基于全基因组序列的弯曲菌特征分析  

Feature analysis of Campylobacter based on whole genome sequences

作　　者：孙磊[1,2,3] 杨臻辉 恽茜 黄金林 SUN Lei;YANG Zhenhui;YUN Xi;HUANG Jinlin(School of Information Engineering,Yangzhou University,Yangzhou 225127,Jiangsu,China;School of Artificial Intelligence,Yangzhou University,Yangzhou 225127,Jiangsu,China;Jiangsu Key Laboratory of Zoonosis,Yangzhou 225009,Jiangsu,China;Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis,Yangzhou 225009,Jiangsu,China)

机构地区：[1]扬州大学信息工程学院,江苏扬州225127 [2]扬州大学人工智能学院,江苏扬州225127 [3]江苏省人兽共患病学重点实验室,江苏扬州225009 [4]江苏省动物重要疫病与人兽共患病防控协同创新中心,江苏扬州225009

出　　处：《生物信息学》2020年第4期254-262,共9页Chinese Journal of Bioinformatics

基　　金：国家重点研发计划项目(No.2018YFD0500500);江苏省人兽共患病学重点实验室资助项目(No.R1805).

摘　　要：空肠弯曲菌(Campylobacter jejuni)和结肠弯曲菌(Campylobacter coli)是引起人类腹泻的主要致病菌。传统生化方法在鉴定弯曲菌时存在步骤多、耗时长、通量低等问题。本研究通过利用生物信息学方法对弯曲菌全基因组进行序列、基因注释、耐药基因、多位点序列分型以及CRISPR-Cas系统等分析,挖掘能够有效区分空肠弯曲菌和结肠弯曲菌的高分辨力特征。实验结果表明,空肠弯曲菌和结肠弯曲菌在基因组序列长度、GC含量、基因数量、多位点序列分型以及CRISPR-Cas系统等方面存在显著差异。同时,研究还发现了一段在空肠弯曲菌基因组中广泛存在的高分辨力CRISPR重复序列。这些特征可用于构建能够准确鉴别空肠弯曲菌和结肠弯曲菌的生物信息学方法。Campylobacter jejuni and Campylobacter coli are the main pathogenic bacteria that cause diarrhea in humans.Traditional biochemical methods have problems such as multiple steps,time consuming,and low throughput when identifying Campylobacter.In this study,several analyses including sequence analyses,gene annotation,drug resistance gene prediction,multilocus sequence typing(MLST),and CRISPR-Cas system finding were performed on the whole genomes of Campylobacter using various bioinformatics methods,thereby exploring highly effective features for distinguishing Campylobacter jejuni from Campylobacter coli.Experimental results manifest that Campylobacter jejuni and Campylobacter coli have significant differences in genome sequence length,GC content,gene number,MLST,and CRISPR-Cas systems.In addition,we found a highly distinguishable CRISPR repeat sequence that is widespread in Campylobacter jejuni.It is concluded that these features can be used to construct bioinformatics tools for identifying Campylobacter jejuni and Campylobacter coli more accurately.

关 键 词：弯曲菌 全基因组 多位点序列分型 CRISPR-Cas系统 

分 类 号：Q93[生物学—微生物学]