BMC Genomics最新文献

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.

Background: Recent advancements in methodologies and technologies have enabled the simultaneous measurement of multiple omics data, which provides a comprehensive understanding of cellular heterogeneity. However, existing methods have limitations in accurately identifying cell types while maintaining model interpretability, especially in the presence of noise.

Methods: We propose a novel method called scMFG, which leverages feature grouping and group integration techniques for the integration of single-cell multi-omics data. By organizing features with similar characteristics within each omics layer through feature grouping. Furthermore, scMFG ensures a consistent feature grouping approach across different omics layers, promoting comparability of diverse data types. Additionally, scMFG incorporates a matrix factorization-based approach to enable the integrated results remain interpretable.

Results: We comprehensively evaluated scMFG's performance on four complex real-world datasets generated using diverse sequencing technologies, highlighting its robustness in accurately identifying cell types. Notably, scMFG exhibited superior performance in deciphering cellular heterogeneity at a finer resolution compared to existing methods when applied to simulated datasets. Furthermore, our method proved highly effective in identifying rare cell types, showcasing its robust performance and suitability for detecting low-abundance cellular populations. The interpretability of scMFG was successfully validated through its specific association of outputs with specific cell types or states observed in the neonatal mouse cerebral cortices dataset. Moreover, we demonstrated that scMFG is capable of identifying cell developmental trajectories even in datasets with batch effects.

Conclusions: Our work presents a robust framework for the analysis of single-cell multi-omics data, advancing our understanding of cellular heterogeneity in a comprehensive and interpretable manner.

Background: The red claw crayfish (Cherax quadricarinatus) is a commercially and ecologically significant species that displays a unique intersex model with an ovotestis gonad and was identified to have functional testes and a vestigial ovary, which was inhibited by insulin-like androgenic gland hormone (IAG), but the underlying molecular mechanisms are still unclear.

Results: In this study, the structure and transcriptomic profiles of ovotestis and female and male gonad was analysis and compared, 406 differentially expressed genes were identified, among which membrane-anchored AG-specific factor (MAG) exhibited significantly greater expression in ovotestis gonads than in male or female gonads. The localization of MAG in type I or II cells of androgenic gland revealed its potential function of IAG hormone synthesis. Furthermore, the analyses of gene regulation relationship revealed that IAG positively regulates MAG expression, while MAG negatively regulates vitellogenin gene (VTG) expression.

Conclusions: Our research suggesting MAG participates in the IAG regulated ovarian suppression in the intersex red claw crayfish, which provides important information on the regulatory mechanism of the ovarian dysplasia in the ovotestis of intersex red claw crayfish. These results will enhance the knowledge of IAG-related pathways in the female reproductive axis, as well as the mechanisms of sexual differentiation in crustaceans.

Background: This cross-sectional study investigated the relationship between genetic variations in monocarboxylate transporter genes and blood lactate production and removal after high-intensity efforts in humans. The study was conducted to explore how genetic variations in the MCT1, MCT2, and MCT4 genes influenced lactate dynamics and to advance the field of sports genetics by pinpointing critical genetic markers that can enhance athletic performance and recovery.

Methods: 337 male athletes from Poland and the Czech Republic underwent two intermittent all-out Wingate tests. Before the tests, DNA samples were taken from each participant, and SNP (single nucleotide polymorphism) analysis was carried out. Two intermittent all-out tests were implemented, and lactate concentrations were assessed before and after these tests.

