BMC genomic data最新文献

Objectives: Haliotis discus hannai, a primary aquaculture species in East Asia, is highly susceptible to viral infections, such as abalone herpesvirus. To facilitate the understanding of antiviral immune mechanisms, we generated a hemocyte transcriptome dataset following stimulation with Polyinosinic: polycytidylic acid (poly[I: C]), a synthetic analog of viral double-stranded RNA. This dataset offers a molecular basis for assessing immune-related genes and pathways in abalone.

Data description: Adult abalones were injected with poly(I:C), and hemocytes were collected at 2 and 7 days post-infection, along with uninfected controls. Total RNA was extracted and sequenced using the Illumina paired-end platform. After quality filtering, de novo assembly with Trinity produced 281,050 transcripts and 214,676 unigenes (N50: 722 bp and GC content: 41.06%). Open reading frames predicted by TransDecoder yielded 18,371 coding sequences. Functional annotation against Non-Redundant Protein, Universal Protein Resource, Protein Families, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes databases identified numerous immune-related genes The raw reads, assembled transcriptome, and annotation files are publicly available in the National Center for Biotechnology Information Sequence Read Archive and Figshare, providing a valuable reference for future studies on the innate immunity of H. discus hannai.

Background: Basella alba L. a widely consumed green leafy vegetable, exhibits considerable nutritional and therapeutic potential attributed to its bioactive constituents. Prior investigations revealed significant variation in phytochemical and antioxidant activity across agro-climatic zones in Sri Lanka, suggesting potential genetic influence. This study is designed to explore underlying genetic variation using RAPD markers to investigate the correlations and contributions of genotype on previously reported bioactivity variation.

Results: From a screening of 15 RAPD primers, four primers (OPA 9, OPA 10, OPA 16, and OPB 10) produced, polymorphic, consistent and clearly scorable banding profiles (under optimized PCR conditions) in B. alba L. collected from 15 Sri Lankan locations. These primers collectively yielded 36 bands, 35 of which were polymorphic, resulting in a high polymorphism rate of 97.2%, confirming the informativeness of the selected primers for genetic diversity analysis. Genetic similarity was assessed using Jaccard's coefficient in NTSYSpc.v2·10e, revealing values ranging from 0.44 to 0.97, with the highest similarity from the samples from Ratnapura and Kandy and the lowest similarity in Ratnapura and Kalutara. A dendrogram constructed via UPGMA grouped the samples into two major clusters and five sub-clusters, demonstrating substantial genetic differentiation influenced by geographic origin. Cluster I included Ratnapura and Kandy, while the remaining samples formed Cluster II and its subgroups, each representing different ecological zones. When compared to the phytochemical and antioxidant clustering data of the previous study, partial correspondence was observed. A Mantel test comparing genetic diversity and biochemical/antioxidant potential revealed a weak negative correlation which was not significantly different. Some of the locations within similar genetic cluster shared similar biochemical traits, while others diverged significantly, indicating that environmental conditions also influence bioactive compound synthesis. Notably, Cluster I (Ratnapura and Kandy) showed both genetic similarity and lower antioxidant traits. Samples from Ella and Polonnaruwa showed similar bioactive traits even though they were grouped into different genetic clusters.

Conclusion: These findings suggest that both genetic makeup and environmental adaptation contribute to observed biochemical diversity in B. alba L. with a clear geographical correlation. This study highlights the value of integrating molecular and biochemical analyses to develop regionally adapted B. alba L. cultivars with enhanced nutritional traits, supporting sustainable agriculture in Sri Lanka and beyond.

Objective: This study presents the whole genome sequence of Staphylococcus aureus strain 37M isolated from cows with subclinical mastitis in Kiruhura district, Uganda. The objective was to characterize the genome to understand the isolate's resistance and virulence potential. The genome sequence accompanying metadata are available under the accession GCA_052439145.1.

Data description: The final assembled genome has a genome size of 2,795,296 bp, Contig N50 (53.2 kb), L50 16, Genome coverage 2.79534e + 06x, Assembly level contigs and a GC content of 32.5%. It contains 2,748 CDSs, 2,819 genes, 2,584 predicted protein-coding genes, 57 tRNA genes, 3 complete rRNAs (23 S), 5 non-coding RNAs and 159 Pseudo Genes. Quality analysis of the genome using CheckM analysis (v1.2.4) revealed 96.72% completeness, and 0.7% contamination. Average Nucleotide Identity (ANI) analysis revealed that the closest type strain to our isolate was Staphylococcus aureus (GCA_000330825.2) with an ANI of 99.04%, 92% assembly coverage, 93.3% type assembly coverage, confirming species-level identity and close relatedness. Screening with the Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB) revealed several genes conferring resistance to different classes of antibiotics: antibiotic (tet(K) and tet(38)- tetracyclines, mepA, aminoglycosides, fluoroquinolones, norA- Fluoroquinolones, LmrS- Macrolides, aminoglycosides, lincosamide, oxazolidinones and blaZ- Beta-lactams, regulatory gene (mepR, arlR and arlS). Virulence factors included: Adherence (icaA, icaB, icaC, icaD, icaR, clfA, ebp, fnbA, fnbB, map, sdrC, sbi, spa,), Secretion system (esaA, esaB, esaC, essA, essB, essC, esxA, esxB), Enzymes (cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G, cap8P, cap8O, cap8N, cap8M, cap8L, mgrA, adsA, geh, srtB, hysA), Iron regulators (isdA, isdB, isdC, isdD, isdE, isdF isdG), Toxin (lukF-PV, lip, sspB, sspC) and Hemolysin (hlb, hld, aur, hlgA, hlgB, hlgC, hly/hla).

Objectives: The fruiting body of Rigidoporus glomeratus is a traditional medicinal herb employed by indigenous ethnic communities in the Gaoligong Mountain region. This fungus is known to be rich in various metabolites, including polyphenols, polysaccharides, flavonoids, terpenoids, and steroids. Despite its significance in traditional medicine, genomic information for R. glomeratus has been scarce. Herein, we report the first de novo assembled whole-genome sequence of R. glomeratus strain YAFMF1018 isolated from the Gaoligong Mountain.

Data description: Whole-genome sequencing of R. glomeratus strain YAFMF1018 was performed using a hybrid approach integrating Illumina NovaSeq and Oxford Nanopore Technologies platforms. The combined data were used for de novo assembly, resulting in a genome size of 38.68 Mb comprising 23 scaffolds, with a GC content of 47.98%. The gene completeness of the assembly was assessed with BUSCO, which revealed a completeness value of 93.9% based on the fungi_odb10 database.