Genomics最新文献

Many studies on the adaptability of Tibetan sheep to hypoxia have been reported, but little attention has been paid to the reproduction of Tibetan sheep living at an altitude of more than 4000 m. In this study, the ovaries of Alpine Merino sheep (AM) living in middle-high altitude areas (2500 m) and the ovaries of Gangba Tibetan sheep (GB) and Huoba Tibetan sheep (HB) living in ultra-high altitude areas (4400 m or more) were collected. Through morphological, transcriptomics and metabolomics, the effects of ultra-high altitude areas on Tibetan sheep ovarian development and the molecular mechanism of sheep's adaptability to ultra-high altitude environment were explored. The results showed that the number of granulosa cells in AM was significantly higher than that in GB and HB. The transcriptome revealed several genes related to follicular development, such as DAPL1, IGFBP1, C5, GPR12, STRA6, BMPER, etc., which were mainly enriched in related pathways such as cell growth and development. Through metabolomics analysis, it was found that the differential metabolites between the three groups of sheep were mainly lipids and lipid-like small molecules, such as Glycerol 3-Phosphate, PC (16: 0 / 18: 3 (9Z, 12Z, 15Z)), mainly enriched in lipid metabolism and other related pathways. The results of combined analysis showed that Tryptophan metabolism and Steroid hormone biosynthesis may have a significant effect on Tibetan sheep follicular development. Some genes (including HSD17B7, CYP11A1, CYP19, HSD3B1, CYP17, etc.) and some metabolites (including Cortisone, 2-Methoxyestrone, etc.) are enriched in these pathways, regulating ovarian and follicular development by affecting estrogen, progesterone, etc.. The results further revealed the molecular mechanism of Tibetan sheep to adapt to the ultra-high altitude environment and maintain normal ovarian and follicular development through the regulation of genes and metabolites.

Chilling stress seriously affects the growth and yield of tomato. Anthocyanin is a typical chilling-induced metabolite with strong antioxidant activity and photoprotective capacity. Here, we found that anthocyanin was also involved in ascorbic acid biosynthesis and glycolysis under chilling stress. SlAN2 is an important positive gene in anthocyanin biosynthesis. The results of physiological indicators showed that SlAN2 overexpression lines (A189) had a greater ability to tolerate cold stress than wild-type (WT) plants. Conjoint analysis of transcriptomics and metabonomics of A189 lines and WT plants was used to analyze the metabolic difference and the cold resistance mechanisms caused by anthocyanin under chilling stress. The anthocyanin accumulated more in A189 than that in WT under chilling stress at 4 °C for 24 h, which led to hexoses and ascorbic acid increased significantly. Results indicate that SlAN2 overexpression reduces the expression of key enzyme genes in glycolytic pathway such as phosphofructokinase (PFK) and pyruvate kinase (PK) genes, weakens glycolysis ability, and promotes accumulation of hexoses in A189 lines at 4 °C for 24 h compared with wild lines. Additionally, ascorbic acid content is increased by up-regulated the genes of ascorbate peroxidase (APX) and dehydroascorbate reductase (DHAR). The increased hexose content can reduce cell osmotic potential, freezing point and synthesize more ascorbic acid, while the increased ascorbic acid content can enhance the ability to scavenge reactive oxygen species, so improves the cold resistance of tomato. The glycolysis and ascorbic acid metabolism pathway mediated by SlAN2 provides a new insight for the molecular mechanism of anthocyanins in improving the cold resistance of tomato and provides a new theoretical basis for cultivating new cold-tolerant tomato varieties.

This study aimed to identify loci (p < 1 × 10^-5) and gene sets (normalized enrichment score (NES) ≥ 3.0) associated with the number of times a heifer is bred to attain a successful pregnancy (TBRD) for Holstein heifers bred by artificial insemination (AI, n = 2754) or that were embryo transfer (ET, n = 1566) recipients. Eight loci were associated (p < 1 × 10^-5) with TBRD in AI bred heifers and four loci were associated with TBRD in ET recipients. The gene set enrichment analysis with SNP data identified one gene set enriched (NES ≥ 3.0) with TBRD in AI bred heifers and two gene sets that were enriched with TBRD in ET recipients. The estimated pseudo-heritability for times bred to AI was 0.063 and 0.043 for ET. The identification of loci associated with embryonic loss aids in the selection of Holstein heifers with higher reproductive efficiencies that are AI bred or that are ET recipients.

Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder, yet its mechanisms remain elusive. This study employed transcriptome sequencing on granulosa cells from 5 PCOS women and 5 controls, followed by bioinformatic analyses. We identified 684 mRNAs and 167 lncRNAs with significant differential expression. Gene Ontology and KEGG analyses highlighted enrichment in immune and inflammatory responses among these genes. Through CytoHubba plug-in and three machine learning algorithms, CCR7 was identified as the hub gene of PCOS, further validated through analysis of GSE65746, GSE34526 and a cohort of eighty subjects (40 PCOS and 40 controls). Furthermore, a competing endogenous RNA network targeting CCR7 was constructed. Immune infiltration analysis unveiled a significant decrease in monocyte infiltration in PCOS women, with CCR7 expression positively correlated to naïve B cells. Our findings suggest CCR7 and related molecules play a crucial role in the pathogenesis of PCOS, potentially serving as biomarkers for the disorder.

