BMC genomic data最新文献

Objective: Mung bean (Vigna radiata) is a leguminous crop of significant economic, nutritional, and ecological importance. Its wild relative, V. radiata var. sublobata, is a wild legume exhibiting strong environmental adaptability and potential economic value. Its rich genetic diversity serves as a critical resource for research on crop stress resistance, thereby offering valuable wild genetic material for mung bean varietal improvement. In this study, we generated transcriptome sequencing data from six distinct tissues of V. radiata var. sublobata, providing a fundamental data for functional genomics research and molecular breeding applications.

Data description: In this study, we performed systematic transcriptomic sequencing analysis on six different tissues of V. radiata var. sublobata, with three biological replicates for each tissue type. Principal component analysis (PCA) demonstrated a significant separation trend among different tissue samples. A total of 19,405 differentially expressed genes (DEGs) were identified through pairwise cross-tissue comparisons. Gene Ontology (GO) enrichment analysis revealed that, relative to leaf tissue, seed tissue exhibited significant up-regulation of genes implicated in energy metabolism, storage processes, and developmental regulation. This study not only provides a tissue-specific gene expression profile for V. radiata var. sublobata but also offers important theoretical foundations and genetic resources for the utilization of wild legume plant resources and molecular breeding.

Objectives: Tribolium castaneum and Drosophila melanogaster are prominent insect model organisms for investigating developmental and evolutionary processes. Both have a significant kit of genetic and molecular tools and a substantial quantity of omic data at their disposal, which makes this species pair suitable for comparative genomic and gene function studies. However, for such comparisons, a rigorous assignment and compilation of the orthologs that these organisms share are essential. Here, we generated and provided a list of orthologous genes between Drosophila and Tribolium, which will be useful for future comparative genomic studies.

Data description: We made use of the reference proteomes of Tribolium castaneum and Drosophila melanogaster to infer phylogenetic orthology using the OrthoFinder platform, and employed the eggNOG 6.0 database and manual phylogenetic tree analyses to assess our results. Our analysis identified more than 9,000 orthologous genes between Drosophila and Tribolium. We posit that this comprehensive list is a valuable resource for comparative studies among these insect species, such as single-cell sequencing or large-scale gene function comparisons. The results are open-access and freely available for download or interactive exploration in iBeetleBase.

Objectives: Heyndrickxia oleronia is a Gram-positive, rod-shaped bacterium originally isolated from termites but has gained clinical importance due to its association with Demodex mites and rosacea, a chronic inflammatory skin disease. Despite its clinical relevance, genomic resources from human-associated environments remain limited, with existing reference genomes derived from ecologically distant sources. This study aimed to provide the first complete genome sequence of H. oleronia EISK28 isolated from human facial skin to support future research on its role in skin health and disease.

Data description: H. oleronia EISK28 was isolated from human facial skin and sequenced using Oxford Nanopore long-read technology. De novo assembly resulted in a single complete circular chromosome of 5,118,808 bp with 164× coverage depth. Structural annotation identified 5,143 genes comprising 4,958 CDSs, 36 rRNAs, 144 tRNAs, 5 non-coding RNAs, and 65 pseudo genes. Functional annotation assigned the predicted CDSs to 22 of 25 COG categories and identified 93 carbohydrate-active enzymes. Secondary metabolite analysis revealed three biosynthetic gene clusters, and genome-based antibiotic resistance profiling predicted 11 resistance genes, while phenotypic testing confirmed resistance to ampicillin and penicillin. Mobile genetic element screening detected 34 insertion sequences, 2 prophages, and 16 genomic islands but no association with antibiotic resistance genes.

Objectives: Marine bacteria are valuable reservoirs of novel carbohydrate-active enzymes (CAZymes) with industrial relevance. A halophilic marine bacterial strain PBL-D1, was isolated from Batu Laut beach in Selangor, Malaysia. The 16S rRNA gene sequence analysis identified strain PBL-D1 as a member of the genus Gaetbulibacter. To date, no enzymes from Gaetbulibacter spp. have been biochemically characterised. The present study reports on the annotated draft genome of Gaetbulibacter sp. PBL-D1 and comparative genome analyses of Gaetbulibacter glycoside hydrolase (GH) enzymes. These findings provide the first genomic insights into the GH repertoire of Gaetbulibacter spp., revealing unexplored enzymes with promising potential for industrial biocatalysis.

Data description: The draft genome of Gaetbulibacter sp. PBL-D1 is 3,433,971 bp in size, has a G+C content of 33.0%, and encodes 3,068 protein-coding genes. The CAZymes analysis revealed that Gaetbulibacter genomes harboured at least nine putative GH-encoding genes, grouped into starch-degrading and β-glucan-degrading enzymes. These enzymes are of industrial importance, particularly in food processing and biofuel production. Collectively, PBL-D1 and other available Gaetbulibacter genomes serve as attractive sources of GH candidates that may be useful in polysaccharide degradation.

Objectives: Pseudolactococcus raffinolactis-a lactic acid-producing bacterium recently reclassified from Lactococcus-demonstrates emerging potential for probiotics and food applications. We report the complete genome of strain GCULR isolated from a stranded spotted seal (Phoca largha) in Korea, to provide genomic data for understanding beneficial bacteria in marine mammals.

Data description: P. raffinolactis strain GCULR was isolated from a stranded spotted seal in Korea, and its whole genome was sequenced using PacBio and Illumina X-10 platforms. Its complete genome comprises a single circular chromosome of 2,270,555 bp with 39.9% GC content and no plasmids. Annotation revealed 2,260 genes, including 2,145 protein-coding sequences, 56 transfer RNAs, 13 ribosomal RNAs, 3 non-coding RNAs, and 43 pseudogenes. Comparative analysis showed an average nucleotide identity of 99.3% with strain WiKim0068, confirming its close relationship with a food-derived isolate. Genome-based screening revealed the presence of several potential virulence- and antimicrobial resistance-associated genes and two intact prophage regions. AntiSMASH analysis predicted a conserved bacteriocin biosynthetic cluster, indicating its functional potential. These findings offer novel insights into the beneficial bacteria in endangered marine mammals and expand our understanding of the ecological and functional diversity of P. raffinolactis.