The Complete Genome Of Serratia Marcescens ESE-2014 And Its Evolutionary Analyses

The species of Serratia are prevalent in the environment,which can be discovered in water,soil,plants,insects,humans and other animals.Serratia marcescens,belongs to the genus Enterobacteriaceae is one of the three ordinary Serratia species.There were 23 Serratia species in the first edition of the “Berger's bacteria manual of systematic bacteriology”.While the total of Serratia species remained was only five in the fifth edition.And the five Serratia species had merged into one species in the eighth edition in 1974,namely S.marcescens.However,with the development of molecular biology,the ninth edition contained eleven Serratia species.After 2004,there are eighteen Serratia species with the new species identified.At the present,the identification of new species mainly depends on the biological characteristics and phylogenetic analysis with 16 S rRNA.The method that utilizes 16 S rRNA as the criterion to classify the microorganisms has an obviously deficiency:16S rRNA carries little evolution information that is scare,and can't construct the reliable phylogentic tree from the aspect of phylogentic analysis.In this study,we used the data of whole genome sequencing of S.marcescens ESE-2014,and combined with other data released from NCBI to discuss the issue of comparative genomics from several aspects.In this study,the project of whole genome sequencing of S.marcescens ESE-2014 was completed.Firstly,the DNA library was constructed and the data was assembled.The size of assembled result is 5,019,494 bp,which have 19 Scaffolds.N50 was extended to 3,111,409 bp,and portray the sketch of genome of S.marcescens only with four incredible nucleotides,N.Then the gaps among Scaffolds were filled up with chain termination method.Finally,the whole genome was obtained.The length of whole genome ESE-2014 was 5,017,639 bp and the GC content was 59.73%.The genome,ESE-2014 was analyzed by some software.Phospholipase is an important enzyme for the hydrolysis of phospholipids.The microorganisms containing the phospholipase A1 mainly includes Yersinia,Streptomyces albidoflavus,Aspergillus,Pseudomonas and Serratia.Our study also analyzed the sequence of phospholipase A1(plaA)and its accessory protein gene(plaS),to discuss the phylogenetic relationships of Enterobacteriaceae.The results are shown below: 1.Analysis of RNA within ESE-2014 genomeS.marcescens ESE-2014,which genome contains 88 tRNAs.The largest number of tRNA is tRNA-Val who can carry valine,and the copy number of that was 9.The second largest number of tRNA is tRNA-Leu,and the copy number of that was 8.One of the tRNAs can carry selenocysteine.And there are also two tRNAs,its function is unclear.The predictions of rRNA show that seven copies of 5S rRNA,six copies of 16 S rRNA operons and six copies of 23 S rRNA operons are found in the genome of S.marcescens ESE-2014.2.Analysis of repeat sequences within ESE-2014 genomeS.marcescens ESE-2014 genome contains many tandem repeats.There are 10 repeats which score above 500 and 22 repeats which score above 100.And there are 77 repeats which score below 100.A total of 225 insertion sequences are predicted,and the insertion sequences of high score are belonged to IS3 family.3.Analysis of prodigiosin gene cluster within ESE-2014 genomeThe strain ESE-2014 contains the gene cluster of prodigiosin which consists of 14 genes,including pig(A~N).We found two types of Serratia species have the gene cluster of prodigiosin via the analysis of 28 strains in seven Serratia species: One type in those strains is that the pig gene clusters inserted in the region between cueR and copA,such as B3R3,U36365 and WW4 strains.Another type is that the pig gene clusters inserted into the region upstream of the cueR and copA,such as AS9,AS12 and AS13 strains.Other species of Serratia contain one or two genes in the gene cluster,and the species of S.proteamaculans 568 and S.marcescens 1122 do not contain this gene cluster.4.Comparative analysis of ORFs in the genome of SerratiaThis study found that the strain ESE-2014 contained 53 specific ORFs,including some hypothetical proteins and enzymes,such as antitermination proteins,portal proteins,scaffold proteins and phage lysozyme.The strain ESE-2014 contains 10 specific ORFs in Serratia.While there are 11 ORFs still unknown,which may be specific in the strain ESE-2014.5.Phylogenetic analysis based on plaA,plaS and 16 S genesIn this study,10 species of Serratia were selected for phylogenetic analysis with the outgroup of Yersinia pestis and Y.enterocolitica.Based on the nucleotide datasets of three genes,the phylogenetic tree was reconstructed by ML,MP and BI methods.The results showed that S.plymuthica may be one of the ancient bacteria symbiotics with slow evolution rate,which maintain some ancient characteristics.While,for S.marcescens,the rate of evolution is faster relatively.At the present,the other infected animals and plants which ancestor of the living organisms in Serratia have not solved.We preliminarily discuss the phylogenetic relationships of Serratia to provide basic information for further study on identifying ancestors of free living bacteria.6.Phylogenetic analysis based on 187 core genesIn order to exploring the phylogenetic relationships of S.ureilytica Niva 51 and S.nematodiphila DZ0503SB1,we selected 36 Serratia strains of 9 species with 187 core genes to construct the ML and NJ phylogenetic tree.Our results indicate that S.ureilytica and S.marcescens U36365 were clustered into one clade,the bootstrap is 100,the two species clustered with S.marcescens RSC-1,and the bootstrap value is 100,they were clustered with S.marcescens,the bootstrap value is high.The stable topological structure demonstrates that S.ureilytica and S.nematodiphila may belong to S.marcescens.From the aspect of phylogentic tree,those strains who secrete prodigiosin can be divided into two clades: Clade I include six strains of S.marcescens,such as ESE-2014,U3636,B3R3,FS14 and WW4.Clade II include three strains of S.plymuthica,such as AS13,AS9 and AS12.In this study,the genome of strain ESE-2014 was sequenced by high-throughput sequencing platform.The gaps among Scaffolds were filled up with chain termination method.We used our data of the genome,and combined with other data released from NCBI to discuss the issue of systematic about S.ureilytica NiVa 51 and S.nematodiphila DZ0503SB1.In addition,our study also analyzed the sequence of plaA and plaS of ESE-2014;we used plaA and plaS to explore the ancestor of ancient bacterial symbionts and free living bacteria of Serratia,our results provide basic information for further study on identifying ancestors of free living bacteria.