Distribution of CRISPR arrays in methanogenic archaea

Abstract:

[Objective] By studying the distribution and origin of clustered regularly interspaced short palindromic repeats (CRISPR) in 51 methanogenic archaea genomes, material exchanges and interaction within methanogenic archaea and other microorganism were inferred, and the genomic divergence among the genomes of methanogenic archaea was characterized. [Methods] we identified all potential CRISPR arrays in the methanogenic archaea by applying the CRISPRdb and CRISPRFinder, and then the components of each CRISPR array were analyzed, where repeats were classified by BLASTClust and spacers were aligned to Refseq viral genome, Refseq plasmid genome and Refseq methanogenic genome respectively to retrieve both taxonomic and functional annotation. [Results] Among the 51 methanogenic archaea, in total 196 CRISPR arrays with 4 355 spacers were identified. The distribution of CRISPR arrays in methanogenic archaea was not even, and the number of spacers in one strain was not proportional to the number of CRISPR arrays in the strain. After clustering on repeat sequences of CRISPR arrays, we found that Mclu1 was the most diverse and representative repeat sequence in methanogenic archaea. Among 4 355 spacers, 388 spacers were assigned with taxonomic information and 266 spacers were assigned with functional annotation. By inferring the origin of each spacer sequence, we found that methanogenic archaea might be attacked by viruses belonging to Poxviridae, Siphoviridae or Myoviridae family. Moreover, and t exchanges of genetic materials among these archaea were observed. [Conclusion] Differences in the distribution and origin of CRISPR arrays in methanogenic archaea genomes were observed and characterized, and these differences might result from the interactions and conditions of their living environment. In this study, we could also infer from CRISPR arrays characterize the genomic divergence among methanogenic archaea.