcription factors like DREB, NAC, MYB, bZIP, and WRKY is discussed. New epigenetic changes, such as m6A RNA methylation and non-coding RNAs, are being discussed as important factors in gene expression. We also mention the most recent genetic engineering, genome editing, omics and synthetic biology approaches that explain the stress response networks and enhance the resilience of cotton. The combination of these molecular and biotechnological solutions gives a platform on which model dynamic regulatory circuits are to be constructed to enhance cotton tolerance in promoting sustainable crop enhancement.

Leaves, the primary photosynthetic organ in plants, provide critical insights into the genetic and epigenetic mechanisms underlying heterosis. This study systematically investigated the leaf phenotypic characteristics, gene expression profiles, and epigenetic regulation through methylation patterns, miRNAs and lncRNAs in two contrasting cotton hybrids, thereby establishing a novel multi-omics framework for heterosis analysis. Our primary innovation is the elucidation of expression level dominance (ELD) and its differential influence on heterotic performance. The Z41S hybrids display superior phenotypic heterosis, which correlates with heightened over-dominant (OD), under-dominant (UD), and paternal expressions (ELD-P). In contrast, the B985S hybrids are characterized by a predominance of maternal expression patterns (ELD-M). We identified CHH-type methylation variations as the major epigenetic regulators influencing dominant gene expression across both hybrids. Differentially methylated regions (DMRs), similarly methylated regions (SMRs), and transposable element distributions significantly impacted heterosis-related gene regulation, particularly through gene body modifications. Furthermore, the joint analysis of multi-omics data revealed that, nine genes including serine/threonine-protein kinase gene, zinc finger BED domain-containing protein RICESLEEPER 3/2, protein tyrosine kinase myosin-6 (Myh6), AGO2, RGA3, LRR and NB-ARC, subjected to multiple epigenetic regulation by miRNAs, lncRNAs, or DNA methylation, are poised to play a pivotal role in the manifestation of strong heterosis in cotton hybrids. These findings establish three fundamental contributions: (1) a comprehensive model integrating genomic and epigenetic regulation of cotton heterosis, (2) identification of parent-specific ELD patterns as molecular predictors of hybrid performance, and (3) characterization of CHH methylation as a critical epigenetic determinant in heterosis manifestation. Our results provide a transformative theoretical framework for optimizing hybrid breeding strategies through targeted manipulation of both genetic and epigenetic factors.

Alternaria alternata is a necrotrophic fungal pathogen with a wide host range, and the black spot disease it causes on Rosa hybrida is the most serious disease, severely limiting the normal growth of Rose. However, the mechanism of this effect in Rose is not fully understood. A resistant cultivar (‘DK’) and a susceptible cultivar (‘OB’) of Rose were selected and a combined physiological, transcriptomic and metabolomic approach was used to investigate the molecular mechanisms of plant resistance to A. alternata. In this study, we found that SOD and PAL levels of Rose increased significantly after A. alternata infection, and the changes were more pronounced in the ‘DK’. Kyoto Encyclopedia of the Genome (KEGG) enrichment analyses showed that differentially expressed genes (DEGs) after A. alternata infestation were enriched in plant-pathogen interaction, plant hormone signal transduction, and metabolic pathways. Two-Way Orthogonal PLS (O2PLS) analysis revealed that flavonoids and phenolic acids had the greatest effect on DEGs. Weighted gene co-expression network analysis (WGCNA) and CCA analyses further demonstrated significant correlations between flavonoid pathways and DEGs. Among the highly correlated transcription factors screened in the green module (WRKY, ERF, NAC) may be involved in flavonoid pathway-mediated resistance to black spot disease in Rose. This study provides a potential transcriptional regulatory network and thus candidate genes for resistance breeding and metabolic engineering in Rose.