BMC Genomics最新文献

Long non-coding RNA (lncRNA) plays important roles in animals and plants. In filamentous fungi, however, their biological function in infection stage has been poorly studied. Here, we investigated the landscape and regulation of lncRNA in the filamentous plant pathogenic fungus Botrytis cinerea by strand-specific RNA-seq of multiple infection stages. In total, 1837 lncRNAs have been identified in B. cinerea. A large number of lncRNAs were found to be antisense to mRNAs, forming 743 sense-antisense pairs, of which 55 antisense lncRNAs and their respective sense transcripts were induced in parallel as the infection stage. Although small RNAs were produced from these overlapping loci, antisense lncRNAs appeared not to be involved in gene silencing pathways. In addition, we found the alternative splicing events occurred in lncRNA. These results highlight the developmental stage-specific nature and functional potential of lncRNA expression in the infection stage and provide fundamental resources for studying infection stage-induced lncRNAs.

Background: Trimethylamine N-oxide (TMAO) is a metabolite produced by gut microbiota, and its potential impact on lipid metabolism in mammals has garnered widespread attention in the scientific community. Bovine fatty liver disease, a metabolic disorder that severely affects the health and productivity of dairy cows, poses a significant economic burden on the global dairy industry. However, the specific role and pathogenesis of TMAO in bovine fatty liver disease remain unclear, limiting our understanding and treatment of the condition. This study aims to construct a bovine fatty liver cell model using an integrated approach that combines transcriptomic, proteomic, and metabolomic data. The objective is to investigate the impact of TMAO on lipid metabolism at the molecular level and explore its potential regulatory mechanisms.

Results: We established an in vitro bovine fatty liver cell model and conducted a comprehensive analysis of cells treated with TMAO using high-throughput omics sequencing technologies. Bioinformatics methods were employed to delve into the regulatory effects on lipid metabolism, and several key genes were validated through RT-qPCR. Treatment with TMAO significantly affected 4790 genes, 397 proteins, and 137 metabolites. KEGG enrichment analysis revealed that the significantly altered molecules were primarily involved in pathways related to the pathology of fatty liver disease, such as metabolic pathways, insulin resistance, hepatitis B, and the AMPK signaling pathway. Moreover, through joint analysis, we further uncovered that the interaction between TMAO-mediated AMPK signaling and oxidative phosphorylation pathways might be a key mechanism promoting lipid accumulation in the liver.

Conclusions: Our study provides new insights into the role of TMAO in the pathogenesis of bovine fatty liver disease and offers a scientific basis for developing more effective treatment strategies.

Background: The fall armyworm (FAW) Spodoptera frugiperda, a highly invasive, polyphagous pest, poses a global agricultural threat. It has two strains, the C-corn and R-rice strains, each with distinct host preferences. This study compares detoxification enzyme gene families across these strains and related Spodoptera species to explore their adaptation to diverse host plant metabolites.

Results: A total of 1,995 detoxification-related genes, including cytochrome P450 monooxygenases (CYPs), carboxylesterases (COEs), glutathione S-transferases (GSTs), UDP-glucuronosyltransferases (UGTs), and ATP-binding cassette transporters (ABCs), were identified across the genus Spodoptera, including S. littoralis, S. litura, S. picta, S. exigua, and both FAW strains. A higher abundance of phase I detoxification enzymes (CYPs and COEs) and GSTs was observed in Spodoptera species, while FAW strains exhibited fewer detoxification genes, with notable differences in copy numbers between the C and R strains. Analyses at the subfamily level revealed significant variation in gene distribution and expression, particularly within phase I and II detoxification enzymes. Expansions in CYP6AE were detected in the C strain, while contractions in GST-ε, CYP9A, CYP4M, UGT33B, and UGT33F occurred in both strains. In contrast, no substantial variation was observed in phase III ABC enzymes. Functional predictions and protein interaction networks suggest a broader expansion of metabolism-related genes in the R strain compared to the C strain.

Conclusions: These findings emphasize the pivotal role of phase I and II detoxification enzymes in host adaptation, providing molecular insights into FAW's capacity for host range expansion, which are crucial for devising targeted and sustainable pest management strategies.

Background: Despite the rapid advancement of high-throughput sequencing, simple sequence repeats (SSRs) remain indispensable molecular markers for various applied and research tasks owing to their cost-effectiveness and ease of use. However, existing SSR markers cannot meet the growing demand for research on lotus (Nelumbo Adans.) given their scarcity and weak connections to the lotus genome.

Methods: Using whole-genome resequencing, active SSR loci were identified throughout the genomes of eight typical Asian lotus. After that, high polymorphism SSR molecular markers were mined from each 2n + 0.5 Mb site on each chromosome (e.g., Chr.1-2.5, 4.5, 6.5 Mb) through four steps: online primer design, primer pair evaluation, agarose gel electrophoresis testing using six Asian lotus, one American lotus, and two their hybrids, and DNA sequence alignment. Finally, the polymerase chain reaction (PCR) efficiency of several SSR markers was validated in 20 Asian temperate lotus, eight Asian tropical lotus, and one American lotus.

