title: DNA-Seq of YT640: piglet fecal
design: Whole-genome sequencing was conducted on selected LAB strains known for their inulin metabolism capabilities. The genomic DNA was extracted from cell pellets derived from centrifugation (4000g, 10 min) of an overnight culture of the LAB strain in liquid MRS medium. The extraction was performed using the Wizard Genomic DNA Purification Kit in accordance with the manufacturers protocol. The purified genomic DNA was quantified using a TBS-380 fluorometer (Turner BioSystems Inc., Sunyvale, A). High-quality genomic DNA samples, exceeding 1 g, were fragmented into 400-500 bp segments using a Covaris M220 Focused Acoustic Shearer, following the manufactures protocol. The Illumina sequencing library was constructed using the EXTflex Rapid DNA-Seq kit (Bioo Scientific Cor. Austin, TX, USA). Paired-end sequencing (2  150 bp) was performed on an Illumina Hiseq X Ten instrument (Illumina Inc., San Diego, CA, USA) with HiSeq X Reagent Kits, according to the manufacturers recommendations (www. illumina.com).Raw sequence data generated from the Illumina platform were processed through bioinformatics analysis. All analyses were performed using the online platform provided by Majorbio Cloud Platform (www.majorbio.com) (Shanghai Majorbio Bio-pharm Technology Co., Ltd.). Initially, raw data were filtered to obtain clean data using Fastp software. These cleaned data were then used for de novo assembly with SOAPdenovo v2.04 to generate genome sequences (contigs) (Luo et al., 2012). Protein-coding genes (CDSs) were predicted using Glimmer v3.0240 (www.cbcb.umd.edu/soware/glimmer), by blasting genes against Clusters of Orthologous Groups (COGs) of proteins and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Genome visualization was carried out using CGview software.
identifiers.namespace: SUB15211072
identifiers.id: PE520