Complete Genome Sequencing And Comparative Genomic Analysis Of Bacillus Velezensis QC-J Strain

Citrus canker is,a citrus bacterial disease,caused by Xanthomonas citri subsp.citri(Xcc).Citrus canker causes crater-like lesions on the fruits and leaves,leading to deciduous,fruit-dropping,and declining tree vigor in severe cases,affecting the fruit taste.Chemical pesticides and other synthetics have been used to prevent and treat the disease.However,the methods have had a significant negative impact on the environment.Biological control reduces the negative impact of agricultural practices on the environment while controlling plant pathogens.Therefore,it is important to study the biological control of citrus canker.In this study,a citrus canker biocontrol strain B.velezensis QC-J isolated from navel orange leaves and twigs in the laboratory was chosen as the study target.In order to reveal its genetic and evolutionary characteristics,clarify its physiological and metabolic mechanisms,colonization ability,antibiotic synthesis ability.In this study,the whole genome sequence of B.velezensis QC-J strain was obtained by Illumina Hi Seq 2500 second-generation sequencing technology,and its genome structure and function were analyzed using a variety of bioinformatics software,and it was compared with the genomes of other homologous strains.The main results are as follows:(1)The whole genome of B.velezensis QC-J was sequenced using the Illumina Hi Seq 2500 system,and the total number of offline reads was 24,280,728,the total number of bases was 3,642,109,200 bp,the sequencing depth was 886,and the percentage of sequencing quality over 99% is 98%.Using SPAdes-3.5.0 software to assemble the filtered reads,18 Scaffolds were obtained.The estimated size of the genome of the strain B.velezensis QC-J is about 3,893,015 bp,and the GC content is 46.4%.(2)A total of 3869 genes,152 tandem repeats and 1 inserted repeat were predicted in the genome.No CRISPRS was found.Two prophage regions are predicted,one is an incomplete prophage and the other is a suspicious prophage.Three gene islands were discovered in the gene island prediction.CARD predicted 59 genes in the genome associated with antibiotics.The CAZyme analysis revealed 71 families containing 203 putative CAZyme genes in QC-J strains.The ability of B.velezensis QC-J strain to synthesize carbohydrate-active enzymes is one of the important factors for its advantages in space competition and nutrition,and it is also one of the factors that inhibit the virulence of the citrus canker pathogen Xcc.The GO annotation analysis revealed that the number of genes related to biological processes is the largest.COG annotation analysis revealed that the number of genes assigned to amino acid transport and metabolism is the largest.KEGG annotation analysis revealed that the metabolic activity of sugars and amino acids of the strain is very active.(3)The phylogenetic tree constructed using the core genomes of 52 strains of B.amyloliquefaciens,B.subtilis,and B.velezensis showed that the QC-J strain belongs to B.velezensis,and the genetic evolution and geographical integration of B.velezensis is very relevant to the growth environment.The pan-genome analysis results of 16 B.velezensis strains showed that the number of core genomes was2029,the number of non-essential genomes was 2516,the number of strain-specific genes was 965,and B.velezensis has an open pan-genome.Through the collinearity analysis of the five strains,the collinearity of the five strains is high,and the collinearity of B.velezensis QC-J and B.velezensis ZF2 is the highest.By analyzing the genomic SNP distribution of B.velezensis QC-J,it is found that the genomic SNP distribution of B.velezensis QC-J is not uniform.The high SNP regions may cause the difference in secondary metabolites of B.velezensis QC-J strain.We found 60 genes related to biofilm synthesis in the B.velezensis QC-J strain and four other strains.The biofilm metabolism pathway constructed by these genes is highly similar to the biofilm metabolism pathway of Bacillus subtilis.The strong biofilm formation ability of B.velezensis QC-J strain is one of its effective ways to inhibit ulcer disease.Fifteen secondary metabolite clusters were identified in the B.velezensis QC-J genome,12 of which are related to antibiotic biosynthesis.And we have found secondary metabolites that can cause induced resistance in plants in 5 strains of B.velezensis.Genomic and comparative genomic analysis showed that B.velezensis QC-J strain can prevent and treat citrus canker through colonization(biofilm formation),antagonism(antibiotic production),carbohydrate active enzymes(CAZymes),and induced resistance(ISR).This article will provide a basis for elucidating its biological control mechanism against citrus canker pathogens and will facilitate future applications.