BMC genomic data最新文献

CGGBP1 is a GC-rich DNA-binding protein which is important for genomic integrity, gene expression and epigenome maintenance through regulation of CTCF occupancy and cytosine methylation. It has remained unclear how CGGBP1 integrates multiple diverse functions with its simple architecture of only a DNA-binding domain tethered to a C-terminal tail with low structural rigidity. We have used truncated forms of CGGBP1 with or without the DNA-binding domain (DBD) to assay cytosine methylation and global gene expression. Proximal promoters of CGGBP1-repressed genes, although significantly GC-poor, contain GC-rich transcription factor binding motifs and exhibit base compositions indicative of low C-T transition rates due to prevention of cytosine methylation. Genome-wide analyses of cytosine methylation and binding of CGGBP1 DBD show that CGGBP1 restricts cytosine methylation in a manner that depends on its DBD and its DNA-binding. The CGGBP1-repressed genes show an increase in promoter cytosine methylation alongside a decrease in transcript abundance when the DBD-deficient CGGBP1 is expressed. Our findings suggest that CGGBP1 protects transcription factor binding sites (TFBS) from cytosine methylation-associated loss and thereby regulates gene expression. By analysing orthologous promoter sequences we show that restriction of cytosine methylation is a function of CGGBP1 progressively acquired during vertebrate evolution. A superimposition of our results and evolution of CGGBP1 suggests that mitigation of cytosine methylation is majorly achieved by its N-terminal DBD. Our results position CGGBP1 DNA-binding as a major evolutionarily acquired mechanism through which it keeps cytosine methylation under check and regulates TFBS retention and gene activity.

Objectives: Wild soybean (Glycine soja), the ancestor of domesticated soybean, retains a higher level of genetic diversity and adaptability to harsh environments, making it highly valuable for breeding. Here, we re-sequenced 69 wild soybean individuals collected by the Shandong Academy of Agricultural Sciences and identified 1,613,162 high-quality SNPs which not only enriches our understanding of the genetic structure of wild soybean, but also provides valuable resources for further genomic research and genetic improvement of soybean.

Data description: In this study, we collected 69 wild soybean accessions from Shandong Province, China, and performed re-sequencing on the DNBSEQ platform, followed by SNPs identification. We then integrated ADMIXTURE, neighbor-joining tree, and principal component analysis to illustrate population characteristics. The results showed that these wild soybean accessions could be divided into three distinct subpopulations, exhibiting significant genetic differences.

Objectives: Mint oil is used in various commercial applications world-wide. Mint oil is typically harvested from commercial clones of peppermint or spearmints. Spearmints are the product of a cross between two diploid species: Mentha longifolia (horse mint) and Mentha suaveolens (apple mint). Peppermints are the product of an additional hybridization step between spearmint and an octoploid Mentha aquatica (water mint). Here, we present a chromosome-scale assembly of the genome of a clone of M. suaveolens. Together with the previously assembled genome of M. longifolia, these assemblies are instrumental in addressing questions regarding the origins of spearmint and peppermint oil and the genomic composition of commercial spearmints, and to start elaborating strategies for mint cultivar improvement.

Data description: A Falcon assembly of the genome of M. suaveolens was generated from 103X coverage of PacBio long reads. Additional scaffolding was conducted by Dovetail Genomics, using a Chicago library, and a HiC library. The resulting assembly had an N50 of 44.7 Mb, and 98.45% of the 536 Mb of the assembly were contained within 12 large superscaffolds. Finally, a genetic map was applied to correct persistent misjoins. Illumina RNA-Seq libraries from a variety of tissues were used to annotate the genome.

Objectives: Cutibacterium acnes is a Gram-positive bacterium commonly found on human skin, particularly in sebaceous areas. While it is typically considered a commensal, specific strain types based on single locus sequence typing (SLST) have been associated with pathogenic conditions or healthy skin. Recently, SLST D1 strains, part of phylotype IA1, have received attention for their potential benefits related to skin health. However, their genetic characteristics remain underexplored. Therefore, the whole genome of C. acnes CN6, an SLST D1 strain isolated from the facial skin of a healthy individual, was sequenced to expand the understanding of SLST D1 strains and identify genomic features that may support skin health.

Data description: The whole genome sequencing of C. acnes CN6 was conducted using MinION reads based on de novo assembly, revealing a single circular complete chromosome. With the length of 2,550,458 bp and G + C content of 60.04%, the genome contains 2,492 genes, including 2,433 CDSs, 9 rRNAs, 46 tRNAs, 4 ncRNAs, and 134 pseudo genes. Previously predicted virulence proteins of C. ances were detected in the genome. Genome comparation with 200 C. acnes strains isolated from healthy facial skin revealed SLST D1 strain-specific genes and a unique variant of the znuC gene in D1 strains.

