BMC Genomics最新文献

Background: DNA methylation is an epigenetic modification that plays an important role in animal and plant development. Among the diverse types of DNA methylation modifications, methylation of cytosines catalyzed by DNA cytosine methyltransferases (DNMTs) is the most common. Recently, we characterized DNA methyltransferase genes including HlDnmt1 and HlDnmt from the Asian longhorned tick, Haemaphysalis longicornis. However, the dynamic expression and functions of these DNMTs at different developmental stages and feeding statuses of the important vector tick H. longicornis remain unknown.

Results: The expression levels of HlDnmt1 and HlDnmt were significantly different at the four developmental stages: eggs, larvae, nymphs, and adults, with the highest expression levels observed in the larval stage. HlDnmt1 and HlDnmt showed different expression trends in the midguts, ovary, Malpighian tubules, and salivary glands of engorged adults, with the highest expression of HlDnmt1 observed in the ovary and the lowest in the midguts; HlDnmt expression was the highest in the midguts and the lowest in the Malpighian tubules. After RNA interference, the relative expression of HlDnmt1 and HlDnmt in H. longicornis decreased significantly, resulting in a significant decrease in the biting rate of H. longicornis. RNA-seq revealed that the differentially expressed genes were mainly enriched in the biological processes of peptide biosynthesis and the cell components of ribosomes. Molecular functions were mainly concentrated on oxidoreductase activity, ribosome structure composition, serine-type endopeptidase activity, molecular function regulators, and endopeptidase inhibitor activity. KEGG enrichment analysis showed that the differentially expressed genes were mainly enriched in autophagy and lysosome pathways, amino sugar and nucleotide sugar metabolism, glyceride metabolism, ribosomes, and other pathways.

Conclusions: HlDnmt1 and HlDnmt played an important role during development and feeding of H. longicornis, and their functions were potentially associated with lysosome pathways. These results provide basic knowledge for understanding the epigenetic regulation of the development of the tick H. longicornis, which sheds light on control strategies for ticks and tick-borne diseases.

Background: It has been reported that the most common post-transcriptional modification of eukaryotic RNA is N6-methyladenosine (m6A). Previous studies show m6A is a key regulator for viral infection and immune response. However, whether there is a pathogen stimulus-dependent m6A regulation in invertebrate shrimp has not been studied.

Results: In this study, we performed a transcriptome-wide profiling of mRNA m6A methylation in shrimp (Marsupenaeus japonicus) after white spot syndrome virus (WSSV) infection by methylated RNA immunoprecipitation sequencing (MeRIP-seq). A total of 15,436 m6A peaks were identified in the shrimp, distributed in 8,108 genes, mainly enriched in the CDS, 3' UTR region and near the stop codon. After WSSV infection, we identified 2,260 m6A peaks with significantly changes, of which 1,973 peaks were significantly up-regulated and 287 peaks were significantly down-regulated. 1,795 genes were identified as differentially methylated genes. GO and KEGG analysis showed that hyper-methylated genes or hypo-methylated genes were highly associated with innate immune process and related to metabolic pathways including HIF-1 signaling pathway, lysine degradation and Wnt signaling pathway. Combined analysis showed a positive correlation between m6A methylation levels and mRNA expression levels. In addition, computational predictions of protein-protein interaction indicated that genes with altered levels of m6A methylation and mRNA expression clustered in metabolism, DNA replication, and protein ubiquitination. ZC3H12A and HIF-1 were two hub genes in protein-protein interaction (PPI) network that involved in immune and metabolism processes, respectively.

Conclusion: Our study explored the m6A methylation pattern of mRNA in shrimp after WSSV infection, exhibited the first m6A map of shrimp at the stage of WSSV induced metabolic reprogramming. These findings may reveal the possible mechanisms of m6A-mediated innate immune response in invertebrates.

Drought, a prevalent abiotic stressor, significantly impacts plant yield and quality. Melatonin (MT), a potent and economical growth regulator, plays a pivotal role in augmenting crop resilience against stress. This study investigated the efficacy of exogenous MT on drought-stressed celery seedlings by comprehensively analyzing phenotypic, physiological, and molecular attributes. The results revealed that exogenous MT mitigated celery seedling damage under drought stress, lowered malondialdehyde (MDA) concentrations, elevated oxidase activities, osmolyte levels, chlorophyll content, and augmented light energy conversion efficiency. Transcriptomic analysis demonstrated that MT could regulate chlorophyll synthesis genes (AgPORA1 and AgDVR2), contributing to heightened photosynthetic potential and increased drought tolerance in celery. Moreover, MT was found to modulate glycolytic pathways, upregulate pyruvate synthesis genes (AgPEP1 and AgPK3), and downregulate degradation genes (AgPDC2 and AgPDHA2), thereby promoting pyruvate accumulation and enhancing peroxidase activity and drought tolerance. The RNA-seq and qRT-PCR analyses demonstrated similar results, showing the same general expression trends. The study elucidates the physiological and molecular mechanisms underlying MT's stress-alleviating effects in celery seedlings, offering insights into MT-based strategies in plant cultivation and breeding for arid environments.

