BMC Genomics最新文献

Haemadipsa yanyuanensis Liu & Song, 1977, is a terrestrial blood-feeding leech whose antithrombotic repertoire remains insufficiently characterized. We present its first chromosome-level genome assembly (165.32 Mb across nine chromosomes; BUSCO: 97.6%) using Nanopore long reads, Hi-C scaffolding, and RNA-seq data. We identified 193 putative antithrombotic genes in 15 putative families, representing a 2.2- to 2.7-fold increase in gene number but reduced family diversity compared with aquatic medicinal leeches, including Hirudo nipponia Whitman, 1886, Hirudinaria manillensis Lesson, 1842, and Hirudo medicinalis Linnaeus, 1758. Notably, the putative bdellin, LDTI, and LCI gene families exhibited marked lineage-specific expansions, ranging from 8.7- to 25-fold relative to those of aquatic leeches. In addition, the putative progranulin gene displayed a distinctive structural organization characterized by 122 cysteine residues and nine tandem repeats. Transcriptomic profiling revealed elevated expression of four expanded putative families, suggesting potential roles in terrestrial blood-feeding adaptation. This chromosome-scale genome provides a valuable resource for investigating anticoagulation mechanisms and may inform the development of next-generation antithrombotic therapeutics.

Background: The Ningxiang pig, a renowned indigenous Chinese breed characterized by exceptional fat deposition, is an ideal model for studying the role of RNA editing in adipose tissue development.

Results: In this study, we constructed a dynamic landscape of RNA editing in subcutaneous adipose tissue across four developmental stages (30, 90, 150, and 210 days) using whole-genome resequencing and transcriptome sequencing data. A total of 86,540 RNA editing sites were identified, with A-to-G conversions being the predominant type (95.73%). These sites were primarily located in intronic regions (80.35%) and highly enriched within the pig-specific SINE retrotransposon PRE-1 (63.08% of all sites). Differential editing analysis revealed 2,023 differentially edited sites (DESs), corresponding to 956 genes, which were significantly enriched in lipid metabolism, insulin signaling, and PI3K-Akt pathway. Temporal clustering analysis identified nine distinct editing patterns, demonstrating stage-specific functional dynamics: early-stage (30 days) events were predominantly involved in catabolic processes; mid-stage events shifted toward PPAR and PI3K-Akt signaling; and late-stage (210 days) events were mainly associated with autophagy and focal adhesion pathways-indicating functional reprogramming of RNA editing during adipogenesis. Integrated protein-protein interaction (PPI) and weighted gene co-expression network analysis (WGCNA) identified hub genes including FOXO3, MAPK1, and PPP2CA, and revealed stage-specific co-editing modules-MEgreen associated with early proliferation and MEturquoise with late-stage maturation.

Conclusions: This study provides a comprehensive RNA editing atlas of adipose development in the Ningxiang pig, revealing its potential role in regulating fat deposition and offering new insights into post-transcriptional regulatory mechanisms in swine.

Background: Chromatin accessibility is a fundamental determinant of genome regulation, enabling transcription factors and RNA polymerase to bind DNA and drive developmental programs. While accessibility landscapes have been studied in model organisms such as Caenorhabditis elegans, almost nothing is known about the regulatory architecture of parasitic nematodes.

Results: We used assay for transposase-accessible chromatin with sequencing (ATAC-seq) to characterise the first genome-wide chromatin accessibility map for Haemonchus contortus - a major pathogen of ruminants and a key model organism for the parasitic nematode order Strongylida, which includes many pathogens of humans and animals. Analysis of embryonated eggs produced ~ 700 million high-confidence reads and identified 22,922 reproducible 'open' chromatin regions. Promoter accessibility was concentrated around transcription start sites and defined 3,897 promoter-accessible genes (~ 20% of the genome). These genes were highly enriched in developmental processes and signalling pathways, including Hippo, Rap1 and FOXO, and showed significantly higher expression across cell types compared with inaccessible genes. Accessible promoters also corresponded disproportionately to genes predicted to be essential, as supported by two independent computational frameworks. Integration with co-expression networks revealed enrichment of promoter-accessible genes in modules linked to translation, protein targeting and proteostasis. Motif analysis identified 378 enriched motifs representing ~ 100 transcription factors, dominated by Homeobox, bHLH, nuclear hormone receptor and Forkhead families, all known regulators of embryogenesis.

Conclusion: This study defines the first chromatin accessibility landscape for a parasitic nematode and delivers a resource for investigating developmental regulation, adaptation and host-parasite interactions.

Background: Gypsophila Radix (Chinese: ShanYin ChaiHu) is a traditional Chinese medicine derived from the dried roots of three Caryophyllaceae species: Silene jenisseensis, Arenaria juncea, and Gypsophila licentiana. Clinically, it is used as an adjuvant therapy for hepatic fibrosis in chronic hepatitis B. However, no reports have yet described the chloroplast genomes of these species. This study aimed to sequence and characterize the chloroplast genomes of these three species and to explore their phylogenetic relationships within Caryophyllaceae.

