BMC Genomics最新文献

Background: tRNA fragments (tRFs) are small non-coding RNAs generated from cleaved tRNA molecules, playing key roles in gene regulation and cellular processes. Produced by ribonucleases like angiogenin and Dicer, tRFs vary in length and function in gene silencing and stress responses. They interact with Argonaute proteins and affect mRNA levels, and are emerging as potential diagnostic and therapeutic targets for diseases such as cancer and neurodegenerative disorders. Given that the skin is the largest organ in mammals, it serves as an ideal model for studying development and various diseases. Therefore, this study investigates tRF expression in sheep skin tissues to understand their regulatory roles during growth and development.

Results: This study analyzed skin tissue from five 1-month-old lambs and five 24-month-old adult Tan sheep using small RNA sequencing and proteomics. Raw sequencing data were filtered and aligned to identify various tsRNAs, while proteomic data were assessed for differential expression. Principal Component Analysis (PCA) revealed distinct separation between juvenile and adult samples based on tsRNA expression patterns, indicating intra-group similarity and inter-group differences. Differentially expressed tsRNAs were identified, with 19 highly expressed tsRNAs at 1 month of age. Proteomic screening identified 932 highly expressed and 835 lowly expressed proteins in the 1-month-old group, with functional enrichment highlighting immunity and inflammation pathways. Predictive analysis of tsRNA target genes intersected with 20 differentially expressed proteins involved in mitochondrial metabolism and stress response.

Conclusion: This study reveals that tsRNAs significantly influence developmental and immune processes in sheep, with distinct expression patterns between juveniles and adults. Future research should validate these findings and further elucidate the functional mechanisms of tsRNA regulation.

Eimeria tenella (E. tenella) infection is a major cause of coccidiosis in chickens, leading to significant economic losses in the poultry industry due to its impact on the cecum. This study presents a comprehensive single-cell atlas of the chicken cecal epithelium by generating 7,394 cells using 10X Genomics single-cell RNA sequencing (scRNA-seq). We identified 13 distinct cell types, including key immune and epithelial populations, and characterized their gene expression profiles and cell-cell communication networks. Integration of this single-cell data with bulk RNA-seq data from E. tenella-infected chickens revealed significant alterations in cell type composition and state, particularly a marked decrease in APOB⁺ enterocytes and an increase in cycling T cells during infection. Trajectory analysis of APOB⁺ enterocytes uncovered shifts toward cellular states associated with cell death and a reduction in those linked to mitochondrial and cytoplasmic protection when infected with E. tenella. These findings highlight the substantial impact of E. tenella on epithelial integrity and immune responses, emphasizing the parasite's role in disrupting nutrient absorption and energy metabolism. Our single-cell atlas serves as a critical resource for understanding the cellular architecture of the chicken cecum and provides a valuable framework for future investigations into cecal diseases and metabolic functions, with potential applications in enhancing poultry health and productivity.

Background: The cytochrome P450 family 2 subfamily C member 9 (CYP2C9) exhibits extensive genetic variability that may influence the metabolism of approximately 16-20% of all drugs. Understanding the frequency and functional impact of the CYP2C9 variants is crucial for the implementation of pharmacogenetics. Our study aims to determine the frequencies of CYP2C9 variants in the Syrian population, contributing to the limited information available for Middle Eastern populations.

Methods: One hundred thirty-eight unrelated individuals from two major Syrian cities (Damascus and Homs) enrolled in this cross-sectional study. Genomic DNA was extracted from peripheral blood and specific PCR amplification products were purified and sequenced. The length of the amplicons allowed for the detection of 17 star alleles (i.e. *2, *8, *14, *20, *26, *33, *40, *41, *42, *43, *45, *46, *62, *63, *72, *73, and *78) in exon three, and seven star alleles (i.e., *3, *4, *5, *24, *55, *66, *68) in exon seven, in addition to two intronic variants. The frequencies of the functionally compromised CYP2C9*2^rs1799853 and CYP2C9*3^rs1057910 alleles were compared to same variants in other populations.

