Genomics最新文献

Glutathione S-transferases (GSTs) constitute a multifunctional enzyme superfamily ubiquitous across diverse organisms, playing crucial roles in detoxification, antioxidant defense, and stress adaptation. Despite extensive studies in plants and mammals, systematic characterization of GSTs in teleosts, particularly in economically and ecologically significant species, remains limited. In this study, we performed a comprehensive genome-wide analysis of the GST gene family in the Plectropomus leopardus, a high-value aquaculture species vulnerable to environmental stressors such as thermal fluctuation. Through integrated bioinformatics approaches, we identified 24 GST genes unevenly distributed across 14 chromosomes, which were phylogenetically classified into 13 distinct subfamilies, with the MAPEG subfamily being the most abundant. Structural analyses revealed considerable diversity in gene architecture and conserved protein motifs, suggesting functional divergence among members. Expression profiling under controlled heat stress demonstrated tissue-specific upregulation of multiple GST genes in both liver and gill tissues, highlighting their active involvement in thermal response mechanisms. Furthermore, collinearity analysis indicated that segmental duplication events have contributed to the expansion of the GST family in P. leopardus, with strong evolutionary conservation observed among related fish species. Our findings not only provide a genomic foundation for understanding GST-mediated stress adaptation in marine teleosts but also offer potential candidate genes for future molecular breeding efforts aimed at enhancing thermotolerance in aquaculture.

Eosinophils are pro-inflammatory cells that play a central role in asthmatic inflammation. However, few studies have examined their methylation profiles in asthma, all relying on microarray-based approaches. Here, an epigenome-wide association study in 183 purified eosinophil samples from the Saguenay-Lac-Saint-Jean asthma family cohort was performed using a custom sequencing panel targeting 4,609,564 CpGs in immune regulatory regions. Two CpG sites in MAEA and SLC9A2 genes, known to be involved in immune function, were significantly associated with asthma, while five additional sites showed suggestive associations. Integration with genotype data (7,829,429 variants) and expression counts (17,513 genes) identified significant quantitative trait loci-mediated regulatory effects. Two CpG sites at Chr1:6,267,177, which is a suggestive association, and Chr2:103,279,574 were linked to expression of EFNA5, GNAQ, and LIMK1, implicating them in eosinophil-driven asthma pathogenesis. This finding offers insights into the asthma's epigenetic architecture, highlighting disease-relevant loci detectable through targeted analysis of eosinophils.

The fat mass and obesity-associated (FTO) gene, though widely studied in human obesity and livestock lipid accumulation, remains poorly understood in bovine adipogenesis. This study investigated its role in bovine adipocytes via overexpression, given its high expression in Guanling cattle adipose tissue. Results demonstrated that FTO significantly increased triglyceride content, adiponectin secretion, and lipid droplet accumulation (P < 0.01). It also upregulated key adipogenic markers (PPARγ, C/EBPβ, FABP4, LPL; P < 0.05). Transcriptomic analysis revealed that FTO promotes adipocyte differentiation and lipogenesis through regulating multiple lipid metabolic pathways. These findings reveal that FTO positively regulates bovine adipocyte differentiation by modulating lipid metabolic networks, thereby filling a critical gap in the understanding of FTO-mediated lipid metabolism in ruminants.

Pork tenderness is a critical determinant of meat quality and is primarily assessed by shear force measurement. In this study, the shear force of the longissimus dorsi muscle was measured in 413 Large White pigs. A genome-wide association study (GWAS) based on imputed data identified multiple loci significantly associated with shear force on chromosomes 5, 8, 13, and 14. Comparison with the PigQTLdb indicated that these four QTLs have not been previously reported. By integrating GWAS results with transcriptomic data from the pigGTEx database, analyses including colocalization, TWAS, and SMR were performed, leading to the identification of two candidate genes, GRM2 and NISCH. PheWAS results showed that NISCH was significantly correlated with palmitoleic acid content, consistent with the positive correlation between palmitoleic acid and shear force in this population. GRM2 was significantly associated with backfat thickness. These results suggest a potential genetic association between fatty acid metabolism and pork tenderness.