Methods: The complete chloroplast genomes of S. jenisseensis, A. juncea, and G. licentiana were sequenced and annotated. Comparative genomic analyses were performed among these species and with representative members of the same family to identify genomic variation, simple sequence repeats (SSRs), and repetitive sequences.

Results: The chloroplast genome of S. jenisseensis, G. licentiana and A. juncea were 161,759 bp, 152,676 bp, and 134,812 bp in length, respectively, showing considerable size variation. A. juncea contained 46 SSRs and 16 repetitive sequences; G. licentiana contained 83 SSRs and 47 repetitive sequences; while, S. jenisseensis had the highest numbers, with 125 SSRs and 50 repetitive sequences, Phylogenetic analysis revealed that these three newly sequenced chloroplast genomes formed well supported subgroups within their respective genera: Silene, Gypsophila, and Arenaria, confirming the monophyly of these genera.

Conclusions: The comparative analysis of repetitive sequence and SSRs provide valuable insights for developing chloroplast genome-based markers. This study enriches the chloroplast genomic resources of Caryophyllaceae and lays a foundation for species identification, evolution studies and the genetic resource utilization of Caryophyllaceae.

Background: Aeromonas hydrophila, a widespread aquatic pathogen, can infect a range of aquatic organisms, such as fish and crustaceans (including Eriocheir sinensis). Understanding the host resistance mechanism against A. hydrophila infection is of significant importance.

Results: In this study, the metabolic and transcriptomic profiles of crabs (E. sinensis) at different stages of A. hydrophila infection (early-infection stage: Ah_6h, mid-infection stage: Ah_24h, and late-infection stage: Ah_72h) were investigated. Metabolomic analysis showed that differentially expressed metabolites were predominantly enriched in purine metabolism pathways. Transcriptomic analysis revealed that the infection might activate the crab's immune response through key signaling pathways, including NF-κB and RIG-I-like receptor pathways, at the early-infection stage, while potentially maintaining immune function throughout infection via apoptosis, phagocytosis, and lysosomal pathways. Notably, the mid-infection stage was the pivotal period in the regulation of the crab's immune response, with the highest levels of differential metabolites and genes. Integrated transcriptomic and metabolomic analysis further highlighted the potential key roles of the tricarboxylic acid (TCA) cycle and purine and pyrimidine metabolisms in the immune response of E. sinensis against A. hydrophila.

Conclusions: These findings provide a better understanding of the immunity of E. sinensis in response to bacterial infection.

Background: Aerobic eukaryotes utilize O₂ to oxidize metabolites and generate ATP. The response to oxygen deprivation leads to migration to locations with more favorable concentrations (aerotaxis), differentiation, metabolic reprogramming, or more global stress responses. In mammals, changes in gene expression are particularly well studied, with the involvement of the Hypoxia-Inducible Factor (HIF-1), which regulates the transcription of hundreds of genes. However, the protist kingdom lacks the HIF-dependent transcriptional response network to adapt to low O₂ levels, and their hypoxic adaptation remains unexplored.

Results: To address the scale and scope of hypoxic responses in protists, we characterized transcriptomic and proteomic changes when the social amoeba Dictyostelium is subjected to low (1%) O₂ under nutritive conditions over 24 h followed by reoxygenation. Remarkably, 32% of the transcripts quantified were differentially expressed during hypoxia, with greatest changes associated with early (1 h) and late phases (24 h). Protein changes were modestly correlated with and generally lagged behind transcriptional changes. Correlated changes were observed for transcripts and proteins associated with various metabolic, anabolic, and catabolic pathways, as well as chromosome organization, cell cycling, vesicular trafficking, and signaling. Interestingly, transcripts associated with the cAMP signaling pathway normally triggered by starvation were also up-regulated during chronic hypoxia. Additionally, we studied the molecular mechanisms driving the transcriptomic response. Analysis of 4 marker genes showed extremely rapid responses that were graded over a range of O₂ levels, with differential responses to inhibitors affecting protein synthesis and mitochondria, suggesting multiple induction mechanisms driving the transcriptomic response.

Conclusion: Overall, the amoebal response to a low but non-toxic O₂-level resulted in massive and temporal remodeling of the transcriptome and proteome. This complex expression changes extend beyond simple metabolic adaptation and point toward a multiprong adaptation strategy.

