BMC genomic data最新文献

Background: Primary carnitine deficiency (PCD) is an autosomal recessive rare disorder of carnitine cycle and carnitine transport caused by pathogenic variants in the SLC22A5 gene. The prevalence of PCD is unclear. This study aimed to estimate the carrier frequency and genetic prevalence of PCD using Genome Aggregation Database (gnomAD) data.

Methods: The pathogenicity of SLC22A5 variants was interpreted according to the American College of Medical Genetics and Genomics (ACMG) standards and guidelines. The minor allele frequency (MAF) of the variants of the SLC22A5 gene in 807,162 individuals was examined to estimate the global prevalence of PCD in nine ethnicities: African/African American (afr), Admixed American (amr), East Asian (eas), Non-Finnish European (nfe), South Asian (sas), Ashkenazi Jewish (asj), Middle Eastern (mid), Finnish (fin) and Remaining individuals (rmi). The global and population-specific carrier frequency and genetic prevalence of PCD were calculated using the Hardy-Weinberg equation.

Results: Total of 213 pathogenic/likely pathogenic variants (PV/LPV) of the SLC22A5 gene were identified according to the ACMG standards and guidelines. The global carrier frequency and genetic prevalence of PCD were 10.6 per thousand (1/95) and 28.2 per million (1/35427), respectively.

Conclusions: The prevalence of PCD is estimated to be 1/35,000 globally, with a range of between 1/450,000 and 1/20,000 depending on ethnicity.

Objectives: The degradation products of chitin exhibit various biological activities, giving them significant application potential. Chitinase-producing bacteria can be isolated from diverse environments such as soil, natural waters, and rhizospheres. However, their chitinolytic activity is often limited, particularly at low temperatures.

Data description: In this study, complete genome sequencing of a cold-adapted chitinolytic Pseudomonas strain, GWSMS-1, revealed a 4,606,781-bp linear chromosome with a G+C content of 59%. The genome encodes 4,599 protein-coding genes, 73 tRNA genes, and 27 rRNA genes. Functional annotation through GO, KEGG, and CAZy databases identified a substantial number of chitinase-encoding genes, which likely contribute to its high chitin-degrading capacity. The genomic insights into GWSMS-1 highlight its potential for applications in chitin degradation and offer valuable gene candidates for further research.

Antibiotic resistance is a major global health concern that caused by the overuse and misuse of antibiotics. Mobile genetic elements have a roles in the transmission of antibiotic resistance genes. The distribution and diversity of antibiotic resistance genes and mobile genetic elements in the microbiome of Sof Umer Cave have yet to be explored. To map the distribution and diversity of antibiotic resistance genes and mobile genetic elements in the microbiome of Sof Umer Cave using high-throughput shotgun sequencing. High-molecular-weight DNA was extracted from homogenized sample using the GeneAll DNA Soil Mini Kit. Purified environmental DNA was sequenced using a NovaSeq PE150. Analysis of the pathogen host interaction database revealed the predominance of pathogenic organisms such as Xanthomonas oryzae, Acinetobacter baumannii, Erwinia amylovora, and Mycobacterium tuberculosis. Similarly, analysis of the virulence factor database confirmed the presence of Type IV pili (VF1240), lipopolysaccharides, capsules, heme biosynthesis (VF0758), and alginate. More than 800 antibiotic resistance genes were identified, with 50% related to glycopeptide resistance, followed by antibiotic resistance genes associated with multidrug efflux pumps (30%), aminoglycoside resistance genes (10%), and unknown genes. A variety of mobile genetic elements were also identified, highlighting their importance in the genetic diversity and adaptation of the microbiome of Sof Umer Cave. These findings underscore the importance of the Sof Umer Cave habitat as a reservoir for antibiotic resistance, emphasizing the need for ongoing monitoring to enhance the understanding and control of antibiotic resistance genes.

Previous genomic characterisation of Rwanda dairy cattle predominantly focused on the One Cow per Poor Family (locally called "Girinka") programme. However, smallholder farmers in Rwanda have benefited from other livestock initiatives and development programmes. Capturing and documenting the genetic diversity, is critical in part as a key contribution to genomic resource required to support dairy development in Rwanda. A total of 2,229 crossbred animals located in all dairy-producing regions of Rwanda were sampled. For each animal, a hair sample was collected and genotyped by using the Geneseek Genomic Profiler (GGP, Neogen Geneseek^®) Bovine 50 K (n = 1,917) and GGP Bovine 100 K arrays (n = 312). The combined dataset was subject to quality control, data curation for use in population genetics and genomic analyses. To assess the genetic structure and diversity of the current population, key analyses for population structure were applied: Principal Component Analysis (PCA), population structure and diversity, admixture analysis, measures of heterozygosity, runs of homozygosity (ROH) and minor allelic frequency (MAF). A dataset of global dairy population of European taurine, African indicus and African taurus (n = 250) was used as reference. Results showed that Rwanda cattle population is highly admixed of diverse pure and crossbred animals with average MAF of 33% (standard error; se = 0.001) with proportion of foreign high yielding (taurine) dairy breeds of Jersey Island (18%); 12% non-Island Jersey and 42% Holstein-Friesian ancestries. Two African Bos taurus and five Bos indicus breeds contributed 28% of their genetics. Genetic distances were highest in Gir and N'dama (0.29); and Nelore and N'dama (0.29). There were 1,331 ROH regions and average heterozygosity were high for Rwanda cattle (0.41 se = 0.001). Asides well-established genes in cattle, we found evidence for a variety of novel and less-known genes under selection to be associated with fertility, milk production, innate immunity and environmental adaptation. This observed diversity offers opportunity to decipher the presence and/or lack of genetic variations to initiate short- and long-term breed improvement programmes for adaptation traits, disease resistance, heat tolerance, productivity and profitability of smallholder dairy systems in Rwanda.