Lobelia seguinii is a plant with great ecological and medicinal value and belongs to Campanulaceae. Lobelia contains lobeline, a well-known compound used to treat respiratory diseases. Nevertheless, lobeline biosynthesis needs further exploration. Moreover, whole-genome duplication (WGD) and karyotype evolution within Campanulaceae still need to be better understood. In this study, we obtained a chromosome-level genome of L. seguinii with a size of 1.4 Gb and 38253 protein-coding genes. Analyses revealed two WGDs within Campanulaceae, one at the most recent common ancestor (MRCA) of Campanula and Adenophora, and another at the MRCA of Lobelioideae. Analyses further revealed that the karyotype of Platycodon grandiflorus represents the ancient type within Asterales. We proposed eight enzymes involved in the lobeline biosynthesis pathway of L. seguinii. Molecular cloning and heterologous expression of phenylalanine ammonia-lyase (PAL), a candidate enzyme involved in the first step of lobeline biosynthesis, verified its function to catalyze the deamination of phenylalanine to cinnamic acid. This study sheds light on the evolution of Campanulaceae and lobeline biosynthesis.

Introduction: With the increasing demand for donkey production, there has been a growing focus on the breeding of donkeys. However, our current understanding of the mechanisms underlying spermatogenesis and maturation in donkeys during reproduction remains limited.

Objectives: This study is to provide a comprehensive single-cell landscape analysis of spermatogenesis and maturation in donkeys.

Methods: In this study, we employed single-cell RNA sequencing to investigate cell composition, gene expression patterns, and regulatory roles during spermatogenesis and maturation in donkeys.

Results: The expression patterns of CDK1, CETN3, and UBE2J1 were found to be indicative of specific germ cells during donkey spermatogenesis. Additionally, the DEFB121, ELSPBP1, and NPC2 genes were specifically identified in the principal cells of the donkey epididymis.

Conclusions: We performed single-cell RNA sequencing to analyze the cellular composition and spatial distribution of donkey testis and epididymis, thereby generating comprehensive transcriptional atlases at the single-cell resolution.

This study investigated the preventive and protective effects of Portulaca oleracea polysaccharides (PP) on Acute liver injury (ALI) in mice and its regulatory effects on intestinal microorganisms, and explored the underlying protective mechanisms. Initially, PP was administered, and then CCl4 was used to induce the mouse ALI model. Serum and liver markers were measured by ELISA. The fecal microbiota was analyzed by 16S rRNA sequencing. The results showed that PP significantly decreased the expression levels of ALT and AST in the serum of mice. The expression levels of MDA, TNF-α, and IL-6 in liver tissue were found to be reduced, while the levels of GSH and SOD increased. At the same time, PP increased the number of Bacteroides, reduced the number of Proteobacteria, activated the GAG degradation pathway, protected the integrity of the intestinal barrier, inhibited oxidative stress and reduced inflammation, thereby assisting the prevention and protection of ALI.

Maize, a vital crop globally, faces significant yield losses due to its sensitivity to cold stress, especially in temperate regions. Understanding the molecular mechanisms governing maize response to cold stress is crucial for developing strategies to enhance cold tolerance. However, the precise chromatin-level regulatory mechanisms involved remain largely unknown. In this study, we employed DNase-seq and RNA-seq techniques to investigate chromatin accessibility and gene expression changes in maize root, stem, and leaf tissues subjected to cold treatment. We discovered widespread changes in chromatin accessibility and gene expression across these tissues, with strong tissue specificity. Cold stress-induced DNase I hypersensitive sites (coiDHSs) were associated with differentially expressed genes, suggesting a direct link between chromatin accessibility and gene regulation under cold stress. Motif enrichment analysis identified ERF transcription factors (TFs) as central regulators conserved across tissues, with ERF5 emerging as pivotal in the cold response regulatory network. Additionally, TF co-localization analysis highlighted six TF pairs (ERF115-SHN3, ERF9-LEP, ERF7-SHN3, LEP-SHN3, LOB-SHN3, and AS2-LOB) conserved across tissues but showing tissue-specific binding preferences. These findings indicate intricate regulatory networks in maize cold response. Overall, our study provides insights into the chromatin-level regulatory mechanisms underpinning maize adaptive response to cold stress, offering potential targets for enhancing cold tolerance in agricultural contexts.

Background: Abnormal programmed cell death (PCD) plays a central role in spermatogenic dysfunction. However, the molecular mechanisms and biomarkers of PCD in patients with nonobstructive azoospermia (NOA) remain unclear.

Methods: The genetic conditions of NOA patients were analysed using bulk transcriptomic, single-cell transcriptomic, single nucleotide polymorphism (SNP), and clinical data from multiple centres. A total of 675 machine learning methods were applied to construct models from 12 different PCDs and to screen for distinctive genes. A new PCDscore system was created to measure the degree of PCD in patients. Using the NOA mouse model, TUNEL, qRT-PCR, Western blotting, and immunohistochemistry (IHC) were utilized to validate the PCD status in NOA testes and the expression levels of hub PCD-related genes (PCDRGs). Mouse testicular samples were used for sequencing of the whole transcriptome. The sequencing results were used to evaluate the correlation between PCD scores and expression of hub genes.

Results: A PCDscore system was built using 12 characteristic PCDRGs chosen by machine learning. PCD scores correlated with gene interaction and immune activity changes. Leydig, Sertoli, and T cells were prominent in cell interactions with PCDscore changes. PCDscore in the NOA mouse testis was increased. Among the 12 PCDRGs, BCL2L14, GGA1, GPX4, PHKG2, and SLC39A8 were strongly linked to spermatogenesis. BCL2L14, GGA1, GPX4, and PHKG2 strongly correlated with PCD statuses. The changes in the expression of these genes may be due to the effects of SNPs, which may lead to the male reproductive system disorders.

Conclusions: Our study provides new insights into PCD-related mechanisms in NOA patients via multiomics and proposes reliable models for the diagnosis of NOA via the use of PCD biomarkers. A deeper understanding of these mechanisms may aid in the clinical diagnosis and treatment of NOA.