Results: A total of 463 SSR markers were developed based on each 2n + 0.5 Mb site of the eight lotus chromosomes (totaling 821.29 Mb). These markers were evenly distributed throughout the lotus genome at a density of 1 SSR per 1.76 Mb. The chromosomal locations of the SSR markers were determined precisely, and the specificity of the primer pairs for each site was verified by sequencing the PCR products. We further provided a set of genome-wide SSR loci, covering 129 per Mb, identified from eight representative Asian lotus, allowing other researchers to independently discover specific SSR markers for particular experiments.

Conclusion: These SSR markers, which have a density of 1 SSR marker per 1.76 Mb in this study, will act as a bridge connecting lotus phenotypes with the genome. This work reveals a novel and convenient strategy for developing highly polymorphic SSR markers at any location throughout the lotus genome, and it sheds light on the development of SSR molecular markers in other plant species.

Background: The evolution and development of flowers are biologically essential and of broad interest. Maize and sorghum have similar morphologies and phylogeny while harboring different inflorescence architecture. The difference in flower architecture between these two species is likely due to spatiotemporal gene expression regulation, and they are a good model for researching the evolution of flower development.

Results: In this study, we generated single nucleus and spatial RNA-seq data for maize ear, tassel, and sorghum inflorescence. By combining single nucleus and spatial transcriptome, we can track the spatial expression of single nucleus cluster marker genes and map single nucleus clusters to spatial positions. This ability provides great power to annotate the single nucleus clusters. Combining the cell cluster resolved transcriptome comparison with genome alignment, our analysis suggested that maize ear and tassel inflorescence diversity is associated with the maize-specific whole genome duplication. Taking sorghum as the outgroup, it is likely that the loss of gene expression profiling contributes to the inflorescence diversity between tassel and ear, resulting in the unisexual flower architecture of maize. The sequence of highly expressed genes in the tassel is more conserved than the highly expressed genes in the ear.

Conclusion: This study provides a high-resolution atlas of gene activity during inflorescence development and helps to unravel the potential evolution associated with the differentiation of the ear and tassel in maize.

Background: WRKY transcription factors (TFs) regulate plant responses to environmental stimuli and development, including flowering. Despite extensive research on different species, their role in the invasive plant Mikania micrantha remains to be explored. The aim of this study was to identify and analyze WRKY genes in M. micrantha to understand their function in flowering and adaptation mechanisms.

Results: By analysing the whole genome of M. micrantha, a total of 77 M. micrantha WRKY (MmWRKY) genes were identified. Based on phylogenetic relationships, sequence alignment, and structural domain diversity, the MmWRKY gene family was preliminarily classified into three major groups and five subgroups: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III. Expression profiles showed tissue-specific expression patterns, with many WRKY genes highly expressed in flowers, indicating potential roles in floral development. Real-time quantitative PCR confirmed that the selected 11 genes were highly expressed in floral tissues, supporting their functional significance in flowering.

Conclusion: In this study, 77 WRKY genes were identified in M micrantha, and their phylogenetic relationships, structural domains, and expression patterns across various tissues and organs were comprehensively analyzed. This work provides a foundation for future functional characterization of WRKY genes in M. micrantha, which may contribute to the development of more effective strategies to control its rapid spread.

Background: The advent of next generation sequencing technologies has enabled a surge in the number of whole genome sequences in public databases, and our understanding of the composition and evolution of bacterial genomes. Besides model organisms and pathogens, some attention has been dedicated to industrial bacteria, notably members of the Lactobacillaceae family that are commonly studied and formulated as probiotic bacteria. Of particular interest is Lactobacillus acidophilus NCFM, an extensively studied strain that has been widely commercialized for decades and is being used for the delivery of vaccines and therapeutics.

Results: Here, we revisit the L. acidophilus genome, which was sequenced twenty years ago, and determined the core and pan genomes of 114 publicly available L. acidophilus strains, spanning commercial isolates, academic strains and clones from the scientific literature. Results indicate a predictable high level of homogeneity within the species, but also reveal surprising mis-assemblies. Furthermore, by investigating twenty one available L. acidophilus NCFM-derived variants, we document overall genomic stability, with no observed genomic re-arrangement or inversions.

Conclusion: This study provides a comparative analysis of the currently available genomes for L. acidophilus and examines microevolution patterns for several strains derived from L. acidophilus NCFM, which revealed no to very few SNPs with strains sequenced at different points in time using different sequencing technologies and platforms. This re-affirms its suitability for industrial deployment as a probiotic and its use as an engineering chassis and delivery modality for novel biotherapeutics.

