BMC genomic data最新文献

Background: The Capra Comune di Sicilia (CCS), also known as Mascaruna, is a Sicilian local goat population first described in 1870 and is currently the focus of a recovery project aimed at its characterization and formal ethnic recognition. To elucidate the ancestral genetic components and selection trajectories of the CCS population, we genotyped 78 CCS goats using the Goat 60 K SNP BeadChip, integrated with genotype data from 1,920 individuals representing 66 goat breeds of Mediterranean and African origin.

Results: CCS exhibited relatively high heterozygosity (0.408), and moderate levels of inbreeding (0.04), an estimated effective population size of 185. Genetic ancestry analysis revealed gene flow from Maltese, Girgentana, Rossa Mediterranea and Saanen populations, alongside evidence of putative Greek ancestry shared with most Mediterranean breeds in our dataset, reflecting Sicily's profound historical and cultural ties with Greece. To better understand the evolutionary trajectories of the CCS population and to explore the potential contribution of Greek goat ancestry, we investigated selection signatures using iHS and ROH analyses. We identified 76 and 31 SNPs intercepting 38 and 12 genes, respectively, under putative selection. Subsequently, we applied XP-nSL and ROH analyses using Greek populations as ancestral references, identifying 21 and 431 SNPs associated with four and 157 genes, respectively, under putative selection. Overall, these selection signature analyses highlighted genes under positive selection related to traits such as milk and meat production, body size and growth, fertility, coat colour, fat deposition, and ear and horn development.

Conclusion: Our findings shed light on the historical and genetic distinctiveness of the CCS population, emphasizing its uniqueness and providing critical insights into its genetic background. This information is essential for supporting informed efforts to formally recognize CCS as a distinct and valuable breed.

The combined use of NGS technologies with bioinformatics tools has significantly advanced research by enabling comprehensive analyses of entire genomes, specific genomic regions of interest, and transcriptomes. Targeted NGS methods, which focus on smaller genome fractions, are widely used to study genetic diseases, epigenetic modifications, microbiomes, and environmental DNA, among other applications. This study aimed to develop a roadmap for detecting and selecting polymorphisms in candidate genes by integrating amplicon NGS-Target techniques with bioinformatics analyses. Sixty-eight genes associated with the hypothalamic-pituitary-gonadal (HPG) axis were selected to develop the amplicon NGS assay, comprising 730 regions that cover a total of 136,274 bp. This method was used to sequence 75 Guzerat cattle, a dual-purpose breed from Brazil, renowned for their high rusticity and adaptability. This Zebu cattle exhibit certain limitations, such as delayed puberty onset, which can reduce reproductive efficiency. Using the GATK protocol a total of 2,600 SNPs and 1,615 indels were detected. A series of consecutive filtering steps (maf, the detection of non-synonymous substitution, phylogenetic amino acid conservation, and biochemical properties) were used, resulting in a subset of 30 candidate SNPs. Then, these polymorphisms were analysed using bioinformatic tools (SIFT, PANTHER, PolyPhen2, and MutPred), identifying 5 SNPs with high effect on the protein. Their structure and stability were estimated using AlphaFold and DDMut. Finally, 3 candidate polymorphisms (IGF1R, LHCGR, TAC3R) with potentially significant effects on the protein remained to be validated through dynamic simulations or in vitro and in vivo experimental assays.

Objectives: Verticillium albo-atrum is one of the most dangerous quarantine pathogen, which is a soil-borne pathogen known for causing verticillium wilt, a disease that affects a wide range of plants, including many economically important crops. However, the lack of high-quality genome resource has greatly limited the research of molecular and evolutionary mechanisms of Verticillium albo-atrum. The highly-quality genome of Verticillium albo-atrum provides a valuable resource for better understanding of the biological characteristics.

Data description: We sequenced and assembled the genome of Verticillium albo-atrum using ONT long reads combined with DNBSEQ-T7 paired-end short reads and anchored 11 contigs into 8 chromosomes using Hi-C chromatin contact information, yielding a 35.95 Mb chromosome-level genome assembly with a N50 of 4.20 Mb. In addition, transcript-based annotation identified 9967 protein-coding genes, of which 84.17% were functionally annotated. BUSCO analysis demonstrated that this genome assembly has a high-level completeness of 96.47% gene coverage.

Objectives: Leuconostoc menseteroides is a species of lactic acid bacteria with established safety, frequently isolated from fermented foods such as kimchi, and is Generally Regarded as Safe (GRAS). This species is used as a starter culture for kimchi fermentation in South Korea. In this study, we aimed to evaluate the probiotic potential of Leconostoc menseteroides B22051, isolated from Panax ginseng C. A. Meyer (Ginseng), through genome analysis by assessing probiotic traits including antibiotic resistance, bacteriocin, and redox genes relevant to both human and livestock applications.

Data description: We isolated a candidate probiotic strain from Panax ginseng Meyer and decoded the complete genome of L. menseteroides B22051. The complete genome was found to be 1,994,797 bp in size with a guanine + cytosine (G + C) content of 37.7%, and is composed of one chromosome (1,943,350 bp) and two plasmids (37,364 bp and 14,083 bp). Genome annotation revealed 71 transfer RNAs, 24 ribosomal RNAs, and 1,987 coding sequences (CDSs). Furthermore, 98.09% and 64.92% of these 1,987 CDSs were assigned to the COG and Gene Ontology classification systems, respectively. Two partial sequences of vanT (32.61% identity) and vanY (34.36% identity) were detected by CARD v3.2.0 analysis, and although in vitro assays confirmed vancomycin resistance, the low sequence identity and absence of a complete van operon indicate that the resistance is intrinsic rather than acquired. An entero_X_chain_beta gene, associated with Enterocin within Bacteriocin Class IIC (chromosomally encoded), along with 28 reductase genes and one oxidase gene identified through Gene Ontology analysis, is present in L. mesenteroides B22051. These genomic findings confirm the probiotic properties of L. menseteroides B22051.