Objective: The pathogenic fungus Diplodia sapinea is of significant importance due to its primary role inducing tip dieback on various Pinus species which are widely distributed throughout the world. The objective of this study is to further provide comprehensive and specific resources for genome assembly and sequence annotation of this important forest pathogen from China, thereby establishing a robust foundation for future studies on its systematics, population genetics, genomics and global movement.

Data description: A high-quality genome of D. sapinea strain ZXD319 was sequenced utilizing the Nanopore PromethION and BGI DNBSEQ-T7 platforms. The assembled genome spans a total length of 36.81 Mb, comprising 14 contigs, with a GC content of 56.80% and an N50 value of 2,972,533 bp. It encompasses 11,200 protein-coding genes and 252 noncoding RNAs. The predicted genes were annotated against multiple public databases, and 1,611 potential virulence genes were identified through the Pathogen Host Interactions (PHI) database. Furthermore, the genome comparative analysis of D. sapinea and related species revealed 11,568 gene clusters and 3,436 single-copy clusters. Phylogenetic analysis indicated a close evolutionary relationship between D. sapinea with D. corticola and D. seriata. The genomic data presented herein serve as a valuable resource for future studies on this globally important pathogen.

Objectives: Lactobacillales, commonly known as lactic acid bacteria (LAB), is an order of Gram-positive, facultatively anaerobic or microaerophilic bacteria characterized by their ability to ferment carbohydrates and produce lactic acid as a major metabolic byproduct. Many species within this group have significant roles in food fermentation, human health, and industrial applications. Here, we report the complete genome sequence of Fructilactobacillus vespulae Mu01, the first sequenced genome of this species. The complete genome sequence of F. vespulae Mu01 is expected to provide valuable insights into the genetics and metabolism of this little-characterized species.

Data description: A novel strain of Fructilactobacillus vespulae was isolated from nectar of Musa paradisiaca L. during a survey for LAB associated with wild and cultivated plants in the metropolitan area of Valencia, Spain. A complete genome was obtained by sequencing with Nanopore long read technology. The genome consists of a chromosome of 1506092 bp and a plasmid of 42437 bp, presenting a GC content of 36 % and 31 %, respectively. The genome includes 1541 genes, with 1450 CDSs, 7 pseudogenes, 18 rRNA encoding genes, 63 tRNAs and 3 ncRNAs.

Background: Cystinosis is a rare autosomal recessive lysosomal storage disorder caused by mutations in the CTNS gene, which encodes cystinosin, a lysosomal cystine transporter. These mutations disrupt cystine efflux, leading to its accumulation in lysosomes and subsequent cellular damage. While more than 140 mutations have been identified, the functional and structural impacts of many nonsynonymous single nucleotide polymorphisms (nsSNPs) remain poorly understood. Nonsynonymous SNPs are of particular interest because they can directly alter protein structure and function, potentially leading to disease. Clinically, cystinosis most often presents with renal Fanconi syndrome, photophobia and vision loss due to corneal cystine crystals, and progressive neuromuscular complications such as distal myopathy and swallowing difficulties This study aimed to identify deleterious nsSNPs in the CTNS gene and evaluate their effects on cystinosin stability, structure, and function via computational tools and molecular dynamics simulations.

Results: From a dataset of 12,028 SNPs, 327 nsSNPs were identified, among which 19 were consistently classified as deleterious across multiple predictive tools, including SIFT, PolyPhen, and molecular dynamics simulations. Stability predictions revealed that most of these mutations destabilize cystinosin, with G308R and G308V located in the sixth transmembrane domain essential for transporter function having the most severe effects. Molecular dynamics simulations revealed that these mutations significantly increase local flexibility, alter hydrogen bonding patterns, and enhance solvent accessibility, resulting in structural perturbations. Notably, D305G and F142S disrupted the transmembrane domains essential for the function of cystinosin, whereas compared with the wild-type protein, G309V resulted in increased stability. Conservation analysis revealed that 16 of the 19 mutations affected highly conserved residues, indicating their crucial roles in the function of cystinosin. Additionally, protein interaction analyses suggested that mutations could impact associations with lysosomal and membrane transport proteins.

Conclusions: This study identified 19 deleterious nsSNPs in the CTNS gene that impair cystinosin stability and function. These findings highlight the structural and functional importance of key residues, such as G308, D305, and F142, which play critical roles in maintaining the active conformation and transport capacity of cystinosin. These insights provide a foundation for future experimental validation and the development of targeted therapeutic strategies to mitigate the effects of pathogenic mutations in cystinosis.