Microbial genome analysis platform – Whole genome sequencing of Morganella morganii and identification of pathogenicity-related genes

• Main Authors: CHEN, YU-TIN, 陳昱廷
• Other Authors: Tang, Chuan Yi
• Format: Others
• Language: en_US
• Published: 2012
• Online Access: http://ndltd.ncl.edu.tw/handle/b337nu

博士 === 國立清華大學 === 資訊工程學系 === 101 === As the sequencing technology advanced, genome of life decode also accelerate, related genome analysis tools also accumulated, comparative genomic analysis is current trend, which could applied to identify gene function and possible pathogenicity mechanism in organism. We develop a software pipeline for microbial genome project, which is suitable to high throughput and short read next generation sequencing analysis. The opportunistic enterobacterium, Morganella morganii, which can cause bacteraemia, is the ninth most prevalent cause of clinical infections in patients at local hospital. It is sometimes encountered in nosocomial settings and has been causally linked to catheter-associated bacteriuria, complex infections of the urinary and/or hepatobiliary tracts infection. To obtain insights into the genome biology of M. morganii and the mechanisms underlying its pathogenicity, the patient isolate strain KT was whole genome sequencing the genome and compared with the genome sequences of related bacteria. Genome backbone build rely on de novo assembly or re-sequence method, many string algorithm applications and developments. Genome backbone build: de novo assembler or re-sequencing compensate with assembler, a mix approach, many string algorithm applications and developments here. In cases, ABySS assembler performs better. Assembly results of two different distance libraries and scaffolder of M. morganii KT, twelve scaffolds remain. Align and fit ten scaffolds in the KT with optical map. PCR and sequencing for gap fill were conduct and toward the completion of the KT genome. In case, the A. baumannii CH 1-43 successful used mix approach and left one gap to complete genome. Genome analysis, use sequence alignment and accumulated organisms’ sequences as comparative genomics resources. The gene prediction, orthologous identification, functional analysis and comparative genomics analysis workflow: Morganella morganii KT and Leptospira santarosai serovar Shermani were successfully find pathogenicity or virulence related functional genes bring from those organisms and novel gene structures. The M. morganii KT possess genomic sequence of 3,826,919-bp sequence contained in 58 contigs has a GC content of 51.15% and includes 3,565 protein-coding sequences, 72 tRNA genes, and 10 rRNA genes. The pathogenicity-related genes encode determinants of drug resistance, fimbrial adhesins, an IgA protease, haemolysins, ureases, and insecticidal and apoptotic toxins as well as proteins found in flagellae, the iron acquisition system, a type-3 secretion system (T3SS), and several two-component systems. Comparison with 14 genome sequences from other members of Enterobacteriaceae revealed different degrees of similarity to several systems found in M. morganii. The most striking similarities were found in the IS4 family of transposases, insecticidal toxins, T3SS components, and proteins required for ethanolamine use (eut operon) and cobalamin (vitamin B12) biosynthesis. The eut operon and the gene cluster for cobalamin biosynthesis are not present in the other Proteeae genomes analysed. The second selected M. morganii PC strain were whole genome sequencing, and compare with KT, genome size are larger 390-kb in length. One ICE of 90-kb were similar ICE Pm1 were appeared, and several prophage gene clusters are mainly contribute to other differences. The strain KT is the first genome sequence of M. morganii, which is a clinically relevant pathogen. Comparative genome analysis revealed several pathogenicity-related genes and novel genes not found in the genomes of other members of Proteeae. Thus, the genome sequence of M. morganii provides important information concerning virulence and determinants of fitness in this pathogen. The M. morganii KT genome deposited in the DDBJ/EMBL/GenBank under the accession number ALJX00000000.