BMC Genomics最新文献

Background: Hericium coralloides is a traditional edible and medicinal mushroom. Light is a key factor in forming fruiting bodies of fungi; however, the effects of different light on the yield and morphogenesis of H. coralloides are still unknown. Therefore, the morphology, yield, and transcriptome of H. coralloides under blue, red, and white light conditions were investigated.

Result: Fruiting bodies under blue light exhibited superior morphological traits, such as milky white color, larger size, elongated stalks, and higher spine count, leading to higher yields. Different light treatments led to dramatic transcriptome changes ranging from 10,827 differentially expressed genes (DEGs) induced by blue light in Blue-4d to 11,375 DEGs induced by red light in Red-4d and accounted for 64.56% to 67.81% of all expressed genes. This massive amount of light-responsive genes has never been reported in fungi. Gene Ontology analysis showed that light affected nearly all aspects of life in H. coralloides; suggesting that the influence of light on fungi may have been underestimated. Blue light-induced yield increment may be achieved by specifically upregulating the growth-related processes such as DNA replication, chromosomes, and cell division.

Conclusions: This study offers preliminary insights into the potential role of blue light in modulating gene expression and yield stimulation in H. coralloides, potentially improving cultivation practice.

Background: Plants possess a high potential for somatic cell reprogramming, enabling the transition from differentiated tissue to pluripotent callus, followed by the formation of de novo shoots during plant regeneration. Despite extensive studies on the molecular network and key genetic factors involved in this process, the underlying epigenetic landscape remains incompletely understood.

Results: Here, we explored the dynamics of the methylome and transcriptome during the two-step plant regeneration process. During the leaf-to-callus transition in Arabidopsis Ler, CG methylation shifted across genic regions, exhibiting a similar number of differentially methylated regions (DMRs) for both hypo- and hypermethylation. Pericentromeric regions underwent substantial CG and extensive CHH hypomethylation, alongside some CHG hypermethylation. Upon shoot regeneration from callus, genic regions displayed extensive reconfiguration of CG methylation, while pericentromeric methylation levels highly increased across all cytosine contexts, coinciding with the activation of the RNA-directed DNA methylation (RdDM) pathway. However, mutation in DEMETER (DME) DNA demethylase gene resulted in significant genic CG redistribution and global non-CG hypomethylation in pericentromeric regions, particularly during shoot regeneration. This non-CG hypomethylation observed in dme-2 mutants was, at least partly, due to RdDM downregulation. The dme-2 mutants affected gene expression involved in pluripotency and shoot meristem development, resulting in enhanced shoot regeneration through a reprogrammed state established by pericentromeric hypomethylation compared to wild type.

Conclusion: Our study demonstrates epigenetic changes, accompanied by transcriptome alterations, during pluripotency acquisition (leaf-to-callus) and regeneration (callus-to-de novo shoot). Additionally, it highlights the functions of the DME demethylase, particularly its close association with the RdDM pathway, which underlies pericentromeric non-CG methylation maintenance. These results provide important insights into the epigenetic reconfiguration associated with cell identity transition during somatic cell reprogramming.

Castration is widely used in poultry and livestock to enhance fat metabolism and improve the flavor, tenderness and juiciness of meat. However, the genetic regulatory mechanism underlying castration consequences have not been clarified. To investigate the key metabolites affecting the quality of capons and the key regulatory mechanisms, Qingyuan partridge roosters were subjected to castration. Metabolic profiling was used to detect differential metabolites in the breast muscle of both capon and control groups. Additionally, an integrative analysis of transcriptomics and proteomics was conducted to explore the genetic regulation mechanisms influencing meat quality. The results indicated that the muscle fiber density and shear force of capons was lower than that of normal chickens, and the fat percentage of capon group (CAM) was higher than control group (COM). The expression of the metabolite inostine-5'-monophosphate (IMP) was lower in capons, and lipid metabolites (PC (10:0/10:0), PC (6:0/13:1), LPC 22:6, LPC 18:2, LPE 18:1, LPE 20:4) were higher in capons. Metabolic pathways were found to be a common signaling pathway in all omics. Glutamate-ammonia ligase (GLUL), acetyl-CoA carboxylase beta (ACACB), 1-acylglycerol-3-phosphate O-acyltransferase 2 (AGPAT2), 4-hydroxy-2-oxoglutarate aldolase 1 (HOGA1) and glutathione S-transferase alpha 2 (GSTA2) regulate the expression of citric acid, arachidonic acid, palmitic acid, isocitric acid, and betaine. These findings highlight the key mechanisms contributing to the meat quality differences between capons and normal chickens.

