Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt.
Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt.
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DOI：
10.1186/1471-2164-15-737
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发表时间：
2014-08-29
期刊：
影响因子：
4.4
通讯作者：
Hauser AR
中科院分区：
文献类型：
--
作者：
Ozer EA;Allen JP;Hauser AR
铜绿假单胞菌是一种重要的机会致病菌，可导致住院和免疫功能低下患者的许多感染。先前的报道估计其6.6Mbp基因组中约10%因菌株而异，因此被称为“辅助基因组”。铜绿假单胞菌辅助基因组内的元件与毒力和抗生素耐药性的差异有关。随着细菌菌株的全基因组测序变得更加普遍和具有成本效益，将需要快速和可靠地鉴定新测序的铜绿假单胞菌基因组中的辅助基因组元件的方法。我们开发了一种鉴定铜绿假单胞菌辅助基因组的生物信息学方法。首先，使用Spine（一种为此目的开发的软件程序），基于12种参考菌株的完整基因组中保守的序列确定核心基因组。核心基因组大小为5.84 Mbp，包含5，316个编码序列。然后，我们开发了名为AGEnt的计算机基因组扣除程序，以从铜绿假单胞菌全基因组中筛选出核心基因组序列，以鉴定这些参考菌株的辅助基因组序列。该分析确定铜绿假单胞菌的辅助基因组范围为总基因组的6.9-18.0%，富含与移动的元件相关的基因，并且由大多数功能未知或不清楚的基因组成。使用这些基因组，我们表明，AGEnt表现良好相比，其他化学上可用的程序，旨在检测辅助基因组元素。然后，我们通过将AGEnt程序应用于两种先前未测序的铜绿假单胞菌菌株PA 99和PA 103的基因组草案，证明了AGEnt程序的实用性。铜绿假单胞菌基因组富含辅助遗传物质。AGEnt程序准确地鉴定了新测序的铜绿假单胞菌菌株的辅助基因组，即使使用草案基因组。随着铜绿假单胞菌基因组以越来越快的速度变得可用，该程序将有助于对该细菌的扩展辅助基因组进行编目，并识别表型和辅助基因组组成之间的相关性。Spine和AGEnt的组合在定义其他细菌物种的附属基因组方面也应该是有用的。本文的在线版本（doi：10.1186/1471-2164-15-737）包含补充材料，可供授权用户使用。
Pseudomonas aeruginosa is an important opportunistic pathogen responsible for many infections in hospitalized and immunocompromised patients. Previous reports estimated that approximately 10% of its 6.6 Mbp genome varies from strain to strain and is therefore referred to as “accessory genome”. Elements within the accessory genome of P. aeruginosa have been associated with differences in virulence and antibiotic resistance. As whole genome sequencing of bacterial strains becomes more widespread and cost-effective, methods to quickly and reliably identify accessory genomic elements in newly sequenced P. aeruginosa genomes will be needed. We developed a bioinformatic method for identifying the accessory genome of P. aeruginosa. First, the core genome was determined based on sequence conserved among the completed genomes of twelve reference strains using Spine, a software program developed for this purpose. The core genome was 5.84 Mbp in size and contained 5,316 coding sequences. We then developed an in silico genome subtraction program named AGEnt to filter out core genomic sequences from P. aeruginosa whole genomes to identify accessory genomic sequences of these reference strains. This analysis determined that the accessory genome of P. aeruginosa ranged from 6.9-18.0% of the total genome, was enriched for genes associated with mobile elements, and was comprised of a majority of genes with unknown or unclear function. Using these genomes, we showed that AGEnt performed well compared to other publically available programs designed to detect accessory genomic elements. We then demonstrated the utility of the AGEnt program by applying it to the draft genomes of two previously unsequenced P. aeruginosa strains, PA99 and PA103. The P. aeruginosa genome is rich in accessory genetic material. The AGEnt program accurately identified the accessory genomes of newly sequenced P. aeruginosa strains, even when draft genomes were used. As P. aeruginosa genomes become available at an increasingly rapid pace, this program will be useful in cataloging the expanding accessory genome of this bacterium and in discerning correlations between phenotype and accessory genome makeup. The combination of Spine and AGEnt should be useful in defining the accessory genomes of other bacterial species as well. The online version of this article (doi:10.1186/1471-2164-15-737) contains supplementary material, which is available to authorized users.
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DOI：
10.1164/ajrccm/139.4.877
发表时间：
1989-04-01
期刊：
AMERICAN REVIEW OF RESPIRATORY DISEASE
影响因子：
--
作者：
FAGON, JY;CHASTRE, J;GIBERT, C
通讯作者：
GIBERT, C
影响因子：
2.1
作者：
Battle SE;Rello J;Hauser AR
通讯作者：
Hauser AR
影响因子：
1.7
作者：
Boisvert, Sebastien;Laviolette, Francois;Corbeil, Jacques
通讯作者：
Corbeil, Jacques
影响因子：
4.2
作者：
Di Nocera PP;Rocco F;Giannouli M;Triassi M;Zarrilli R
通讯作者：
Zarrilli R
影响因子：
3.6
作者：
FinckBarbancon, V;Goranson, J;Frank, DW
通讯作者：
Frank, DW