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克里斯普尔比较工具包:快速识别,可视化和分析克里斯普尔数组多样性

Alan J Collins¹, Rachel J Whitaker^1,2

¹Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA and University of Illinois Urbana-Champaign, Urbana, Illinois, USA.

The CRISPR journal

|July 17, 2023

概括

我们开发了CRISPR比较工具包 (CCTK) 来自动化CRISPR间隔器的分析以确定微生物菌株的类型. 这个工具重建了菌株历史,推断了进化关系,有助于微生物基因组学研究.

科学领域:

微生物基因组学微生物基因组学
分子生物学分子生物学
生物信息学是一种生物信息学.

背景情况:

通过特定序列的间距向,CRISPR-Cas系统赋予微生物对移动遗传元素 (MGE) 的免疫力.
克里斯普尔隔离器在微生物菌株之间具有很高的变异性,因此它们适合用于高分辨率的菌株类型化.
目前还缺乏使用CRISPR间隔器数据重建微生物菌株历史的自动化工具.

研究的目的:

开发一个用于分析CRISPR数组关系的自动化工具包.
为了使微生物菌株历史和进化途径的重建使用CRISPR间距数据.
为CRISPR阵列分析提供一个统一的平台,包括遗传学推断.

主要方法:

开发CRISPR比较工具包 (CCTK),一个命令行应用程序.
整合用于识别CRISPR数组,比较数组关系 (CRISPRdiff) 和推断家族遗传树 (CRISPRtree) 的工具.
实施一种新的工具,用于预测MGE内部的距离目标.

主要成果:

CCTK成功地识别了CRISPR数组并分析了它们的关系,可视化了与CRISPRdiff.diff.的相似之处.
克里斯普树从数组关系中推断出家族遗传树,提供了关于进化史的假设.
该工具包统一了多个CRISPR分析功能,包括从数组数据中推断族系的第一个方法.

结论:

克里斯普尔比较工具包 (CCTK) 为分析克里斯普尔间隔器演变提供了必要的自动化工具.
CCTK促进了微生物菌株的类型和演化史的重建.
这一工具包代表了应用CRISPR-Cas系统用于微生物种群遗传学研究的重大进步.

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