PhasomeIt: an 'omics' approach to cataloguing the potential breadth of phase variation in the genus Campylobacter.
PhasomeIt: an 'omics' approach to cataloguing the potential breadth of phase variation in the genus Campylobacter.
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DOI：
10.1099/mgen.0.000228
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发表时间：
2018-11
影响因子：
3.9
通讯作者：
Bayliss CD
中科院分区：
文献类型：
--
作者：
Aidley J;Wanford JJ;Green LR;Sheppard SK;Bayliss CD
超变简单序列重复序列（SSR）是相位变异（PV）的驱动因素，其基因表达的随机，高频，可逆开关是几种致病细菌物种的共同特征，包括人类病原体空肠弯曲菌。在这里，我们研究的分布和保护已知的和假定的SSR驱动的相位可变基因-相体-在弯曲杆菌属。PhasomeIt是一种新的程序，专门用于快速鉴定SSR介导的PV。该程序检测每个SSR的位置、类型和重复次数。每个SSR与特定基因及其推定的表达状态连锁。其他产出包括SSR驱动的相位可变基因和“核心相体”-PV基因在系统发育分组中的最小集合的保护。77个完整的弯曲杆菌基因组序列的分析检测到一个“核心相组”的保守的PV基因在每个物种和大量的罕见的PV基因很少，或没有，在其他基因组序列的同源物。分析一组部分基因组序列，与食物链相关的元数据，检测到的证据相组和源主机之间的弱链接的致病分离物的序列类型（ST）-828，但不是ST-21或ST-45复合物。在弯曲杆菌属的相体的调查提供了重叠的证据，但独特的机制，PV介导的适应特定的生态位。这表明，相体可能参与宿主的适应和传播的弯曲杆菌。最后，这个工具是可塑性的，并将有效用的研究在不同的细菌物种的其他重复元件的分布和基因的影响。
Hypermutable simple sequence repeats (SSRs) are drivers of phase variation (PV) whose stochastic, high-frequency, reversible switches in gene expression are a common feature of several pathogenic bacterial species, including the human pathogen Campylobacter jejuni. Here we examine the distribution and conservation of known and putative SSR-driven phase variable genes – the phasome – in the genus Campylobacter. PhasomeIt, a new program, was specifically designed for rapid identification of SSR-mediated PV. This program detects the location, type and repeat number of every SSR. Each SSR is linked to a specific gene and its putative expression state. Other outputs include conservation of SSR-driven phase-variable genes and the ‘core phasome’ – the minimal set of PV genes in a phylogenetic grouping. Analysis of 77 complete Campylobacter genome sequences detected a ‘core phasome’ of conserved PV genes in each species and a large number of rare PV genes with few, or no, homologues in other genome sequences. Analysis of a set of partial genome sequences, with food-chain-associated metadata, detected evidence of a weak link between phasome and source host for disease-causing isolates of sequence type (ST)-828 but not the ST-21 or ST-45 complexes. Investigation of the phasomes in the genus Campylobacter provided evidence of overlapping but distinctive mechanisms of PV-mediated adaptation to specific niches. This suggests that the phasome could be involved in host adaptation and spread of campylobacters. Finally, this tool is malleable and will have utility for studying the distribution and genic effects of other repetitive elements in diverse bacterial species.
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影响因子：
14.9
作者：
Lin WH;Kussell E
通讯作者：
Kussell E
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
2.6
作者：
Cooper, Kerry K.;Cooper, Margarethe A.;Joens, Lynn A.
通讯作者：
Joens, Lynn A.
DOI：
10.1111/j.1749-6632.2012.06584.x
发表时间：
2012-01-01
期刊：
EFFECTS OF GENOME STRUCTURE AND SEQUENCE ON VARIATION AND EVOLUTION
影响因子：
--
作者：
Bayliss, Christopher D.;Palmer, Michael E.
通讯作者：
Palmer, Michael E.
DOI：
10.1098/rspb.2011.0146
发表时间：
2011-12-07
影响因子：
4.7
作者：
Libby, Eric;Rainey, Paul B.
通讯作者：
Rainey, Paul B.