Results: Sprinters more frequently exhibited the haplotype TAC in the MCT2 gene, which was associated with an increase in the difference between maximum lactate and final lactate concentration. Additionally, this haplotype was linked to higher maximum lactate concentration and was more frequently observed in sprinters. The genotypic interactions AG/T- and GGxT- (MCT1 rs3789592 x MCT4 rs11323780), TTxTT (MCT1 rs12028967 x MCT2 rs3763979), and MCT1 rs7556664 x MCT4 rs11323780 were all associated with an increase in the difference between maximum lactate concentration and final lactate concentration. Conversely, the AGxGG (MCT1 rs3789592 x MCT2 rs995343) interaction was linked to a decrease in this difference. The relationship between maximum lactate concentration and genotypic interactions can be observed as follows: when ATxTT (MCT2 rs3763980 x MCT4 rs11323780) or CTxCT (MCT1 rs10857983 x MCT2 rs3763979) genotypic combinations are present, it leads to a decrease in maximum lactate concentration. Similarly, the combination of CTxCT (MCT1 rs4301628 x MCT2 rs3763979), CT x TT (MCT1 rs4301628 x MCT4 rs11323780), and CTxTT (MCT1 rs4301628 x MCT2 rs3763979) results in decreased maximum lactate concentration.

Conclusions: The TAC haplotype (rs3763980, rs995343, rs3763979) in the MCT2 gene is associated with altered lactate clearance in sprinters, potentially affecting performance and recovery by elevating post-exercise lactate concentrations. While MCT4 rs11323780 is also identified as a significant variant in lactate metabolism, suggesting its role as a biomarker for sprinting performance, further investigation is necessary to clarify underlying mechanisms and consider additional factors. Based on elite male athletes from Poland and the Czech Republic, the study may not generalize to all sprinters or diverse athletic populations. Although genetic variants show promise as biomarkers for sprinting success, athletic performance is influenced by a complex interplay of genetics, environment, and training extending beyond MCT genes.

Solute carriers (SLC) are integral membrane proteins responsible for transporting a wide variety of metabolites, signaling molecules and drugs across cellular membranes. Despite key roles in metabolism, signaling and pharmacology, around one third of SLC proteins are 'orphans' whose substrates are unknown. Experimental determination of SLC substrates is technically challenging, given the wide range of possible physiological candidates. Here, we develop a predictive algorithm to identify correlations between SLC expression levels and intracellular metabolite concentrations by leveraging existing cancer multi-omics datasets. Our predictions recovered known SLC-substrate pairs with high sensitivity and specificity compared to simulated random pairs. CRISPR-Cas9 dependency screen data and metabolic pathway adjacency data further improved the performance of our algorithm. In parallel, we combined drug sensitivity data with SLC expression profiles to predict new SLC-drug interactions. Together, we provide a novel bioinformatic pipeline to predict new substrate predictions for SLCs, offering new opportunities to de-orphanise SLCs with important implications for understanding their roles in health and disease.

Background: Soybean (Glycine max (L.) Merr.) is a crucial crop due to its high plant protein and oil content. Previous studies have shown that soybeans exhibit significant heterosis in terms of yield and protein content However, the practical application of soybean heterosis remains difficult, as the molecular mechanisms underlying photoperiod-sensitive genic male sterile (PGMS) is still unclear.

Results: This study characterized the PGMS line 88-428BY, which is sterile under short-day (SD) conditions and fertile under long-day (LD) conditions. To elucidate the genetic basis for this trait, we collected anthers, from 88-428BY under SD and LD conditions at three developmental stages, resulting in the identification of differentially expressed genes (DEGs) (2333, 2727 and 7282 DEGs, respectively) using Illumina transcriptome analysis. Using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, we fund that among the DEGs, enriched genes were associated with photoperiod stress, light stimulus, oxidation-reduction processes, multicellular organism development and protein phosphorylation. Additionally, weighted correlation network analysis identified four modules (blue, brown, red, and yellow) that were significantly correlated with PGMS, revealing co-expressed hub genes with potential regulatory roles. Functional annotation of 224 DEGs with|KME| >0.9 across the four modules in seven databases highlighted their involvement in light stimulus, oxidation-reduction processes, multicellular organism development, and protein phosphorylation, suggesting their importance in soybean PGMS. By integrating fertility-related genes previously identified by other studies with the DEGs from our analysis, we identified eight candidate genes associated with the photosensitive sterility in soybeans.

