Genomic variation in Salmonella enterica core genes for epidemiological typing.
Genomic variation in Salmonella enterica core genes for epidemiological typing.
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沙门氏菌核心基因的基因组变异，用于流行病学分类。
DOI：
10.1186/1471-2164-13-88
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发表时间：
2012-03-12
期刊：
影响因子：
4.4
通讯作者：
Ussery DW
中科院分区：
文献类型：
--
作者：
Leekitcharoenphon P;Lukjancenko O;Friis C;Aarestrup FM;Ussery DW
高通量基因组测序的技术进步使全基因组测序（WGS）可作为细菌分型的常规工具。需要鉴定相关基因和变异的标准化程序，以便在研究之间和随着时间的推移进行比较。核心基因-在一个属或物种的所有（或大多数）成员中保守的基因-是研究遗传学和流行病学中基因组变异的潜在良好候选者。我们基于73个公开的沙门氏菌基因组确定了一组2，882个核心基因簇，并评估了它们作为分型靶点的价值，比较了全基因组分型和传统方法，如16 S和MLST。基于核心基因变异的共识树比16 S和MLST提供了更好的分辨率;泛基因组家族树与共识树相似，但具有更高的置信度。核心基因可以分为两类：少数高度变异的基因和较大的保守核心基因，具有低变异。对于最可变的核心基因，氨基酸序列的变化高于相应的核苷酸序列，表明存在对导致氨基酸变化的突变的正选择。核心基因组内的基因组变异对于研究分子进化和为细菌基因组分型提供候选基因是有用的。识别具有不同变异程度的基因是重要的，特别是在趋势分析中。
Technological advances in high throughput genome sequencing are making whole genome sequencing (WGS) available as a routine tool for bacterial typing. Standardized procedures for identification of relevant genes and of variation are needed to enable comparison between studies and over time. The core genes--the genes that are conserved in all (or most) members of a genus or species--are potentially good candidates for investigating genomic variation in phylogeny and epidemiology. We identify a set of 2,882 core genes clusters based on 73 publicly available Salmonella enterica genomes and evaluate their value as typing targets, comparing whole genome typing and traditional methods such as 16S and MLST. A consensus tree based on variation of core genes gives much better resolution than 16S and MLST; the pan-genome family tree is similar to the consensus tree, but with higher confidence. The core genes can be divided into two categories: a few highly variable genes and a larger set of conserved core genes, with low variance. For the most variable core genes, the variance in amino acid sequences is higher than for the corresponding nucleotide sequences, suggesting that there is a positive selection towards mutations leading to amino acid changes. Genomic variation within the core genome is useful for investigating molecular evolution and providing candidate genes for bacterial genome typing. Identification of genes with different degrees of variation is important especially in trend analysis.
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影响因子：
14.9
作者：
Benson DA;Karsch-Mizrachi I;Lipman DJ;Ostell J;Sayers EW
通讯作者：
Sayers EW
影响因子：
3.3
作者：
Boxrud, David;Monson, Timothy;Besser, John
通讯作者：
Besser, John
影响因子：
3.7
作者：
Friis C;Wassenaar TM;Javed MA;Snipen L;Lagesen K;Hallin PF;Newell DG;Toszeghy M;Ridley A;Manning G;Ussery DW
通讯作者：
Ussery DW
DOI：
10.1126/science.1182395
发表时间：
2010-01-22
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Harris SR;Feil EJ;Holden MT;Quail MA;Nickerson EK;Chantratita N;Gardete S;Tavares A;Day N;Lindsay JA;Edgeworth JD;de Lencastre H;Parkhill J;Peacock SJ;Bentley SD
通讯作者：
Bentley SD
影响因子：
2.9
作者：
Binnewies, Tim T.;Motro, Yair;Ussery, David W.
通讯作者：
Ussery, David W.