Objectives: Purple blotch, caused by the necrotrophic pathogen Alternaria porri, is one of the most economically significant diseases of onion and allied crops. While the virulent nature of many Alternaria spp. has been identified, the pathogenic repertoire of A. porri is still unknown. The objective of this work was to sequence the genome of A. porri using the PacBio SMRT sequencing strategy and analyse the repertoire of CAZymes, secondary metabolites, secretome and effectors in A. porri. Our research group is working to identify onion germplasm with purple blotch resistance and to understand the genetics of the pathogen. The reported de-novo assembly will contribute to the analysis of potential variants and the gene repertoire contributing to the virulence and pathogenicity of the purple blotch pathogen.

Data description: Long-read sequencing on a PacBio Sequel II system resulted in a 32.98 Mb (20 contigs) assembly with an N50 of 2, 657, 264 bp, the longest contig length of 5.05 Mb, and a GC content of 51.06%. The Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis resulted in 99.7% genome completeness at the Dothideomycetes lineage, representing a high-quality genome assembly. AUGUSTUS ab initio analysis resulted in 9875 protein-coding genes. Of the 6776 pathogenicity-related genes, 537 genes with effector functions were identified. Likewise, the glycoside hydrolases (434) were the most dominant group of the total 837 predicted CAZymes. The assembled genome of A. porri showed distinctive similarities to the genomes of A. alternata and A. brassicicola, the causal agents of leaf blight of onion and leaf spot of Brassica crops, respectively.

Background: Coronary artery disease (CAD) significantly contributes to global fatalities. Recent studies have demonstrated the crucial roles of sortilin1 (SORT1) and sestrin1 (SESN1) in lipid metabolism, as well as their involvement in the development of CAD. The aberrant expression or activity of SORT1 can consequently lead to metabolic and vascular diseases. Sestrins, including SESN1, play a crucial role in helping cells survive by maintaining metabolic balance while also reducing oxidative stress (OS). OS contributes to the progression of atherosclerosis-related diseases, such as CAD. The study aimed to compare the gene expression of SORT1 and SESN1 in peripheral blood mononuclear cells (PBMCs), alongside serum OS markers, in CAD patients and controls.

Materials: The case-control study included 49 CAD patients and 40 controls. The expression of the SORT1 and SESN1 genes was quantified using qRT-PCR, and the expression of the SORT1 protein was evaluated by western blotting. OS markers, including total oxidation status (TOS), total antioxidant capacity (TAC), and malondialdehyde (MDA), were measured using spectrophotometric and fluorometric methods.

Results: SORT1 gene and protein expressions were similar between groups. CAD patients had a non-significant decrease in SESN1 gene expression. MDA levels were significantly higher in CAD patients, whereas TOS and TAC levels did not differ significantly.

Conclusion: For atherosclerosis-related disorders like CAD, MDA shows potential as a non-invasive, easy-to-use, affordable, and stable biomarker. Further research is needed to elucidate the precise roles of SORT1 and SESN1 in CAD pathogenesis.

Background: Inflammatory bowel disease (IBD) is occasionally associated with ophthalmic diseases, including iridocyclitis (IC). The co-occurrence of IBD and IC has been increasingly observed, possibly due to shared genetic structures.

Methods: A three-part analysis was executed utilizing genome-wide association study (GWAS) data on IBD and IC. First, the overall genetic correlation between the two traits was observed using linkage disequilibrium score regression (LDSC). Subsequent to this, a local genetic correlation analysis was conducted utilizing the heritability estimation from summary statistics (HESS) methodology. Finally, the conditional/conjunctional false discovery rate (cond/conjFDR) statistical framework was utilized to ascertain the degree of genetic overlap between the two traits.

Results: Positive overall correlations were observed among IBD, ulcerative colitis (UC), and IC, encompassing both acute/subacute and chronic IC presentations. While a significant correlation was identified between Crohn's disease (CD) and IC, it was not evident for acute/subacute or chronic IC (P > 0.05). Notably, IBD (encompassing CD and UC) demonstrated local genetic correlations with IC and acute/subacute IC, with pronounced enrichment notably on chromosomes 1 and 6, though such correlations were not observed with chronic IC. The conjFDR analysis confirmed the genetic overlap between the two diseases. The shared genes overlapping between IBD (encompassing CD and UC) and IC were IL23R, GPR35, and ERAP1. For acute/subacute IC and chronic IC, there were six overlapping genes (GPR35, RPL23AP12, IL23R, SNAPC4, ERAP1, and INAVA) and one overlapping gene (INAVA), respectively.