Conclusions: This study enhances the understanding of PGMS in soybean and establishes the genetic basis for a two-line hybrid seed production system in soybean.

Background: The accumulation of cadmium (Cd) in ryegrass (Lolium multiflorum Lamk.) as a widely used pasture plant poses a serious risk to food safety. This study aimed to investigate the differences in phenotypes, physiology, and expression of metal transporters between four ryegrass genotypes (diploid/tetraploid and Cd-tolerant/sensitive).

Results: The diploid/Cd-sensitive genotypes were found to uptake, accumulate, and translocate more Cd compared to the tetraploid/Cd-tolerant genotypes. Cd with more soluble components facilitated the transfer of Cd from root to shoot in the sensitive genotypes. Tetraploid and Cd-tolerant Chuansi No.1 accumulated less Cd in shoots but higher ratio in root cell wall, making it a promising model for studying the mechanisms of plant resistance to Cd stress. The complex regulatory system and dilution effect contributed to the lower uptake and accumulation of Cd in tetraploid genotypes. Moreover, tetraploid genotypes exhibited higher expression of genes that promoted Cd efflux, which could contribute to their lower Cd accumulation.

Conclusions: Overall, this study sheds light on the physiological and transcriptional mechanisms of Cd uptake and accumulation by different polyploids, providing guidance for ryegrass breeding and soil improvement.

Background: In plants, FK506-binding proteins (FKBPs) have been shown to participate in various biological processes such as photosynthetic system reaction, stress response, and growth and development. However, the roles of FKBPs in cotton are less well known.

Results: In this study, we investigated FKBP family genes on a genome-wide scale in four Gossypium species. A total of 147 FKBP genes were identified from these four Gossypium species and placed into three classes based on phylogenetic analysis. Collinearity analysis indicated that whole-genome duplication events and segmental duplication events were the main sources of gene amplification during the evolution of FKBP genes. Conserved motif, expression profiles and cis-acting elements prediction of the GhFKBPs analysis revealed that GhFKBPs were differentially expressed in different tissues and under abiotic stress. qRT-PCR analysis showed that some GhFKBPs were predominantly expressed in leaves. The analysis of cis-acting elements prediction revealed that MYB, MYC and ERE related binding sites in the promoters of GhFKBP genes were the most abundant. Furthermore, the composition and distribution of these cis-acting elements exhibited differences between homologous GhFKBP gene pairs. Silencing of GhFKBP13 in cotton resulted in disruption of chloroplast structure and starch metabolism disorders.

Conclusions: Taken together, 147 FKBP family genes in four Gossypium species are comprehensively characterized, and GhFKBP13 play a critical role in chloroplast biogenesis in upland cotton.

Background: An alternative approach to investigate associations between genetic variants and disease is to examine deviations from the Hardy-Weinberg equilibrium (HWE) in genotype frequencies within a case population, instead of case-control association analysis. The HWE analysis requires disease cases and demonstrates a notable ability in mapping recessive variants. Allelic heterogeneity is a common phenomenon in diseases. While gene-based case-control association analysis successfully incorporates this heterogeneity, there are no such approaches for HWE analysis. Therefore, we proposed a gene-based HWE test (gene-HWT) by aggregating single-nucleotide polymorphism (SNP)-level HWE test statistics in a gene to address allelic heterogeneity.

Results: This method used only genotype count data and publicly available linkage disequilibrium information and has a very low computational cost. Extensive simulations demonstrated that gene-HWT effectively controls the type I error at a low significance level and outperforms SNP-level HWE test in power when there are multiple causal variants within a gene. Using gene-HWT, we analyzed genotype count data from a genome-wide association study of six cancer types in Japanese individuals and suggest DGKE and ANO3 as potential germline factors in colorectal cancer. Furthermore, FSTL4 was suggested through a combined analysis across the six cancer types, with particularly notable associations observed in colorectal and prostate cancers.

Conclusions: These findings indicate the potential of gene-HWT to elucidate the genetic basis of complex diseases, including cancer.