Rice eating and cooking quality (ECQ) is a key determinant of consumer preference and market value, governed by complex genetic and biochemical mechanisms. This study aimed to dissect the genetic architecture underlying three major ECQ-related traits including amylose content (AC), gelatinization temperature (GT), and gel consistency (GC), using a panel of 243 diverse rice accessions through a genome-wide association study (GWAS), epistatic interaction analysis, haplotype analysis, and gene expression profiling. Phenotypic evaluation revealed extensive variability for all three traits, accompanied by high narrow-sense heritability estimates, indicating strong genetic control. Based on the FarmCPU model, 29 significant SNPs corresponding to 23 quantitative trait loci (QTLs)-11 for GT, 6 for GC, and 6 for AC-were identified across 10 chromosomes. Among them, qAC6-1, overlapping with the Waxy (WX1/GBSS1) gene, was determined as the major locus for AC; qGC2-1 on chromosome 2 emerged as the principal region governing GC; and three major GT-related QTLs (qGT6-1, qGT6-2, qGT6-3) were located near the SSIIa gene on chromosome 6. Epistatic analysis revealed 18 significant interactions (4 for AC, 6 for GC, and 8 for GT), underscoring the polygenic and interactive nature of rice quality traits. Haplotype analysis within qGC2-1 identified three haplogroups, among which H001-defined by the SNP combination "G/T/G/A"-was associated with superior gel consistency. Functional annotation and RNA-Seq expression profiling identified 12 candidate genes potentially involved in ECQ regulation, including WX1, Amy2A, IRX9, OsNAC1, PMEI25, and OsFbox132. Quantitative RT-PCR validated the expression of key genes (WX1, Amy2A, and IRX9) at different seed developmental stages in high- and low-quality rice genotypes. Overall, the integration of genomic, haplotypic, and transcriptional analyses provides new insights into the molecular control of rice grain quality. The identified QTLs, candidate genes, and favorable haplotypes serve as valuable genomic resources for marker-assisted selection and molecular breeding strategies aimed at developing rice varieties with superior eating and cooking qualities.

Background: Crustacean aquaculture is one of the most important food sectors globally and projected to grow. It is a source of nutritious and economic animal protein in many countries. As the global demand for sea food increases, and with an increase in climatic and pathogenic threats to the industry, curating our current knowledge about crustaceans, as well as generating new tools and resources to help minimise the impact of various diseases on the sustainability of the industry is of the utmost importance to increase the resilience of the farmed animal stocks. The main aim of this pilot study was to create a new cell atlas for Pacific whiteleg shrimp (Litopenaeus vannamei) hepatopancreas which encapsulates both the different hepatocyte cell states as well as the various supporting cells found throughout the hepatopancreas, while developing a new method for nuclei isolation and data analysis in the species.

Results: We developed new protocols for TST-based nuclei isolation which could be used to successfully isolate and process crustacean-derived nuclei for single nuclei RNA-sequencing analysis with minimal nuclei degradation using frozen hepatopancreas tissue from healthy L. vannamei adults. The bioinformatic analysis that followed allowed us to create a new cell atlas for the hepatopancreas which details the different hepatocyte cell states. Additionally, we built up on the existing knowledge by also analysing the multiple supporting cell clusters such as IECs, fibroblasts and myocytes, which helps improve our understanding of the characteristics of this immune-related organ.

Conclusion: Overall, 4005 cells were assigned to nine different clusters. Distinct marker genes suggest unique functions of each hepatocyte subtypes and adjacent supportive cells. The new TST-based isolation method for frozen or archived nuclei is particularly useful for processing difficult samples, such as the hepatopancreas, minimise stress and dissociation bias while allowing for greater flexibility between tissue sampling and processing times. Combining the knowledge gained through this study with past and future work in other penaeid shrimp species will allow us to create a powerful resource that will help uncover new knowledge about these important species, especially in the field of stress and immunity.

Mitochondrial DNA (mtDNA) is a crucial genetic marker for tracing maternal ancestry, understanding population history, and identifying disease-associated variants. Northern Pakistan, particularly the Kohistani and Gilgiti populations, lies at a historically significant crossroads of human migration, yet remains genetically understudied. Previous studies on these populations have primarily focused on the mtDNA control region, limiting insights into their genetic diversity, demographic history, and health-related mutations. A comprehensive whole mitogenome analysis is essential to bridge this gap and provide a more complete understanding of their genetic landscape. This study presents the first whole mitogenome analysis of the Kohistani and Gilgiti populations, leveraging next-generation sequencing to examine 120 complete mitochondrial genomes. This approach allows for a more detailed exploration of genetic diversity, population structure, and disease-associated mutations. Our primary focus is to investigate population history, genetic affinities, and clinically relevant mtDNA variations in these groups, contributing to both evolutionary genetics and precision medicine. We observed high genetic diversity, with balancing selection evident in the Gilgiti population and signals of recent expansion in the Kohistani group. Additionally, we identified mtDNA mutations associated with Leber's Hereditary Optic Neuropathy (m.11778G > A, m.14484T > C), which are well established pathogenic variants known to exhibit incomplete penetrance in other populations, as well as MIDD and MELAS (m.3243 A > G) and metabolic syndrome (m.10398 A > G), revealing population-specific health risks that warrant cautious interpretation. These findings highlight the importance of population-specific genetic studies for disease risk assessment and healthcare planning. By characterizing the mitogenomic landscape of these populations, our study provides critical insights into the genetic history in Kohistani and Gilgiti population and biomedical significance. Overall, this work not only enriches our understanding of human migration dynamics in Northern Pakistan but also establishes a valuable reference for future anthropological and biomedical research.