Analysis Of Conserved Microsatellite Loci And Their Functions In Ebolavirus Genomes

Microsatellites are nucleic acid sequences that are tandem repeated multiple times in series by 1-6 nucleotides,and also can be called simple sequence repeats(SSRs).Microsatellites are widely distributed in eukaryotes,prokaryotes and viruses,with length polymorphism,motif diversity and non-random distribution characteristics.Microsatellites are highly variable and vary widely among individuals,and these mutations may be related to genomic structure and function.Therefore,the emergence and fixation of microsatellites may contribute to the diversity and evolution of the genome.There are also many microsatellites in Ebolavirus genomes,including both coding and non-coding regions.In the past,comprehensive analysis of microsatellites was generally based on the proportion,relative abundance,relative density,and GC content in the viral genomes.Little is known about the relationship between microsatellite and viral genome function and structure.This research mainly explores from the following two aspects:1.Analysis of conserved microsatellites in the terminal non-coding regions of Ebolavirus genomes(Chapter 2)In this chapter,we downloaded 219 genomes from the public database NCBI,which belong to five species of the Ebolavirus genus,and selected all the complete genomes with relatively complete sequencing in the database.We conducted a comprehensive analysis of the microsatellite of the complete genomes and terminal region sequences in Ebolavirus.Using Clustal W software for sequence alignment to detect the diversity between different sequences,the sequence diversity of the complete genome of Ebolavirus in intraspecific is small,but in interspecies is large,especially in the terminal non-coding regions.Using IMEx software to extract microsatellites from 219 samples,five conserved microsatellite loci among different species were found in the complete genomes.In addition,we observed that four of these were located on the terminal non-coding regions.Therefore,the sequences of the terminal non-coding regions were further explored,and the analysis showed that the terminal non-coding region sequence has lower interspecies sequence similarity and higher microsatellite conservation.Using RNA secondary structure prediction methods,it was shown that the four of conserved microsatellites which well base-paired to help forming conserved stem-loop structures mainly appeared in the terminal non-coding regions.Therefore,we speculate that the conserved microsatellites in the Ebolavirus genomes may contribute to the formation of the conserved stem-loop structures.These results suggest that the conserved microsatellites may be evolutionary selected to form conserved secondary structures in 5',3' terminals of Ebolavirus genomes.It may help to understand the biological significance of microsatellites in Ebolavirus and also other virus genomes.2.Analysis of conserved microsatellites in the coding regions of GP gene in Ebolavirus genomes(Chapter 3)In this chapter,we further explore the conservative microsatellite loci found in Chapter 2.Among the only five conserved loci in Ebolavirus genomes of five species,one is located in the coding region of the GP gene,in addition to the conserved loci of terminal non-coding regions that have been thoroughly studied.By comparing GP CDs sequences in 219 samples and microsatellite statistics,it was found that the sequence similarity of GP CDs was significantly lower than that of the complete genomes,but the microsatellite conservative rate was significantly higher.The amino acid sequences of three different proteins(GP1,2,s GP,ss GP)encoded by GP gene were found to be related to the conserved microsatellites.The Uni Prot KB database was used to query the corresponding protein functional sites,and the conserved microsatellite was at the important protein functional sites.Among them,the RNA editing function acts on the conserved microsatellite site.By deleting or inserted A residues,different codons are generated to translate the structural protein and two secreted proteins necessary for Ebolavirus to maintain normal life.In addition,the phenomenon of microsatellite expansion occurred in conserved microsatellites,resulting in different coding effects of RNA editing,so that the RNA produced by them translated the accurate protein.These results may mean that conserved microsatellites can only be preserved by functional choice and have an indispensable role in Ebolavirus genomes.