Background: The demand for food is expected to grow substantially in the coming years. To address this challenge, especially in the context of climate change, a deeper understanding of genotype-phenotype relationships is crucial for improving crop yields. Recent advances in high-throughput technologies have transformed the landscape of plant science research. However, there is an urgent need to integrate and consolidate complementary data to understand the biological system.

Results: We introduce AgroLD, a knowledge graph that uses Semantic Web technologies to seamlessly integrate plant science data. AgroLD is designed to facilitate hypothesis formulation and validation within the scientific community. With approximately 1.08 billion triples, it integrates and annotates data from more than 151 datasets across 19 distinct sources.

Conclusion: The overarching goal is to provide a specialized knowledge platform addressing complex biological questions in the plant sciences, including gene participation in plant disease resistance and adaptive responses to climate change.

Backgroud: Although Cinnamomum camphora's metabolic composition has been well studied, flavonoid distribution across its tissues remains poorly understood. This study combined transcriptome and metabolomic analyses on leaf, stem, and root tissues to uncover the synthesis pathway of flavonoids and to identify key regulatory genes.

Results: Metabolomic analysis revealed 2,893 metabolites, which can be divided into secondary metabolite 1,213(41.93%), primary metabolite: 622 (21.50%) and others: 1,058 (36.57%). As for the secondary metabolite, flavonoids were the most abundant (28%), followed by terpenoids (27%) and phenolic acids (12%). Differential metabolites were identified using VIP > 1, |log2 fold change|≥ 1, and p < 0.05 criteria, showing tissue-specific flavonoids distribution. For example, rutin, quercetin 3-o-alpha-l-rhamnoside, and quercetin were abundant in leaves and stems, while 2-hydroxyisoflavanone naringenin, fustin, and catechin were predominant in roots. Transcriptome analysis indicated that a total of 2,043 differentially expressed genes (DEGs) were identified, with the most considerable number found in the leaf-to-root comparison. The KEGG enrichment analysis of DEGs showed significant changes in pathways related to flavonoid and phenylpropanoid biosynthesis. Correlation analysis indicated that key enzyme genes including CcPAL_1, CcF3H_1, CcF3_H, CcCHS_1, CcC4H_2, CcANR_1, Cc4CL_9, Cc4CL_7 and Cc4CL_1 play positive regulatory roles in the accumulation of downstream metabolites, whereas CcPAL_4, CcPAL_2 and CcC4H_1 exert negative regulation on downstream metabolites. In addition, we have identified several bHLH and MYB transcription factors that may regulate flavonoid biosynthesis. Finally, qRT-PCR validation confirmed the RNA sequencing results.

Conclusions: This research elucidates the spatial variations in the accumulation profiles of flavonoid metabolites across different tissues and offers crucial insights into the regulatory mechanisms of flavonoid metabolism in C. camphora. Consequently, it laid a foundation for further research on the flavonoid biosynthetic pathway of C. camphora.

Background: Epigenome-wide association studies (EWAS) are a highly promising approach that can inform precision environmental health. However, current EWAS are underpowered and increasing sample sizes will require substantial resources. Therefore, alternative approaches for identifying candidate biomarkers through EWAS are critical. Here, we provide proof of principle that maximizing exposure variance in EWAS enables effective candidate biomarker detection, even in small sample sizes.

Methods: We profiled genome-wide DNA methylation in whole blood from individuals from Madre de Dios, Peru, with either high methylmercury (MeHg) exposure (> 10 µg/g total hair mercury; N = 16) or low MeHg exposure (< 1 µg/g total hair mercury; N = 16).

Results: We identified nine differentially methylated CpG sites (FDR < 0.05), which is comparable to the number identified by much larger EWAS. The most significantly different CpG site was in an intronic enhancer of the SLC5A7 gene, which encodes the L-type amino acid transporter 1 (LAT1) that facilitates MeHg transport. Our Gene Ontology and transcription factor motif enrichment analyses identified genes involved in outcomes linked to MeHg toxicity, including immune response, neurotoxicity, and type 2 diabetes (T2D).

Conclusions: Similar EWAS in global populations with known high exposure variance can be leveraged to develop targeted, custom sequencing panels and microarrays limited to replicated, validated biomarkers of a given exposure.

Objective: Streptococcus hominis is a recently described species within the genus Streptococcus, yet its genomic characteristics remain poorly understood, particularly in the context of the oral microbiome. Previously, only two complete genomes from non-oral sources were available. To address this gap, we sequenced and analyzed S. hominis strain KHUD_010, isolated from the subgingival biofilm of a healthy Korean adult.

Data description: Genomic DNA from KHUD_010 was extracted and confirmed as S. hominis by 16 S rRNA gene sequencing. Whole-genome sequencing using the PacBio Sequel II platform generated 135,974 HiFi reads (N50: 10,345 bp). De novo assembly with SMRT Link v11.0 produced a single circular chromosome of 1,883,665 bp with 39.04% GC content. Annotation via the NCBI Prokaryotic Genome Annotation Pipeline predicted 1,793 protein-coding genes, four rRNA operons (5 S, 16 S, 23 S), and 120 tRNAs. BUSCO analysis showed 99.1% completeness. Comparative genomics with NSJ-17 and UMB6992B revealed 1,416 core, 223 dispensable, and 398 strain-specific gene clusters. KHUD_010 harbored 18 unique gene clusters comprising 20 genes, mostly assigned to COG category L (replication, recombination, repair). This high-quality genome expands the genomic landscape of S. hominis and provides a valuable reference for future studies on oral microbiome diversity and host adaptation.