Exogenous Source Studies Of Spacer Sequences In Regularly Clustered Intervals Of Short Palindromic Repeats

It was discovered in recent years that clustered regularly interspaced short palindromic repeats (CRISPRs) are structures closely related to the horizontal genetic transfer of prokaryotes, such as archaea and eubacteria. CRISPRs are considered as an adaptive immune structure of prokaryotes. The interspaced repeats structure in CRISPR is considered exogenous genes. Therefore, it is of great importance to study the patterns of the interspaced repeats in order to understand the functions and working mechanisms of CRISPR and the patterns of horizontal transfers of bacterial genes.This project studies the interspaced sequencing of CRISPR systems in all the prokaryotes whose genes have been completely sequenced. It discovers the patterns of their distribution, understands the origins of interspace sequenced bacteriophage and plasmid, and thus provides preliminary data for future research.MethodologyOut of existing CRISPR database, we collect CRISPR systems and interspaced sequence data of 2762 bacterial genes. We also organize data of 1444 bacteriophage genes and 4598 plasmid genes as published by the GenBank Database. We use the BLASTN software to make similitude comparisons between interspaced sequence data and bacteriophage and plasmid genomes, which are put into X2 tests.Results1. Out of 2762 bacterial genomes, we find 1940 genomes that have definite or possible CRISPR structures and 90096 interspaced sequences. Most genomes contain 1 to 50 interspaced sequences (1414/1940, 72.9%). Only 58 (58/1940, 3.0%) genomes have more than 250 interspaced sequences, including 13 (13/150, 8.6%) archaea and 45 (45/2612,1.7%) eubacteria. The difference is statistically significant (X2=29.98,p<0.01).2. The similitude comparison of the interspaced sequences: 1055 interspaced sequences of 245 bacterial genomes have been found, successfully matching 363 bacteriophages. The match rate is as low as 0.12%. 201 spacer sequences are found in 104 bacteria, successfully matching 320 plasmids.Conclusions1. There are significant differences in the number of interspaced sequences of CRISPR systems in bacterial genomes. Archaea genomes contain more interspaced sequences in their CRISPR systems.2. In the similitude comparisons,only a small percentage of interspaced sequences originate from bacteriophages and plasmids due to low discovery rate of bacterial and bacteriophages ' genomes, indicating that more in-depth study could significantly raise success rates.