Results: Of the 24 exonic alleles investigated, only the *2, *3, *41, and *46 alleles were detected at frequencies of 14.8%, 8.3%, 1.45%, and 0.72%, respectively, with 43.5% of the study subjects carrying at least one dysfunctional variant. The genotype frequencies observed were as follows: *1/*1 (56.5%), *1/*2 (23.9%), *2/*2 (0.7%), *3/*1 (12.3%), *2/*3 (4.3%), *3/*3 (0%), *1/*41 (0.7%), *2/*41 (0%), *3/*41 (0.7%), *1/*46 (0.7%), *46/*2 (0%), and *46/*3 (0%). Moreover, frequencies of the rs933120 and rs933119 intronic alleles were 12.3% and 6.1%, respectively. A high linkage disequilibrium (LD) was found (D'=0.78) between the intronic rs933119 and exonic rs1799853 (*2 allele).

Conclusions: This study provides evidence for high prevalence of the CYP2C9 *2 and *3 alleles, and consequently the intermediate and poor metabolizer phenotypes in Syrians. Two rare putative function-relevant variants (*41 and *46) were detected in three individuals. These findings pave the path to the efforts for implementing CYP2C9 pharmacogenetics-based personalized pharmacotherapy in this Middle Eastern population.

Background: The basic helix-loop-helix (bHLH) transcription factors play important physiological functions in the processes of plant growth, development, and response to abiotic stresses. However, a comprehensive genome-scale study of the ginger bHLH gene family has not been documented.

Results: In this study, 142 ZobHLH genes were identified in the ginger genome. Using Arabidopsis bHLH proteins as a reference, ZobHLH genes were classified into 15 subfamilies and unevenly distributed on 11 chromosomes of ginger. Sequence characterization, multiple sequence alignment, phylogenetic analysis, conserved protein motifs and exon-intron distribution patterns were conducted to further analyze the evolutionary relationships among these ZobHLH proteins. The results of the duplicated event analysis demonstrated that the pivotal role of segment duplication in promoting the expansion of the ZobHLH gene family. Additionally, analysis of cis-regulatory elements as well as protein interaction networks indicated the potential involvement of ginger ZobHLH family proteins in plant growth and development, and response to adversity stress. RNA-seq and RT-qPCR results showed that ZobHLH083 and ZobHLH108 play key roles in response to salt stress and waterlogging stress, respectively.

Conclusion: In this study, we systematically analyzed the characteristics of ZobHLH proteins in ginger, discovering that these genes play critical roles in ginger rhizome expansion and response to salt and waterlogging stresses. The present study provides a theoretical foundation for the further research on ZobHLHs and will help to explore the functional properties of ZobHLH genes.

Background: The genus Cuscuta L. (Convolvulaceae), commonly known as dodder, is a holoparasite plant that relies on host plants for nutrition, leading to significant genomic changes, particularly in plastomes. This dependency has led to significant reductions and modifications in their plastomes compared to autotrophic plants. In contrast to the well-conserved plastomes of photosynthetic plants, Cuscuta exhibits substantial genomic reductions reflecting the loss of photosynthetic functions and associated genes.

Result: This study examines eight plastomes within Cuscuta and reconstructs the phylogenetic relationships among 40 Cuscuta taxa using five other genera as an outgroup. The size of plastid genome varies significantly, with the smallest being 60 kb and the largest 121 kb, highlighting extensive genomic reduction. In special cases, the subgenera Cuscuta exhibit the loss of inverted repeats, distinguishing from them other subge within the Cuscuta genus. This reduction is most pronounced in genes related to photosynthesis, such as atp, pet, psa, psb, and ycf genes, particularly in the subg. Grammica (Lour.) Peter. The study also notes the frequent and independent loss of the plastid genes infA, rpl23, rpl32, rps15, and rps16 across various angiosperm lineages, often involving transfer to the nuclear genome. In parasitic plants like Cuscuta, the ndh genes, crucial for photosynthesis, are often lost. The study also highlights that in the subg. Grammica, the matK and rpo genes, along with trnR-ACG genes, are lost in parallel, indicating that these parasitic plants do not need matK and rpo genes after the loss of ndh genes for survival. Analysis of selective relaxation pressure on plastid genes shows a reductive trend, with genes such as atp, pet, psa, psb, rpo, and ycf progressively becoming pseudogenes over time, with housekeeping genes like rpl and rps expected to follow. However, the pseudogenization process is specific to the subg. Grammica, Pachystigma (Engelm.) Baker & C.H.Wright, and Cuscuta, rather than in the subg. Monogynella (Des Moul.) Peter, Engl. & Prantl (ancient clade species).