Background: Efficient capture and use of resources is critical for optimal plant growth and productivity. Both shoot and root growth are essential for resource acquisition, namely light and CO₂ by the shoot and water and mineral nutrients by roots. Soybean [Glycine max (L.) Merr.], one of the most valuable crops world-wide, uses an additional strategy, symbiotic N fixation (SNF), for N acquisition. SNF relies on development of specialized root organs known as nodules, which represent a distinct C sink. The genetic diversity of C partitioning in N fixing soybean to shoots, roots, and nodules has not been previously investigated but is valuable to better understand consequences of differential C allocation and to develop genetic resources, including identification of quantitative trait loci (QTLs).

Results: A diversity panel of 402 soybean genotypes was phenotyped outdoors in a deep-tube system without addition of mineral N to measure allocation of biomass to the shoot, root, and nodules, as well as to determine nodule number, mean nodule biomass, and total shoot N accumulation. Wide ranges in phenotypes were observed for each of these traits, demonstrating extensive natural diversity in C partitioning and SNF in soybean. Using a set of 35,647 single nucleotide polymorphism (SNP) markers, we identified 121 SNPs tagging 103 QTLs that include both 84 novel and 19 previously identified QTLs for the eight examined traits. A candidate gene search identified 79 promising gene models in the vicinity of these QTLs. Favorable alleles of QTLs identified here may be used in breeding programs to develop elite cultivars with altered C partitioning.

Conclusions: This study provides novel insights into the diversity of biomass allocation in soybean and illustrates that the traits measured here are heritable and quantitative. QTLs identified in this study can be used in genomic prediction models as well as for further investigation of candidate genes and their roles in determining partitioning of fixed C. Enhancing our understanding of C partitioning in plants may lead to elite cultivars with optimized resource use efficiencies.

Great Bay Estuary (GBE), within the rapidly warming Gulf of Maine, has experienced significant ecological shifts this century due to naturalization of invasive species. The range expansion of the American blue crab (Callinectes sapidus) currently underway from the mid-Atlantic northward brings the possibility of similar ecological shifts. This study accounts recent trapping and diet analysis of C. sapidus in GBE. Diet is an important component of understanding how the blue crab range expansion may affect GBE ecosystem functions. Across all sites and trap types, 27 blue crabs were captured. Metagenomic analysis of shotgun sequencing techniques were used on the gut contents of blue crabs captured. Most specimens had > 50% Eukaryote sequences. Overall results of this gut content study confirm a mixed diet indicative of an opportunistic feeder. Using metagenomics to analyze the diet of blue crabs as they establish viable populations in GBE will be a useful tool for predicting how these range expanding organisms are interacting within this important estuarine ecosystem, which will promote sustainable development by informing end users who may be affected by these crabs to help them meet their needs in the present and future. This project falls within Global Goal SDG14: Life Below Water.

Background: Gene set tests can pinpoint genes and biological pathways that exert small to moderate effects on complex diseases like Type 2 Diabetes (T2D). By aggregating genetic markers based on biological information, these tests can enhance the statistical power needed to detect genetic associations.

Results: Our goal was to develop a gene set test utilizing Bayesian Linear Regression (BLR) models, which account for both linkage disequilibrium (LD) and the complex genetic architectures intrinsic to diseases, thereby increasing the detection power of genetic associations. Through a series of simulation studies, we demonstrated how the efficacy of BLR derived gene set tests is influenced by several factors, including the proportion of causal markers, the size of gene sets, the percentage of genetic variance explained by the gene set, and the genetic architecture of the traits. By using KEGG pathways, eQTLs, and regulatory elements as different kinds of gene sets with T2D results, we also assessed the performance of gene set tests in explaining more about real phenotypes.

Conclusions: Comparing our method with other approaches, such as the gold standard MAGMA (Multi-marker Analysis of Genomic Annotation) approach, our BLR gene set test showed superior performance. Combining performance of our method in simulated and real phenotypes, this suggests that our BLR-based approach could more accurately identify genes and biological pathways underlying complex diseases.

Background: Sugar beets (Beta vulgaris L.) are grown worldwide and suffer economic loss annually due to curly top disease caused by the beet curly top virus (BCTV). The virus is spread by the beet leafhopper (BLH), Circulifer tenellus Baker. Current management strategies rely on chemical control and planting BCTV-resistant sugar beet genotypes. However, the genetic mechanism underlying BCTV resistance in sugar beet is unknown. This study aimed to determine these mechanisms by comparing a resistant (EL10) and susceptible (FC709-2) sugar beet genotype using host plant suitability (no-choice), host preference (choice) assays, and transcriptomic analysis.

