Molecular Evolution Of Genomic Recombination And Reassortinent

Genetic recombination is an important factor to change and shape genome and itsrelevant phenotypes. Gene transfer or reassortment and recombination in the naturehappen quite frequent between different species or individuals, which lays the foundationfor evolution of species. There are many manners for genome transfer and recombinationin the nature, including conjunction of bacteria, transduction in cells being infected byvirus, gene shifting and rearrangement mediated by insertion sequence and transposons,and virus reassortment in virus infection and genome recombination of different DNAmolecules. It is of vital significance to discuss the molecular evolution mechanism ofRNA and DNA genome recombination. In order to better understand the influence ofgenome recombination on different types of genome evolution, we need to test therecombination event of two different types of genome sequence, that is, RNA and DNA.This research employs bioinformatics to analyze and explain RNA viruses and the avianmitochondrial genome recombination event, and discussed the influence of genomechanges incurred by recombination or reassortment on the reconstruction of speciesevolution history and population genetic models.This research studies RNA genome reassortment and recombination with avianinfluenza virus H6N1and the MERS-CoV as the case study, and studies DNA genomerecombination phenomena with Anseriformes mitochondrial genome as the case study.Based on the GISAID (Global Initiative on Sharing Avian Influenza Datadatabase), NCBIGenBank database and METAMIGA database (Metazoan Mitochondrial GenomesAccessible database), we mainly discuss the following questions:1) the genomecharacteristics and reassortment origin of the human-infecting H6N1influenza virus;2)genome characteristics and recombination analysis of the MERS-CoV;3) the selectivemodel of the functional genes of MERS-CoV;4) analysis of Anseriformes mitochondrialgenome recombination. The research findings are as follows: 1. Genome characteristics and reassortment origin of the human-infecting H6N1influenza virusThis research first reports the reasssortment origin of virus and genomecharacteristics related to virus pathogenicity. The phylogenetic analysis indicate that thefirst case of human infection with H6N1(A/Taiwan/2/2013/H6N1) is brought byreassortment of H6N1virus and H5N2virus. Apart from PB1gene, the other sevengenome segments were all separated from H6N1(A/chicken/Taiwan/A2837/2013) virusisolated from the chickens. The two H6N1viruses originated frommultiple-reassortment of H6N1virus lineage from2003to2004, H6N1virus lineage from2009to2010and several cases of2012year H5N2. Though this reassortment event hasnot caused large-scale H6N1influenza pandemic, we assumed that the surfacehemagglutinin decoding gene HA and neuraminidase decoding gene NA has not resultedin significant changes of H6N1virus antigenicity. Besides, this research finds out thatspecial amino acids existing in several binding sites of surface hemagglutinin receptors inthe human-infecting H6N1virus are different from those of the other H6N1virus, such asthe186nt (H3) in the upstream of the receptor binding site. The analysis finds out that themutation from Proline (P) to Leucine (L) may change H6N1virus recognition andcombination affinity.2. Genome characteristics and recombination analysis of the MERS-CoVThe34sequences of MERS-CoV genome in this research include250singlenucleotide polymorphism sites. There is a missing of17nucleotides in the open readingframe of ORF4b gene of Bisha1/2012and Riyadh1/2012, and6nucleotides indels innucleocapsid (N) of England-Qatar/2012and England1/2012. According to phylogeneticrelationship and polymorphic sites, MERS-CoV is divided into A, B, C and D genetypesand a transitional genetype. Besides, this research finds out that there exists recombinationsignal among BtCoV/133/2005, BtCoV/HKU4-1, BtCoV/HKU5-1andErinaceusCoV/2012-216/GER/2012. However, no recombination site with highconfidence within MERS-CoV is found. This provides the prerequisite for the research ofthe seletive model that virus gene experiences. This research finds out that theMERS-CoV membrane gene (M) had experienced a stepwise evolutionary pathway.Before the virus infection, glycoprotein better adapted itself to the host through changing itself. Later, it was experiencing neutral selective evolution. In MERS-CoV, ORF3openreading frame may encode constructive protein or interferon antagonism to regulate theinternal virus genome replication efficiency or pathogenicity, which is significantlyinfluenced by positive selection in the evolution process between genome B and genomeC. Research finds out that in the first period, the ORF3gene experiences the change fromnegative selection to positive selection evolution. It is assumed that the protein plays animportant role in adapting to the host.3. Analysis of Anseriformes mitochondrial genome recombinationThis research has sequenced three mitochondrial complete genomes of Anseriformesspeices (Bean Geese, Swan Geese and Mandarin Duck), and analyzes the genomestructure and characteristic, phylogeny and some geological distribution of Anseriformesbirds. All these lay certain foundation for the DNA genome recombination analysis ofAnseriformes mitochondrial genomes. This research finds out that there are9differentrecombination events happening to the five genome sequence in20mitochondrialgenomes. Of them, the most possible genome recombination event is found in the SwanGeese mitochondrial genomes sequenced in this research. The recombination happens in1093to2052bp within its genome. Anseriformes phylogenetic analysis and geologicaldistribution analysis provides certain evidence for the occurring of recombination cases.