Conclusion: The study of Cuscuta plastomes reveals the profound impact of parasitism on genome evolution, highlighting the complex interplay of gene retention and loss through phylogenomic approaches. This research enriches our understanding of plant genome evolution and the intricate host-parasite relationships. It also sheds light on the evolutionary history and genomic adaptations of Cuscuta, illustrating the diverse strategies enabling subg. Grammica, Pachystigma, Cuscuta, and Monogynella thrive as parasitic species. These findings provide valuable insights into the molecular mechanisms underlying parasitism and its impact on plastid genome organization.

Background: Interspecific hybrid combinations of Larimichthys crocea × Larimichthys polyactis exhibit heterosis in terms of growth traits; however, the molecular regulatory mechanism underlying this phenomenon remains unclear. DNA methylation plays a pivotal role in regulating gene expression and is involved in growth and development processes. In this study, we comprehensively investigated intricate regulatory processes by integrating transcriptome and methylome datasets from brain, liver, and muscle tissues.

Results: We analyzed a total of 72 sequence datasets, including transcriptome and genome-wide DNA methylome data, from 36 tissue samples using LC, LP, LPC and LCP. We elucidated the distinct expression patterns of these four populations and examined their interactions with DNA methylation. Our findings revealed diverse DNA methylation profiles and demonstrated a greater number of hypo-DMRs in hybrid yellow croakers than in their parental lines. The majority (86 ~ 92%) of these DMRs were observed within the CG context. Moreover, we found that most DMRs were located within promoter regions as well as exons and introns. A total of 1288 DMEGs were identified through correlation analysis between DNA methylation and transcriptional activity. Functional enrichment analysis revealed that most of the DMEGs were significantly enriched in pathways related to the protein export pathway, proteasome, terpenoid backbone biosynthesis, ubiquitin-mediated proteolysis, autophagy-other pathway. Furthermore, we screened candidate growth-related genes, such as stat2, capn2, akt1, mTOR, and mef2aa. Among these, the expression levels of capn2, mTOR, and akt1 exhibited a positive correlation with DNA methylation levels, whereas the expression levels of stat2 and mef2aa showed a negative correlation. These findings suggest that alterations in DNA methylation patterns may promote growth advantages in hybrid yellow croaker by modulating the expression of these genes.

Conclusions: Epigenetic changes exert distinct influences on genes related to growth heterosis. The presented data establish a foundation for comprehending the epigenetic and transcriptomic alterations underlying the growth of hybrid yellow croaker, thereby providing preliminary insights into the molecular mechanisms of growth heterosis. These findings have significant implications for breeding programs aimed at enhancing yellow croaker production.

Ensuring sufficient gRNA transcript levels is critical for obtaining optimal CRISPR-Cas9 gene editing efficiency. The standard gRNA scaffold contains a sequence of four thymine nucleotides (4T), which is known to inhibit transcription from Pol III promoters such as the U6 promoter. Our study showed that using standard plasmid transfection protocols, the presence of these 4Ts did not significantly affect editing efficiency, as most of the gRNAs tested (55 gRNAs) achieved near-perfect editing outcomes. We observed that gRNAs with lower activity were T-rich and had reduced gRNA transcript levels. However, this issue can be effectively resolved by increasing transcript levels, which can be readily achieved by shortening the 4T sequences. In this study, we demonstrated this by modifying the sequences to 3TC. Although the 3TC scaffold modification did not improve editing efficiency for already efficient gRNAs when high vector quantities were available, it proved highly beneficial under conditions of limited vector availability, where the 3TC scaffold yielded higher editing efficiency. Additionally, we demonstrated that the 3TC scaffold is compatible with SpCas9 high-fidelity variants and ABEmax base editing, enhancing their editing efficiency. Another commonly used natural Cas9 variant, SaCas9, also benefited from the 3TC scaffold sequence modification, which increased gRNA transcription and subsequently improved editing activity. This modification was applied to the EDIT-101 therapeutic strategy, where it demonstrated marked improvements in performance. This study highlights the importance of shortening the 4T sequences in the gRNA scaffold to optimize gRNA transcript expression for enhanced CRISPR-Cas9 gene editing efficiency. This optimization is particularly important for therapeutic applications, where the quantity of vector is often limited, ensuring more effective and optimal outcomes.

