A strain of Lactiplantibacillus plantarum ZJ316 was screened from the feces of a newborn baby in Zhejiang, China. After long-term laboratory acid adaptation domestication, its genome underwent at least 2% changes. Domestication was carried out through continuous passage until an acid resistant mutant strain was finally isolated and named Lactiplantibacillus plantarum ZJ316PV. The purpose of this study is to reveal the effects of acid adaptive domestication on the genome and probiotic properties of bacterial strains, for reference by other researchers.
1 For genome assembly, The filtered subreads were assembled by Hifiasm v0.12 software, and then circlator v1.5.5 was taken to cyclizing assembly genome.
2 For genome component prediction, Coding genes prediction was performed by Prodigal v2.6.3. The GenBlastA v1.0.4 program was used to scan the whole genomes after masking predicted functional genes. Putative candidates were then analyzed by searching for non-mature mutations and frame-shift mutations using GeneWise v2.2.0. Transfer RNA (tRNA) genes were predicted with tRNAscan-SE v2.0, Ribosome RNA (rRNA) genes were predicted with Infernal v1.1.3. Repetitive sequences were predicted using RepeatMasker. PhiSpy v2.3 is used for prophage prediction and CRT v1.2 was used for CRISPR identification. IslandPath-DIMOB v0.2 was used to predict genomic island in genome. antiSMASH v5.0.0 was used to predict secondary metabolic gene clusters, and PromPredict v1 was used for promoter prediction.
3 For functional annotation, the predicted protein were blast (e-value: 1e-5) against Nr,Swiss-Prot,TrEMBL,KEGG,eggNOG, Blast2go was used for GO annotation. Further more, the pathogenicity and drug resistance can be researched by blast against CAZy, TCDB, CARD, PHI databases.
4 For subcellular localization, the subcellular localization information is one of the key features to protein function research, secretory proteins were detected by SignalP, after transmembrane proteins were filterd by TMHMM, the candidate secretory proteins can be got.
5 For methylation analysis, use SMRT Link v8.0.0 to predict the methylation sites and possible nucleotide motifs recognized by methyltransferases on the final genome assembly results. Less...