Conclusion: This study confirms the existence of a shared genetic structure between IBD and IC, providing a biological basis for their comorbidity. Additionally, this finding has significant implications for preventing and treating these two diseases.

Objectives: Chicken (Gallus gallus), as the most economically important poultry, is a classical and ideal model for studying the mechanism of vertebrate developmental biology and embryology. However, the sex determination and differentiation in chicken is still elusive, which limited the application and slowed down many basic studies in chicken.

Data description: We applied PacBio Iso-seq to multiple spatiotemporal embryo-gonad tissues in the male and female chicken, which contain the blastoderm (E0, un-differentiation stage), genital ridge (E3.5-6.5, sex-differentiation stage) and gonads (E18.5, full-sex-differentiation stage). We obtained 51,479 and 48,356 full-length transcripts in male and female chicken embryo, respectively. The comprehensive annotated and evaluated these transcripts. The 1,293 and 1,556 candidate lncRNAs, 5,766 and 4,211 AS events in male and female. Collectively, our data constitutes a grand increase in the known number of lncRNA, AS (Alternative splicing) and Poly(A) during chicken embryo sex-differentiation and plays an important role in improving current genome annotation. In the meantime, the data will be enriched the functional studies in other birds.

The root architecture, more seminal roots, and Deeper roots help the plants to uptake the resources from the deeper soil layer to ensure better growth. The Gibberellic acid-sensitive (GA-sensitive) Rht genes are well known for increasing drought tolerance in wheat. Much work has been performed on the effect of these genes on the plant agronomic traits and little work has been done on the effect of Rht genes on seminal roots and root architecture. This study was designed to evaluate 200 wheat genotypes under normal and osmotic stress. The genotypes were sown in the solution culture and laid under CRD factorial arrangement with three replications and two factors i.e., genotypes and treatments viz. normal and osmotic stress (20% PEG-6000) applied one week after germination. The data was recorded for the root traits. Results demonstrated that out of 200 genotypes, the GA-sensitive Rht13 gene was amplified in 21 genotypes with a fragment length of 1089 bp. In comparison, the GA-insensitive Rht1 gene was amplified in 24 genotypes with a band size of 228 bp. From 200 wheat genotypes, 122 genotypes produced 5 seminal roots, 4 genotypes 4 seminal roots, and 74 genotypes 3 seminal roots. The genotypes G-3 (EBW11TALL#1/WESTONIA-Rht5//QUAIU#1), G-6 (EBW01TALL#1/SILVERSTAR-Rht13B//ROLF07) and G-8 (EBW01TALL#1/SILVERSTAR-Rht13B//NAVJ07) produced 5 seminal roots and have longer coleoptile (> 4.0 cm), root (> 11.0 cm) and shoot (> 17 cm) under normal and osmotic stress. Furthermore, Ujala 16, Galaxy-13, and Fareed-06 produced 3 seminal roots and have short coleoptile (< 3 cm), root (< 9.0 cm) and shoot (< 10.0 cm). These results showed that the genotypes showing the presence of GA-sensitive Rht genes produced a greater number of seminal roots, increased root/shoot growth, and osmotic stress tolerance compared to the genotypes having GA-insensitive Rht genes. Thus, the Rht13 gene improved the root architecture which will help to uptake the nutrients from deeper soil layers. Utilization of Rht13 in wheat breeding has the potential to improve osmotic stress tolerance in wheat.

Objective: Paracidovorax avenae (Pa) is the causative agent of red stripe disease in sugarcane and belongs to the Gram-negative β-Proteobacteria. Red stripe is a major bacterial disease of sugarcane worldwide. Limited genome sequences of Pa can be used for exploring the phylogenetic and genetic diversity analysis in this pathogen at the complete genome level. In this study, a whole genome sequence of Pa CNGX08 strain isolated from sugarcane in China was assembled and annotated.

Data description: Genome assembly data from second- and third-generation sequencing revealed that the entire genomic sequence of Pa CNGX08 strain causing red stripe in sugarcane, consisted of a 5,625,582 bp circular chromosome with a GC content of 68.97%. In total, 4,915 protein-coding genes were annotated. Additionally, 9 ribosomal RNAs and 52 transfer RNAs were identified. This genomic resource will facilitate the genome-based taxonomic classification of the genus Paracidovorax and the exploration of pathogenic mechanisms underlying sugarcane red stripe disease caused by Pa.