Revealing the microbial diversity and functional annotation during postharvest storage of sweet cherry using metagenomics.

Isolation and identification of plant growth-promoting endophytic bacteria from Eclipta prostrata (L.) L. and its metagenomic evidence through functional annotation

Deep learning revolutionizes protein research: Advances in structure prediction, functional annotation, and engineered design.

Mechanistic insights into cardiovascular toxicity induced by polycyclic aromatic hydrocarbons using Benzo[a]pyrene (BaP) as an example.

S⁰-S²⁻ co-substrate system achieves efficient nitrite accumulation under high alkalinity and ultra-short HRT: Multidimensional responses and metabolic regulation mechanism.

Genome-Wide Comparison Analysis of Brucella Attenuated Vaccine Strain BA0711 and Brucella Wild-Type Strain M28 and Establishment of a Dual qPCR Differentiation Method.

Downregulated ECHS1 and HADH-mediated fatty acid β-oxidation contributes to mitochondrial dysfunction in salivary glands of Sjögren's syndrome.

Genome-wide association analysis to identify novel candidate genes and genomic model optimization to predict acute low-temperature stress resilience in olive flounder (Paralichthys olivaceus).

Antidepressant effects of combined eucommia-gastrodia extract via modulation of the HIF-1α-EPO/cAMP-CREB-BDNF pathway: An integrated network pharmacology and in vivo study.

Effects of tea polyphenols on intestinal barrier, antioxidant capacity, and cecal microbiota in lion-head geese.

This dataset presents the draft genome of Ochrobactrum anthropi strain Nas42, isolated from metal-contaminated estuarine sediments of the Red River Delta, Vietnam. Genomic DNA was extracted from the isolate and sequenced using the Illumina MiSeq platform, followed by de novo assembly and functional annotation. The generated dataset comprises a 4,605,092 bp draft genome assembled into 27 contigs with a GC content of 56.11%, containing 4,356 protein-coding sequences. Notably, in silico whole-genome comparison supported its taxonomic assignment to O. anthropi , demonstrating 99.37% Average Nucleotide Identity (ANI) with strain PBO and the absence of IS711 insertion sequences, a genomic feature characteristic of Brucella species but absent in Ochrobactrum . Additionally, the annotated dataset highlights 45 genes associated with metal resistance, including those encoding resistance to cobalt, zinc, cadmium, and copper. This genomic resource can be reused by the scientific community to investigate metal resistance determinants, explore microbial adaptation mechanisms in polluted estuarine environments, and support phylogenomic analyses of the Ochrobactrum–Brucella complex.

Genomic characterization and global lineage-plasmid context of a bla NDM-5-harboring Escherichia coli ST3014 isolate.

This dataset presents the high-quality whole-genome sequence of Deinococcus wulumuqiensis FBCC-B5220, a bacterium exhibiting extracellular protease activity isolated from freshwater sediment in Korea. The genome was assembled using a hybrid approach combining Illumina and PacBio platforms, resulting in five contigs totaling 3458,218 bp with a G + C content of 66.0%. Functional annotation identified 3239 protein-coding sequences, including a specialized repertoire of 45 protease-related genes, such as zinc metalloproteases, ATP-dependent proteases, and serine proteases. Phylogenomic and 16S rRNA gene analyses confirmed its taxonomic identity as D. wulumuqiensis, with ANI (97.2%) and dDDH (78.2%) values. The genome sequence and annotation files are available in the NCBI database under the accession number JBSRRC000000000. This dataset provides a high-quality genomic reference for comparative studies within the genus Deinococcus and serves as a primary resource for identifying protease-related genes with potential industrial relevance.

Serine proteases and serine protease inhibitors identified from the venom gland transcriptome of Rhitymna verruca.

Shotgun metagenomic dataset of microbial communities in the water column of the Flores Sea, Indonesia.

Accurate protein domain annotation is essential for inferring protein function, and databases such as Pfam provide sequence-derived signatures for thousands of domain families. Because protein structure is more evolutionarily conserved than sequence, structure-based searches can detect homologous relationships even at low sequence identity (typically below 30%), where pairwise sequence aligners often lose sensitivity. Here, we leverage AlphaFold-derived structures of Pfam domain instances to systematically evaluate structure-based versus sequence-based methods for Pfam annotation. We benchmarked three structural aligners (Reseek, Foldseek, TM-align) against sequence-based methods (MMseqs, HMMER) using both exhaustive all-against-all searches and a split-family design that enables direct comparison of pairwise and profile-based ranking performance. We also evaluated residue-level alignment accuracy using Pfam multiple sequence alignments as reference and investigated whether profile-derived information can improve structural hit ranking. In all-against-all searches, Reseek achieved the highest sensitivity up to the first false positive (AUC = 0.85), outperforming Foldseek (0.81), TM-align (0.76), and MMseqs (0.46). In split-family evaluation, HMMER remained superior (maximum F1 = 0.991), highlighting the continued strength of sequence-profile approaches for family-level annotation. Performance varied substantially across domain families, with average sequence identity emerging as the strongest predictor of success. Structural aligners consistently produced more accurate residue-level mappings than pairwise sequence methods. Finally, incorporating profile-derived information via rescoring improved structural annotation performance for short domains, suggesting a path toward profile-informed structure-based domain annotation.

Zymoseptoria tritici, the causal agent of Septoria tritici blotch (STB), poses a critical threat to wheat (Triticum aestivum L.) production in temperate Europe, underscoring the need for durable genetic resistance. Here, we screened 151 winter wheat varieties at the seedling stage using a mixed inoculum of five virulent isolates. Disease severity was quantified at 14, 21, and 28 days post-inoculation to calculate the area under the disease progress curve. We observed broad phenotypic variation, with higher susceptibility in Southern European germplasm. A genome-wide association study identified three significantly resistant loci: IWB5774 on chromosome 2D, and IWB72742 and IWB11406 on chromosome 1B. Functional annotation mapped these markers to high-priority candidate genes, including a TaBx3D-like protein, the endomembrane trafficking regulator WDR91, and NAP1, a nucleosome assembly factor involved in stress signaling. These findings provide robust molecular markers for breeding and nominate specific targets for functional validation of STB resistance mechanisms.

Improving end-use quality in bread wheat (Triticum aestivum) requires dissecting the genetic basis of complex processing traits and deploying robust prediction pipelines in breeding. We performed genome-wide association studies (GWASs) using 1767 high-quality single-nucleotide polymorphisms generated by genotyping-by-sequencing in a diverse Canada Western Red Spring panel phenotyped near Swift Current, SK, from 2009 to 2019 for grain protein content, milling yield, mixing energy, water absorption, and doughextensibility. The analysis detected significant marker-trait associations on 13 chromosomes, recovering signals at Rht-B1 and Glu-1 and revealing multiple additional signals that may represent previously unreported loci in this germplasm and environmental context, consistent with polygenic control. We then evaluated genomic selection using GBLUP (Genomic Best Linear Unbiased Predictor) and BayesB with and without including significant GWAS hits as fixed effects; gains in predictive accuracy were generally negligible, although water absorption showed modest improvement, compatible with fewer, larger effect loci. Functional annotation of genes near associated variants implicated stress responses, protein metabolism, and grainfilling. Together, these results refine the genetic architecture of Canadian wheat quality and support integrating GWAS-informed biology with genome-wide prediction to accelerate quality-by-design breeding.

Functional annotation of the aberrantly methylated genes in atrial myocytes of patients with atrial fibrillation

Draft genome sequence of Leuconostoc mesenteroides isolated from fermented kodo millet: Genomic insights into probiotic and anti-diabetic potential.