Polygonatum odoratum, a valuable medicinal herb, faces severe cultivation constraints due to continuous cropping (CC) obstacles, yet the physiological and molecular mechanisms in its rhizome remain unclear. This study integrates physiological and transcriptomic analyses comparing CC and first-cropping plants. Under CC stress, rhizomes exhibited reduced diameter, root length, and root number, along with decreased antioxidant enzyme activities and polysaccharide content, but increased malondialdehyde levels and 3 types of phenolic acids. RNA-seq identified 3357 upregulated and 1215 downregulated DEGs. KEGG analysis revealed downregulation in plant hormone signal transduction, particularly in IAA-related genes, while the JA, CTK, and ABA pathways, along with key carbohydrate metabolism processes, were upregulated. Moreover, exogenous NAA application promotes the root growth in the rhizome of P. odoratum. These results uncover hormone signaling reprogramming and metabolic shifts underlying CC responses, offering novel insights and a theoretical basis for mitigating cropping obstacles in medicinal plants.

To elucidate neutrophil heterogeneity in rheumatoid arthritis (RA) synovium, we performed single-cell RNA sequencing on 8 RA patients (66,539 cells), stratified by neutrophil infiltration status. Infiltrating neutrophils predominantly displayed inflammatory C1 (Chemokine⁺) and C3 (S100A8/A9⁺) phenotypes. Co-expression analysis (hdWGCNA) identified two functional modules (M3/M4) enriched in NF-κB and type I interferon signaling. Furthermore, these neutrophils actively reshaped the synovial microenvironment via CXCL, IL1, and MIF communication pathways. Transcriptional inference and comparative in silico knockouts revealed the NF-κB/STAT3 axis as a candidate regulatory node, with NFKB1 uniquely perturbing S100A8/A9 effector genes. Key findings, including M4 module activation and its correlation with systemic inflammatory markers (ESR/CRP), were validated in an independent bulk RNA-seq cohort (n = 19). This study comprehensively characterizes RA neutrophil inflammatory reprogramming and nominates the NF-κB/STAT3 axis for future functional validation.

Nekemias grossedentata, a perennial woody vine and the primary source of vine tea, is valued for its medicinal and edible properties. Its leaves contain key bioactive compounds, such as flavonoids (notably dihydromyricetin) and polyphenols, which determine the core quality of vine tea. However, overexploitation threatens wild populations, leading to germplasm resource depletion and loss of genetic diversity, underscoring the urgent need for effective conservation and breeding strategies. Therefore, this study aimed to clarify the genetic diversity, construct a core germplasm collection, and screen elite accessions to support the conservation and sustainable utilization of N. grossedentata. Using principal component analysis on 10 leaf phenotypic traits from 190 samples across eight production regions, this study identified total leaf flavonoid content (contribution rate: 0.810) as the key factor influencing phenotypic variation. Based on transcriptome data previously obtained by our group from different tissues, 25,009 EST-SSR primer pairs were developed, from which 18 stable and polymorphic EST-SSR markers were screened. Utilizing these markers to assess population and individual genetic diversity revealed a high level of genetic diversity in N. grossedentata: average Shannon's diversity index (0.880), expected heterozygosity (0.497), and observed heterozygosity (0.194). Based on these analyses, a core germplasm collection comprising 19 representative accessions from eight geographic origins was constructed. Finally, based on the catechin quality index (CQI) of these 19 core accessions, six elite accessions were selected: GD-10, GX-13, GX-15, GX-18, GX-21, and HN-31. These accessions exhibit high genetic diversity, high CQI (>100), and high total flavonoid content (>20%), making them suitable for direct use as core parental materials. This study provides the first systematic evidence of high genetic diversity in N. grossedentata resources, successfully establishing a core germplasm collection while identifying elite accessions to offer a scientific foundation for conservation, evaluation, and breeding utilization.

Despite having an established backbone phylogeny of Elaeagnaceae, the intrageneric relationships within Elaeagnus L. remain elusive, and family-wide plastome evolution is poorly explored. We analyzed 71 plastomes of 62 species, including four newly sequenced Elaeagnus samples, to reconstruct phylogenies using protein-coding genes (PCGs), intergenic spacers (IGS), and complete sequences. Among these datasets, PCGs provided the strongest resolution, clarifying interspecific and infraspecific relationships within Hippophae L. However, Elaeagnus topologies remained poorly resolved across all datasets, consistent with a history of rapid evolutionary radiation. Plastome structure was highly conserved in Elaeagnaceae, except for lineage-specific IR expansion in Hippophae. Additionally, we identified repeat sequences and signals of positive selection. This study provides essential plastomic resources for understanding the phylogenetic complexity and adaptive evolution of Elaeagnaceae.