摘要
【背景】功能作图(functional mapping)模型是基于统计方法的分析生物体动态复杂性状发育的全基因组作图方法,旨在定位性状发育过程中的数量性状位点(quantitative trait loci,QTL),将功能作图应用于微生物研究有助于解析复杂的互作过程。【目的】利用功能作图定位两种微生物在动态生长发育过程中发挥显著作用的QTL,通过基因功能注释找到影响微生物表型生长的基因。【方法】将大肠杆菌和金黄色葡萄球菌各100个菌株单独培养和一一配对共同培养,将取得的各菌株生长丰度表型数据和单核苷酸多态性(single nucleotide polymorphism,SNP)数据进行关联分析,找到同一物种在不同培养条件下对生长起作用的显著QTL。【结果】通过功能作图分析,在大肠杆菌中定位到217个QTL,金黄色葡萄球菌中定位到152个QTL;通过功能聚类和基因注释分析发现,QTL所在候选基因中金黄色葡萄球菌scdA、sdrC、sdrD、ftsA和大肠杆菌phr、nagC、eptA、ppsA、priA、flim基因对微生物的生长发挥了较大作用。【结论】本文借助功能作图定位了大肠杆菌和金黄色葡萄球菌在竞争互作中的关键基因,研究成果不仅为功能作图在微生物研究中的应用奠定了基础,更为解析微生物复杂的相互作用机制提供了新的思路。
[Background]Functional mapping is a genome-wide mapping method that uses statistics to analyze the development of dynamic and complex traits in organisms,with the aim of locating quantitative trait loci(QTL)during the development of traits.The application of functional mapping to microbiological studies can unravel complex interactions.[Objective]To locate significant QTLs in the growth and development of two microorganisms by functional mapping,and to identify the key genes affecting the phenotypic growth of the microorganisms functional annotation.[Methods]One hundred strains of Escherichia coli and 100 strains of Staphylococcus aureus were cultured separately or paired together for co-culture.The phenotypic data and SNP data obtained from each strain were used for correlation analysis to locate the significant QTL of the same species under different culture conditions.[Results]The functional mapping identified 217 QTL in E.coli and 152 QTL in S.aureus.The functional clustering and gene annotation analysis showed that scdA,sdrC,sdrD,and ftsA in S.aureus and phr,nagC,eptA,ppsA,priA,and flim in E.coli might play a role in the microbial growth.[Conclusion]We identified the key genes involved in the competitive interactions between E.coli and S.aureus by employing functional mapping.Our results not only provide fundamental data for the application of functional mapping in microbial research but also offer a new idea for deciphering the complex mechanisms of microbial interactions.
作者
尹丽新
李彩凤
何晓青
邬荣领
金一
YIN Lixin;LI Caifeng;HE Xiaoqing;WU Rongling;JIN Yi(College of Biological Sciences and Technology,Beijing Forestry University,Beijing 100083,China)
出处
《微生物学通报》
CAS
CSCD
北大核心
2023年第9期3784-3799,共16页
Microbiology China
基金
中央高校基本科研业务费专项资金项目(2021ZY64)。
关键词
大肠杆菌
金黄色葡萄球菌
竞争互作
功能作图
显著数量性状位点
Escherichia coli
Staphylococcus aureus
competitive interaction
functional mapping
significant quantitative trait loci
