Comparative Analysis Of The Completed Genome Sequences Of Pectobacterium Carotovorumresulted From The Different Sequencing Methods

High-throughput sequencing technologies(High throughput sequencing)are also called "Next generation sequencing technology".Compared with the previous indoor cultivation,fingerprint technology,denaturing gradient gel electrophoresis(DGGE)cloning sequencing and the sequencing of the first generation technology,High-throughput sequencing technologies have particularly obvious advantages:fast sequencing speed and big flux,more information on species classification and functional genes data and lower cost,simpler operation compared to the first generation of sequencing.At present,the second generation sequencing technique has been comprehensively developed and extensive utilized.Meanwhile,The third generation sequencing technology(single molecular sequencing technology)is developed rapidly with lower cost and more reads in long sequences,and more and more attentions of many scientific research communities were paid on.Based on this,the completed genome sequencing analysis of Pectobacterium carotovorum subsp.carotovorum(Pcc)were carried out in different sequencing techniques for the more accurate sequence,and comparing different techniques,further evaluating them.1.Illumina Hiseq sequencing platform was used as the second generation sequencing technology for the completed genome sequencing analysis of Pectobacterium carotovorum subsp.carotovorum(Pcc)in this work.A completed genome of 4,899,898 bp in length was obtained after the assembling of the reads.According the functional annotations by Kyoto Encyclopedia of Genes and Genomes(KEGG),the gens for membrane transportation were up to 911 in quantity and set the group with the highest abundance in PccS1,which are might benefit for the cells of this bacterium toadaption in different environments.Meanwhile,genes for the components of T3SS were the largest in number by analysis of the secreted protein annotations than for other secretion systems,which suggested that the pathogenic process of PccS1 mainly through Ⅲ secretion system(T3SS).In summary,this study explores the pathogenic mechanism of Pcc and provides technical support for disease prevention and control strategies.2.The third generation sequencing technology of whole genome sequencing analysis of Pectobacterium carotovorum subsp.carotovorum(Pcc):The third generation sequencing technology also called single molecule real-time technology.It has huge potential for its high speed,long sequence output and lower cost.We used the three generations of sequencing technologies adopted PacBio RS Ⅱ sequencing model,to get whole genome sequencing analysis of Pectobacterium carotovorum subsp.carotovorum,and DNA sequencing data have analyzed and we got detailed genomic information,such as genomic profiles,genome analysis,and gene function annotation.This study measured that PccS1’s genome is 4896358 bp,which might include 4520 genes.We construct metabolic pathways by KEGG database to obtain a total of 4197 proteins,which have definite biological function through.3.The comparison of two kinds of sequencing technology:(1)New DNA sequencing technologies help us get comprehensive and precise genome with lower prices to analyze the genome,transcriptome and protein interactions.The second generation sequencing technology can obtain relatively short,but the high accuracy sequences,to assemble the whole genomes,but its operation processes require more steps;Third generation sequencing operation is simpler,the sequencing read is longer,and the cost is lower.But it has more proportion of the wrong bases.The second generation sequencing technology is more extensive application,for the useful data analysis platform and robust database.While single molecule sequencing technology is still in the preliminary stage of development,so it has a lot of challenges in this respect.(2)The genome length is 3540 bp longer and the number of genes is 222 more measured by second generation sequencing platform than third generations of sequencing for PccS1 genome sequencing.In addition,the second generation sequencing platform measured the number of 892 more COG gene than three generation sequencing.In general,the second generation sequencing technology is more convenient in practice.Compared with the third generation sequencing technology,its data analysis and processing is available,which make it easier to use with a lot of report.Although single molecule sequencing technology is rapid development,it faces challenges in various aspects.With the constant improvement of database technology and data analysis,single molecule sequencing technologies are expected to get an extensive application in the near future.