Genomic Analysis Of Streptomyces Albulus ZPM And Sogatella Furcifera

Part I:Streptomyces species are Gram-positive bacteria that predominantly inhabit highly complex and competitive soil environments.The secondary metabolites produced by Streptomyces species have been the sources of antibiotics,anti-tumor drugs and immunosuppressive agents.In the current study,a strain of Streptomyces albulus,S.albulus ZPM,was isolated from the soil,which produces the homopolymer antibiotic s-PL with shaking flask yield of?0.79 g/L.The genome sequencing,assembly and annotation of S.albulus ZPM were performed.And the results showed that S.albulus ZPM has a linear genome,which consists of 9,784,577 bp with 9,073 genes and has a GC content of 72.2%.Comparative genomics revealed that the core genome region was harbored in the middle of the S.albulus ZPM chromosome,whereas the variable genome region was at both ends of the chromosome.The genome houses 44 gene clusters for secondary metabolite biosynthesis,in which 20 gene clusters are involved in the biosynthesis of polyketides and non-ribosomally synthesized peptides,including the Pls NRPS gene cluster.The regulatory mechanism of?-PL synthesis,particularly in vivo,is still unclear.In order to identify the genes involved in?-PL synthesis,high-throughput sequencing was further performed,and genetic variants were identified from pooled libraries consisting of the 30 highest-yield mutants?group-H?or 30 lowest-yield mutants?group-L?selected from the 180 mutants generated by either chemical mutagens or UV radiation.When combining the group-L-and group-H-specific genetic variants,162 genes with non-synonymous SNP were identified,which were enriched in transportation and metabolism of carbohydrate,as well as transcription and energy production.HrdD,encoded by SAZ 4132,is a sigma factor that shows the most sensitive response to pH change,containing a non-synonymous mutation?A132V?in mutant strains with lower?-PL yields.Electrophoretic mobility shift assays showed that the pls gene is likely regulated by transcriptional activator HrdD.The data obtained in this study will facilitate future studies to improve the yield of?-PL,improvement and optimization industrial bioprocesses.Part?:Sogatella furcifera is an important phloem sap-sucking and plant virus-transmitting migratory insect of rice.plant.Because of its high reproductive potential,dispersal capability and transmission of plant viral diseases,S.furcifera causes considerable damage to rice grain production.A total of 241.3 Gb of raw reads from the whole genome of S.furcifera were generated by Illumina sequencing using different combinations of mate-pair and paired-end libraries from 17 libraries with distinct sizes ranging between 180 bp and 40 kbp.The final genome assembly was 720 Mb,with average N50 contig size of 70.7 kb and scaffold N50 of 1.18 Mb,which was consistent with the estimated genome size determined by flow cytometry and k-mer frequency.The completeness of assembly was estimated using several different methods and the result showed that 99.59%?247/248?of core CEGMA genes and 91.7%?2,453/2,675?of BUSCO genes were covered.Genome annotation,assisted by RNA-seq data?different developmental stages?,identified 21,254 protein-coding genes,of which 70%genes showed homology with known functional proteins.To obtain a global overview of S.furcifera development,the transcriptomes of eight differentially developmental stages,including embryo?emb?,1^st-5^th instar nymphs?1in,2in,3in,4in,and 5in?,5-day-old adult?5d?and 10-day-old adult?10d?,were investigated using RNA-seq,with pairwise comparisons between each pair of developmental stages.A total of 4,166 genes were identified as significant differently expressed genes?DEGs?,which can be clustered into eight different patterns.The expression levels of specific genes at each developmental stage were investigated,for example,chitinase,which is coupled with insect growth and exoskeleton development,showed high expression in 5th instar nymphs.Vitellogenin was highly expressed in 5-day-old and 10-day-old adults,suggesting that they are essential for the S.furcifera reproduction process.The assembled genome and transcriptome of S.furcifera will be a valuable resource for ecological and virus-host interaction studies of this pest.