Whole Genome Sequencing And Identification Of Chitinase Family Genes Of Two Biocontrol Streptomyces Strains

Streptomyces sp.FT05 W and Streptomyces sp.ZEA71 I are biocontrol strains showed antagonisms to a variety of plant pathogens.In order to understand their classifications,Multilocus Sequence Analysis(MLSA)were conducted based on the 16 S rDNA,gyrB,rpoB,atpD,and recA genes.Phylogenetic tree was constrcted by Mega 6.0 with related sequences from 56 Streptomyces strains.The results indicated that Streptomyces sp.FT05 W is a close species of S.griseoplaus,while Streptomyces sp.ZEA17 I is a close species of S.griseobrunneus.Draft genome sequences from Streptomyces sp.FT05 W and ZEA71 I were obtained from Miseq PE300 and Illumina Hiseq sequencing platforms for better understanding the characteristcs of the two strains.Raw data of Streptomyces sp.FT05 W showed that the genome obtained6,914,188 reads with an average length of 301 bp.The qualities of reads1 were 91.60% higher than 20(Q20),82.94% higher than 30(Q30).Meanwhile,the qualities of reads2 were 83.99%higher than 20(Q20),72.00% higher than 30(Q30).The number of reads1 N bases is 130 bp,and the number of reads2 N bases is 74 bp.The GC content of reads1 was 63.99%,and the GC content of reads2 was 64.79%.With annotation by SPAdes,the full-length of genome was 7,699,129 bp,consisting by 1836 contigs and 7,343 protein-coding genes(GenBank Accession number:NZ_QGMR00000000).Raw data of Streptomyces sp.ZEA17 I showed that the genome obtained5,915,444 reads with average length 301 bp.The qualities of reads1 were 89.98 % higher than 20(Q20),78.71% higher than 30(Q30).Meanwhile,the qualities of reads2 were 73.26% high than20(Q20),57.93% higher than 30(Q30).The number of reads1 N bases is 36 bp,and the number of reads2 N bases is 571 bp.The GC content of reads1 was 66.93%,and the GC content of reads2 was 68.46%.Based on SPAdes annotation,genome was 7,526,731 bp in full length,made up by1,956 contigs.Total 6,881 protein-coding genes were also predicted(GenBank Accession number:NZ_QGMS01000000).In general,whole genome sequencing studies could promote the exploration of gene functions in biocontrol Streptomyces.Furthermore,we comducted genome annotation,comparative genomics,and other bioinformatical analysis to better undertand the genome of the two strains.Among them,eight chitinase family genes were identified from Streptomyces sp.FT05 W genome,of which ChiD,ChiO and ChiP are regarded as potentially new genes.Meanwhile,from Streptomyces sp.ZEA17 Igenome,10 chitinase family genes were identified,of which ChiD,ChiI,ChiQ and ChiT are regarded as potentially new genes.According to the phylogenetic tree of chitinase family genes constructed by MEGA 6.06,in Streptomyces sp.FT05 W genome,six genes belongs to Family 18 and 1 gene belongs to Faimly 19.In the genome of Streptomyces sp.ZEA17 I,nine genes belongs to Family 18 and 1 gene belong to Family 19.The 19 family chitinase is able to degrade the chitin,which is main component of the fungal cell wall,and play a major role in the biocontrol mechnisms of Streptomyces species.Further ioinformatical analysis of the chitinase family genes were performed by using a variety of softwares,including Protparam.Moreover,qPCR analysis was conducted to quantify the expression of chitinase family genes in Streptomyces sp.FT05 W.The relative expression level of all 18 Family genes were higher than the 19 Family gene,and ChiD gene showed the highest expression level.Additoonally,msiK,dasR and ChiR genes from Streptomyces coli genome were used as reference genes to explore potential regulators of chitinase in Streptomyces sp.FT05 W.It was sure that msiK gene exist in its genome,and attemption to knock it from the genome was conducted.All these above information would provide basis to further explore its chitinase regulators.