Results: Host plant suitability assays revealed no significant differences in adult survival or nymph production between viruliferous and non-viruliferous BLH on either genotype, suggesting that BCTV resistance is not directly associated with reduced beet leafhopper fitness. However, host preference assays showed that viruliferous BLH preferred settling on the susceptible genotype, FC709-2, compared to the resistant genotype, EL10 whereas the non-viruliferous BLH showed no preference. RNA-sequencing analysis of BCTV-inoculated (viruliferous BLH-fed) and mock-inoculated (non-viruliferous BLH-fed) plants at day 1, 7, or 14 post-inoculations highlighted dynamic and contrasting responses between the two genotypes. The resistant genotype had differentially expressed transcripts (DETs) associated with jasmonic acid and abscisic acid biosynthesis and signaling. DETs associated with stress mitigation mechanisms and reduction in plant primary metabolic processes were also observed. In contrast, the susceptible genotype had DETs associated with opposing phytohormones like salicylic acid and auxin. Moreover, this genotype exhibited an upregulation in DETs involved in volatile organic compounds (VOCs) production and increased primary plant metabolic processes.

Conclusions: These results provide novel insight into the opposing transcriptional responses underlying BCTV resistance and susceptibility in sugar beet. Understanding and classifying the mechanisms of resistance or susceptibility to BCTV infection in sugar beet is beneficial to researchers and plant breeders as it provides a basis for further exploration of the host plant-virus-vector interactions.

Nanopore sequencing enables detection of DNA methylation at the same time as identification of canonical sequence. A recent study validated low-pass nanopore sequencing to accurately estimate global methylation levels in vertebrates with sequencing coverage as low as 0.01x. We investigated the applicability of this approach to plants by testing three plant species and analysed the effect of technical and biological parameters on estimate precision and accuracy. Our results indicate that higher coverage (0.1x) is required to achieve accuracy in assessing plant global methylation comparable to that in vertebrates. Shorter read length and a closer sequence match between sample and reference genome improved measurement accuracy. Application of this method in Vitis vinifera showed consistent global methylation levels across different leaf sizes, and different sample preservation and DNA extraction methods, whereas different varieties and tissue types did exhibit methylation differences. Similarly, distinct methylation patterns were observed in different genomic features. Our findings suggest the suitability of this method as a low-cost screening tool for validation of experimental parameters, developmental time courses, and to assess methylation status for different modification types and sequence contexts at the level of whole genome or for abundant genomic features such as transposable elements.

NF-Y is a class of heterotrimeric transcription factor composed of three subunits; NF-YA, NF-YB, and NF-YC. This complex binds to the CCAAT box found in eukaryotic promoters and is involved in the plant development and proliferation at various stages. Although many studies were conducted on NF-Y gene family in various species, but no study has been reported yet in switchgrass (Panicum virgatum L.). In this study, 47 PvNF-Y genes (17 PvNF-YA, 18 PvNF-YB, and 12 PvNF-YC) have been identified and named according to their subfamily. Chromosome location analysis revealed that all 47 PvNF-Y genes are randomly distributed across nine chromosomes. Moreover, multiple sequence alignment showed the DNA-binding domain and NF-YA/NFYB interacting domains flanking with non-conserved domains. In addition, prediction of functional similarities among PvNF-Ys genes phylogenetic tree was constructed corresponding to Arabidopsis. The gene structure, conserved domains and motifs analysis of PvNF-Ys genes demonstrated their specificity and functional conservation. Cis-regulatory elements analysis identified numerous key CREs that are significantly associated with light, hormone, stress and plant development responses. Expression profiling indicated higher expression levels of many PvNF-YA genes during drought and heat stress. Additionally, qRT-PCR analysis showed that some PvNF-Ys genes have high expression level in root. In conclusion, the findings of this study could provide a foundation for further cloning and functional analysis of NF-Y genes in switchgrass.

Panax ginseng is an important medicinal plant in China and is classified into two types: cultivated ginseng (CFCG) and mountain-cultivated ginseng (MCG). The two types of genetic varieties are the same, but the growth environments and management practices are different, resulting in substantial differences in their taproot morphology. Currently, there is a paucity of research on the internal mechanisms that regulate the phenotypic differences between cultivated ginseng and mountain-cultivated ginseng. In this study, we explored the potential mechanisms underlying their phenotypic differences using transcriptomic and metabolomic techniques. The results indicate that the taproot thickening of CFCG was significantly greater than that of MCG. Compared with MCG-4, MCG-10, and MCG-18, the diameters of the taproots of CFCG-4 increased by 158.96, 81.57, and 43.21%, respectively. Additionally, the contents of sucrose and starch in the taproot, as well as TRA and DHZR, were markedly elevated. Transcriptome analysis revealed that compared with MCG of different age groups, genes associated with starch and sucrose metabolism pathways (PgSUS1, PgSPS1, PgSPS3, and PgglgC1) were significantly upregulated in CFCG-4, whereas genes involved in the phenylpropanoid biosynthesis pathway (PgPER3, PgPER51, and PgPER12) were significantly downregulated in CFCG-4. This imbalance in the metabolic pathways suggests that these genes play crucial roles in ginseng taproot thickening. PgbHLH130 and PgARF18 may be key regulators of transcriptional changes in these pathways. These findings elucidate the molecular mechanisms governing ginseng taproot thickening, and have important implications for enhancing the overall quality and value of ginseng.