Background: The common Eastern bumble bee Bombus impatiens is native to North America and is the main commercially reared pollinator in the Americas. There has been extensive research on this species related to its social biology, applied pollination, and genetics. The genome of this species was previously sequenced using short-read technology, but recent technological advances provide an opportunity for substantial improvements. This species is common in agricultural and urban environments, and heavy metal contaminants produced by industrial processes can negatively impact it. To begin to identify possible mechanisms underlying responses to these toxins, we used RNA-sequencing to examine how exposure to a cocktail of four heavy metals at field-realistic levels from industrial areas affected B. impatiens worker gene expression.

Results: PacBio long-read sequencing resulted in 544x coverage of the genome, and HiC technology was used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high quality, chromosome-level assembly. The sequenced genome size is 266.6 Mb and BRAKER3 annotation produced 13,938 annotated genes. The genome and annotation show high completeness, with ≥ 96% of conserved Eukaryota and Hymenoptera genes present in both the assembly and annotated genes. RNA sequencing of heavy metal exposed workers revealed 603 brain and 34 fat body differentially expressed genes. In the brain, differentially expressed genes had biological functions related to chaperone activity and protein folding.

Conclusions: Our data represent a large improvement in genomic resources for this important model species-with 10% more genome coverage than previously available, and a high-quality assembly into 18 chromosomes, the expected karyotype for this species. The new gene annotation added 777 new genes. Altered gene expression in response to heavy metal exposure suggests a possible mechanism for how these urban toxins are negatively impacting bee health, specifically by altering protein folding in the brain. Overall, these data are useful as a general high quality genomic resource for this species, and provide insight into mechanisms underlying tissue-specific toxicological responses of bumble bees to heavy metals.

Background: Pueraria is a widely cultivated medicinal and edible homologous plant in Asia, and its tuberous roots are commonly used in the food, nutraceutical, and pharmaceutical industries. "Gange No. 5" is a local variety of Pueraria montana var. thomsonii (Bentham) M.R. Almeida (PMT) in Jiangxi Province, China. After optimizing its cultivation technique, we shortened the cultivation cycle of this variety from two years to one year, suggesting that the regulatory mechanism of the endogenous hormone system during tuberous root expansion may have changed significantly. In this study, we focused on the molecular mechanisms of endogenous hormones in promoting tuberous root expansion during one-year cultivation of "Gange No. 5".

Results: The mid-late expansion period (S4) is critical for the rapid swelling of "Gange No. 5" tuberous roots during annual cultivation. At S4, the number of cells increased dramatically and their volume enlarged rapidly in the tuberous roots, the fresh weight of a single root quickly increased, and the contents of multiple nutrients (total protein, total phenol, isoflavones) and medicinal components (puerarin, puerarin apigenin, and soy sapogenin) were at their peak values. We compared the transcriptomes and metabolomes of S1 (the pre-expansion period), S4, and S6 (the final expansion period), and screened 42 differentially accumulated hormone metabolites and 1,402 differentially expressed genes (DEGs) associated with hormone biosynthesis, metabolism, and signaling. Most Auxin, cytokinins (CKs), jasmonic acids (JAs), salicylic acid (SA), melatonin (MLT), and ethylene (ETH), reached their maximum levels at S1 and then gradually decreased; however, abscisic acid (ABA) appeared in S6, indicating that most of the endogenous hormones may play a key role in regulating the initiation of tuberous root expansion, while ABA mainly promotes tuberous root maturation. Notably, multiple key genes of the 'Tryptophan metabolism' pathway (ko00380) were significantly differentially expressed, and COBRA1, COBRA2, YUCCA10, IAA13, IAA16, IAA20, IAA27, VAN3, ACAA2, and ARF were also identified to be significantly correlated with the expansion of "Gange No. 5" tuberous roots.

Conclusions: Our study has revealed how endogenous hormone regulation affects the expansion of "Gange No. 5" tuberous roots. These findings offer a theoretical foundation for improving the yield of PMT tuberous roots.

Background: Calcium-dependent protein kinases (CDPKs) phosphorylate downstream target proteins in response to signals transmitted by free calcium ions (Ca²⁺, one of the second messengers) and thus play important regulatory roles in many biological processes, such as plant growth, development, and stress response.

