| Delftia tsuruhatensis MTQ3 was isolated from the rhizosphere of tobacco.As a environmental friendly PGPR,MTQ3 had a antagonism against the Ralstonia solanacearum,which was formerly reported to cause tobacco bacterial wilt.In this study,we analysed the genome sequence of MTQ3 and identified the functional genes by using gene knockout technology,in order to explore the molecular mechanisms of antagonism.We focus on identifying the function of genes related to siderophore biosynthesis.Based on the Illumina HiSeq 2500 platform,the draft genome sequence of MTQ3 was obtained by whole genome shotgun sequencing,and the accession number of NCBI was LCZH00000000.The length of genome was 6.27 Mb with a G+C content of 66.79%.It consists of 136 contigs,12 scaffolds after the finally assemble.The total number of coding sequences(CDS)was 5005,10 rRNA genes,72 tRNA genes,1 noncoding RNA and 13 pseudogenes were also found.According to the annotation,numerous genes responsible for biosynthetic of antibiotic substances such as bacteriocin or NRPS.In addition,MTQ3 also possesses many genes related to adaptation in rhizosphere environments.The phylogenetic analyses suggested that strain MTQ3 have a high homology with Delftia tsuruhatensis.We make the comparative genome analysis of four sequenced Delftia(MTQ3,391,SPH-1 and Cs1-4)which revealed the genetic relationship between these strains.The general features of the four genomes showed the variation in genome size.Genome size varies between 5.7Mb in MTQ3 to 6.7Mb in SPH-1.Meanwhile,chromosome coding DNA sequences(CDS)changing between 4103 in strain 391 and 6040 in SPH-1.The(G+C)mol% of the species share the mean value 66.60% and no strain drifts from the mean value by >0.3%.That indicates the genetic relationship between the species to some extent.The orthologous and unique genes analyses showed that MTQ3,Cs1-4,SPH-1,and 391 shared 2540 orthologous genes totally.MTQ3 shared 4470,4414,and 2782 orthologous genes with Cs1-4,SPH-1,and strain 391,respectively.The clusters of orthologous groups(COG)based analysis showed that the genes of these four genomes show some similarities in distribution trend.For the four genomes,genes related with transcription,amino acid transport and metabolism,lipid transport and metabolism indicated the relative abundant functional category.The genome of MTQ3 take up a great proportion of genes indicated carbohydrate transport and metabolism compared with other three genomes.Meanwhile we compared the NRPS gene cluster between the four genomes which indicated that not all Delftia own identical cluster of NRPS.That maybe stand for adaptations of a strain to their specific environment.To reveal the molecular mechanisms of antagonism,several genes related with the biosynthetic of antibiotic substances were knocked out to obtain mutants MTQ3-Δ1941,MTQ3-Δ1945,MTQ3-Δ1946,MTQ3-Δ00865,MTQ3-Δ02705,MTQ3-Δ11480 and MTQ3-Δ12420,respectively.Compared with the wild type strain MTQ3,these mutants maintained its role in antagonism against the bacterial wilt of tobacco.It maybe suggested that above genes irrelevant to the antagonism.However the three NRPS mutants(MTQ3-Δ1941,MTQ3-Δ1945,MTQ3-Δ1946)lost their ability to produce siderophore.The results indicated that siderophore could be biosynthesized by the NRPS modular multienzymes in MTQ3.The NRPS gene cluster which included orf-1941,orf-1945,and orf-1946 occupied for siderophore production.The siderophore produce by MTQ3 was carboxylates.This research aims to study the antagonistic mechanisms of MTQ3 which was first isolated from the rhizosphere of tobacco.Through genomic analysis,numerous genes responsible for biosynthetic of antibiotic substances were presented,which maybe difficult to find the antagonistic substance.However,complete genome annotation can also provid information for the study of the genes function in molecular level,which has a great significant for further research. |