Background: The sequencing of non-model species has increased exponentially in recent years, largely due to the advent of novel sequencing technologies. In this study, we construct the Reference Genome of the Spanish toothcarp (Aphanius iberus (Valenciennes, 1846)), a renowned euryhaline fish species. This species is native to the marshes along the Mediterranean coast of Spain and has been threatened with extinction as a result of habitat modification caused by urbanization, agriculture, and its popularity among aquarium hobbyists since the mid-twentieth century. It is also one of the first Reference Genome for Euro-Asian species within the globally distributed order Cyprinodontiformes. Additionally, this effort aims to enhance our comprehension of the species' evolutionary ecology and history, particularly its remarkable adaptations that enable it to thrive in diverse and constantly changing inland aquatic environments.

Results: A hybrid assembly approach was employed, integrating PacBio long-read sequencing with Illumina short-read data. In addition to the assembly, an extensive functional annotation of the genome is provided by using AUGUSTUS, and two different approaches (InterProScan and Sma3s). The genome size (1.15 Gb) is consistent with that of the most closely related species, and its quality and completeness, as assessed with various methods, exceeded the suggested minimum thresholds, thus confirming the robustness of the assembly. When conducting an orthology analysis, it was observed that nearly all genes were grouped in orthogroups that included genes of genetically similar species. GO Term annotation revealed, among others, categories related with salinity regulation processes (ion transport, transmembrane transport, membrane related terms or calcium ion binding).

Conclusions: The integration of genomic data with predicted genes presents future research opportunities across multiple disciplines, such as physiology, reproduction, disease, and opens up new avenues for future studies in comparative genomic studies. Of particular interest is the investigation of genes potentially associated with salinity adaptation, as identified in this study. Overall, this study contributes to the growing database of Reference Genomes, provides valuable information that enhances the knowledge within the order Cyprinodontiformes, and aids in improving the conservation status of threatened species by facilitating a better understanding of their behavior in nature and optimizing resource allocation towards their preservation.

Background: Rubber tree (Hevea brasiliensis Muell. Arg.) is a significant commercial crop in tropical areas worldwide, with rubber production threatened by Tapping Panel Dryness (TPD). Rubber tree virus 1 (Capillovirus uniheveae; RTV1) was identified in rubber tree samples with TPD symptoms through RNA-seq. However, its genetic diversity may have hindered the detection of RTV1 via RT-PCR, complicating the further identification of RTV1 as the causative agent of TPD. To assess RTV1 prevalence and genomic diversity, rubber tree bark samples with TPD syndrome were collected from various sites in Hainan, China, for RNA-seq and RTV1 genome determination.

Results: Twenty complete RTV1 genomes were determined from 22 samples with TPD syndrome via RNA-seq and RT-PCR. Using degenerate primers based on conserved sequences in the 3'- and 5'-UTR, 20 complete RTV1 genomes were identified directly from 48 trees affected by TPD via RT-PCR. The 40 RTV1 genome sequences showed significant variations, particularly in the RdRp domain. Phylogenetic analysis of full-genome nucleotide sequences divided RTV1 isolates into three phylogroups (A, B, and C), with phylogroup A being the most prevalent (67.5%). Similar results were observed based on RdRp and CP phylogenetic analysis. Additionally, mixed infections with different genotypes were identified in the same tree. Notably, no genetic recombination was observed among different phylogroups, while ten recombination events were identified within phylogroup A.

Conclusions: RTV1 was identified in approximately 50% of samples with TPD syndrome collected in Hainan, China, with phylogroup A being the most prevalent. Considerable variations were observed in RTV1 nucleotide sequences among different phylogroups. These findings lay a foundation for accurate diagnostics, etiological characterization, and elucidation of the evolutionary relationships of RTV1 populations, providing a strong guarantee for obtaining virus-free rubber tree seedlings, and promoting the healthy and sustainable development of rubber tree plantations.