Comparison Of The Predictions Of Prokaryotic Genomic Islands And Analysis Of Prokaryotic Essential Genes In Genomic Islands

Prokaryotes including bacteria and archaea are playing an imperative role in the field of health,medicine,environment and energy.Genomic islands(GIs)usually contain clusters of horizontally transferred genes.It is reported that these genes are closely related to pathogenicity,drug resistance,secretion,antibiotics and metabolism.Large amounts of genomic islands prediction tools have been developed based on sequence composition method,such as IslandPath,SIGI-HMM,Zisland Explorer,and comparative genomics method like Island-Pick and MobilomeFINDER.However,it is crucial to choose the most suitable approaches among a wide variety of GIs prediction algorithms.Here,comparative analyses of GIs prediction results in prokaryotes are performed from chapter one to two.Features and functional classifications associated with GIs are firstly introduced in the thesis.Then,genomic island databases and other web resources have been detailed presently.Lastly,GIs in 28 organisms have been predicted with several representative methods.With a further comparison with experimentally verified GIs,the distinctions of these methods can be realized.Furthermore,functional analysis of GIs has been carried out based on the reliable GIs prediction results in prokaryotes.For instance,the study on potential drug resistance genes can help further detect drug-resistant mechanism which will give clue to detect new antibiotics and antimicrobials targets.Essential genes and statistical analysis of these genes in GIs have been researched in the chapter three and four.Essential genes are thought to encode proteins that carry out the basic functions to sustain a cellular life.Firstly,the experimental methods and database associated with essential genes are detailed in the thesis.After that,the essential genes in 28 prokaryotes have been analyzed by a statistical method and the conclusion that essential genes in GIs are significantly fewer than those outside GIs has been reached.Lastly,the function of 362 essential genes found in GIs has been explored further by BLAST against the Virulence Factor Database(VFDB)and the phage/prophage sequence database of PHAge Search Tool(PHAST).Consequently,several toxin-related proteins and repressors encoded by these essential genes are found in GIs.The comparative analysis of essential genes in genomic islands will not only shed new light on the development of the prediction algorithm of essential genes,but also give a clue to detect the functionality of essential genes in genomic islands.