Background: Anorexia nervosa (AN) is a polygenic, severe metabopsychiatric disorder with poorly understood aetiology. Eight significant loci have been identified by genome-wide association studies (GWAS) and single nucleotide polymorphism (SNP)-based heritability was estimated to be ~ 11-17, yet causal variants remain elusive. It is therefore important to define the full spectrum of genetic variants in the wider regions surrounding these significantly associated loci. The hypothesis we evaluate here is that unrecognised or relatively unexplored variants in these regions exist and are promising targets for future functional analyses. To test this hypothesis, we implemented a novel approach with targeted nanopore sequencing (Oxford Nanopore Technologies) for 200 kb regions centred on each of the eight AN-associated loci in 10 AN case samples. Our bioinformatics pipeline entailed base-calling and alignment with Dorado and minimap2 software, followed by variant calling with four separate tools, Sniffles2, Clair3, Straglr, and NanoVar. We then leveraged publicly available databases to characterise these loci in putative functional context and prioritise a subset of potentially relevant variants.

Results: Targeted nanopore sequencing effectively enriched the target regions (average coverage 14.64x). To test our hypothesis, we curated a list of 20 prioritised variants in non-coding regions, poorly represented in the current human reference genome but that may have functional consequences in AN pathology. Notably, we identified a polymorphic SINE-VNTR-Alu like sub-family D element (SVA-D), intergenic with IP6K2 and PRKAR2A, and a poly-T short tandem repeat (STR) in the 3'UTR of FOXP1.

Conclusions: Our results highlight the potential of targeted nanopore sequencing for characterising poorly resolved or complex variation, which may be initially obscured in risk-associated regions detected by GWAS. Some of the variants identified in this way, such as the polymorphic SVA-D and poly-T STR, could contribute to mechanisms of phenotypic risk, through regulation of several neighbouring genes implicated in AN biology, and affect post-transcriptional processing of FOXP1, respectively. This exploratory investigation was not powered to detect functional effects, however, the variants we observed using this method are poorly represented in the current human reference genome and accompanying databases, and further examination of these may provide new opportunities for improved understanding of genetic risk mechanisms of AN.

Background: Thyroid hormone (T3) has an inhibitory effect on tissue/organ regeneration. It is still elusive how T3 regulates this process. It is well established that the developmental effects of T3 are primarily mediated through transcriptional regulation by thyroid hormone receptors (TRs). Here we have taken advantage of mutant tadpoles lacking both TRα and TRβ (TRDKO), the only receptor genes in vertebrates, for RNA-seq analyses to investigate the transcriptome changes underlying the initiation of tail regeneration, i.e., wound healing and blastema formation, because this crucial initial step determines the extent of the functional regeneration in the later phase of tissue regrowth.

Results: We discovered that GO (gene ontology) terms related to inflammatory response, metabolic process, cell apoptosis, and epithelial cell migration were highly enriched among commonly regulated genes during wound healing at either stage 56 or 61 or with either wild type (WT) or TRDKO tadpoles, consistent with the morphological changes associated with wound healing occurring in both regenerative (WT stage 56, TRDKO stage 56, TRDKO stage 61) and nonregenerative (WT stage 61) animals. Interestingly, ECM-receptor interaction and cytokine-cytokine receptor interaction, which are essential for blastema formation and regeneration, were significantly enriched among regulated genes in the 3 regenerative groups but not the non-regenerative group at the blastema formation period. In addition, the regulated genes specific to the nonregenerative group were highly enriched with genes involved in cellular senescence. Finally, T3 treatment at stage 56, while not inducing any measurable tail resorption, inhibited tail regeneration in the wild type but not TRDKO tadpoles.

Conclusions: Our study suggests that TR-mediated, T3-induced gene regulation changed the permissive environment during the initial period of regeneration and affected the subsequent patterning/outgrowth period of the regeneration process. Specifically, T3 signaling via TRs inhibits the expression of ECM-related genes while promoting the expression of inflammation-related genes during the blastema formation period. Interestingly, our findings indicate that amputation-induced changes in DNA replication-related pathways can occur during this nonregenerative period. Further studies, particularly on the regenerative microenvironment that may depend on ECM-receptor interaction and cytokine-cytokine receptor interaction, should provide important insights on the regulation of regenerative capacity during vertebrate development.

This study aimed to investigate the temporal accumulation of odor fatty acids (OFAs) in the dorsal subcutaneous adipose tissue, and uncover their dynamic regulatory metabolic pathways from the transcriptomic perspective in lambs from birth to market. Thirty-two Hulun Buir lambs were selected and randomly assigned to four different sampling stages following their growth trajectories: neonatal (day 1), weaning (day 75), mid-fattening (day 150), and late-fattening (day 180) stages. Results indicated that the contents of three OFAs increased progressively as lambs matured, with the most drastic change occurred at mid-fattening vs. weaning. The dynamic transcriptomic profiles exhibited two distinct phases, with differentially expressed genes (DEGs) before weaning were involved in immune homeostasis, whereas those after weaning were associated with nutrient metabolism. Furthermore, DEGs involved in lipid metabolism and branch-chain amino acid degradation pathways exhibited surge in expression at mid-fattening vs. weaning, with acetyl-CoA and branched-chain-CoA as intermediates, and driven by regulation of PPAR and AMPK signaling pathways. Overall, our findings provided novel insight into the critical time window and pivotal candidate genes of OFA synthesis in the adipose tissue, which will assist with the targeted development of nutritional strategies to inhibit OFA accumulation of lambs.