Results: A bioinformatic analysis, as well as thorough evolutionary and expression investigations, were conducted to confirm previous reports of functional evidence for plant CDPKs. Using the Phytozome database's BLAST search engine and the HMM search tool in TBtools software, we discovered that CDPKs are well conserved from green algae to flowering angiosperms in various gene family sizes. Additional investigations of the obtained CDPKs revealed high conservation of domain and motif numbers, gene architectures, and patterns. However, this conservation differed among plant species. Phylogenetic analysis demonstrated that the CDPK gene family diverged from a common ancient gene. Similarly, investigations into plant interspecies evolutionary relationships revealed common ancestral plant species, suggesting speciation of plants and evolution based on plant adaptation and diversification. A search for the driving force of CDPK gene family expansion revealed that dispersed duplication events, among other duplication events, contributed largely to CDPK gene family expansion. Gene localization analysis in P. trichocarpa  demonstrated that most CDPK genes are localized within several cell organelles and bind other kinases and proteins to perform their biological functions efficiently. Using RNA-seq data and qPCR analyses, we postulated that PtCDPKs play functional roles in abiotic stress responses by regulating cold, heat, drought and salt stress to varying extents.

Conclusion: The CDPK genes are well conserved in plants and are critical entities in abiotic stress regulation, and further exploration and manipulation of these genes in the future may provide solutions to some of the challenges in agriculture, forestry and food security.

Background: Heat stress (HS) can affect the physiology and metabolism of animals. HS-induced intestinal inflammation in pigs is a common disease, causing severe diarrhea, that can result in substantial economic losses to the pig industry, but the molecular mechanisms and pathogenicity of this disease are not fully understood. The objective of this study was to identify the differentially expressed genes (DEGs) and long noncoding RNAs (DELs) related to inflammation in the colon tissues of pigs under constant (1, 7, and 14 days) HS.

Results: LncRNA and targeted gene interaction networks were constructed. GO annotation and KEGG pathway analyses were subsequently performed to determine the functions of the DEGs and DELs. The results revealed 57, 212, and 54 DEGs and 87, 79, and 55 DELs in the CON/H01, CON/H07, and CON/H14 groups, respectively. KRT85, CLDN1, S100A12, TM7SF2, CCN1, NR4A1, and several lncRNAs may be involved in regulating the development of intestinal inflammation. GO analysis indicated that the DEGs and DELs were enriched in a series of biological processes involved in the innate immune response, RAGE receptor binding, and positive regulation of the ERK1 and ERK2 cascades. KEGG pathways related to inflammation, such as the tight junction (TJ) and MAPK signaling pathways, were enriched in DEGs and DELs.

Conclusions: This study have expanded the knowledge about colon inflammation-related genes and lncRNA biology in pigs under HS; analyzed the the lncRNA‒mRNA interaction for HS-induced intestinal inflammation. These results may provide some references for our understanding of the molecular mechanism of the intestinal response to HS in pig.

Background: Therapeutic targets supported by genetic evidence from genome-wide association studies (GWAS) show higher probability of success in clinical trials. GWAS is a powerful approach to identify links between genetic variants and phenotypic variation; however, identifying the genes driving associations identified in GWAS remains challenging. Integration of molecular quantitative trait loci (molQTL) such as expression QTL (eQTL) using mendelian randomization (MR) and colocalization analyses can help with the identification of causal genes. Careful interpretation remains warranted because eQTL can affect the expression of multiple genes within the same locus.

Methods: We used a combination of genomic features that include variant annotation, activity-by-contact maps, MR, and colocalization with molQTL to prioritize causal genes across 4,611 disease GWAS and meta-analyses from biobank studies, namely FinnGen, Estonian Biobank and UK Biobank.

Results: Genes identified using this approach are enriched for gold standard causal genes and capture known biological links between disease genetics and biology. In addition, we find that eQTL colocalizing with GWAS are statistically enriched for corresponding disease-relevant tissues. We show that predicted directionality from MR is generally consistent with matched drug mechanism of actions (> 85% for approved drugs). Compared to the nearest gene mapping method, genes supported by multi-omics evidences displayed higher enrichment in approved therapeutic targets (risk ratio 1.75 vs. 2.58 for genes with the highest level of support). Finally, using this approach, we detected anassociation between the IL6 receptor signal transduction gene IL6ST and polymyalgia rheumatica, an indication for which sarilumab, a monoclonal antibody against IL-6, has been recently approved.

Conclusions: Combining variant annotation, activity-by-contact maps, and molQTL increases performance to identify causal genes, while informing on directionality which can be translated to successful target identification and drug development.