产甲烷古菌中CRISPR簇的研究

Distribution of CRISPR arrays in methanogenic archaea

【目的】通过对51个产甲烷古菌基因组中成簇的规律间隔短回文重复序列(Clustered regularly interspaced short palindromic repeats,CRISPR)的组成和来源进行研究,推测产甲烷古菌与环境中其他微生物的物质交换和相互作用,在基因组水平上阐述产甲烷古菌之间的遗传差异。【方法】利用CRISPRdb和CRISPRFinder,找出产甲烷古菌基因组中所有潜在的CRISPR簇。对CRISPR簇的基本组成部分进行分析:利用BLASTCLUST对重复序列(Repeat)进行分类;分别将间隔序列(Spacer)与Refseq病毒基因组、Refseq质粒基因组和Refseq产甲烷古菌基因组进行比对,从而获得间隔序列的物种来源和功能信息的注释。【结果】在51个产甲烷古菌中共找到了196个CRISPR簇,这些CRISPR簇中包含了总共4 355条间隔序列。在这些产甲烷古菌中,CRISPR簇的分布是不均匀的,且每个物种的间隔序列数量与其CRISPR簇数量是不成正比的。在对重复序列进行分类之后,发现Mclu1是分布最广且最具代表性的一类重复序列。在4 355条间隔序列中有388条具有物种注释信息,266条具有功能注释信息。从CRISPR簇间隔序列的来源来看,产甲烷古菌曾受到来自Poxiviridae、Siphoviridae以及Myoviridae属病毒的攻击,并且产甲烷古菌之间存在比较广泛的遗传物质交换。【结论】产甲烷古菌基因组中的CRISPR簇在组成和来源上存在较大的差异,这些差异与它们的生存环境有较大的关系。从CRISPR簇的角度阐述了产甲烷古菌之间基因组序列的差异。

[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.