Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies.
Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies.
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DOI：
10.1093/femsle/fny069
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发表时间：
2018-05-01
影响因子：
2.1
通讯作者：
Tucker NP
中科院分区：
文献类型：
--
作者：
Beaton A;Lood C;Cunningham-Oakes E;MacFadyen A;Mullins AJ;Bestawy WE;Botelho J;Chevalier S;Coleman S;Dalzell C;Dolan SK;Faccenda A;Ghequire MGK;Higgins S;Kutschera A;Murray J;Redway M;Salih T;da Silva AC;Smith BA;Smits N;Thomson R;Woodcock S;Welch M;Cornelis P;Lavigne R;van Noort V;Tucker NP
细菌假单胞菌菌株a390 T是最近描述的这一物种的模式菌株，在这里，我们提出了它的高邻接草图基因组。为了庆祝第16届国际假单胞菌会议，使用Ion Torrent半导体和Oxford Nanopore方法的独特组合对P. baetica菌株a390 T的基因组进行了测序，作为社区主导的合作项目的一部分。使用具有长Nanopore读数的高质量Ion Torrent序列得到快速、高邻接性和高质量的16-重叠群基因组序列。全基因组系统发育分析将Baetica置于荧光假单胞菌群的P. koreensis分支内。细菌假单胞菌与其他假单胞菌主要基因组特征的比较。这表明它是一种适应性很强的生物，是该属的典型。该菌株最初是从患病的楔唯一鱼的肝脏中分离的，基因型和表型分析表明，它对渗透胁迫和土霉素具有耐受性。在这里，我们提出了高质量的基因组草图的细菌病原体，已被证明是导致疾病的鱼类养殖设施的细菌baetica。
Pseudomonas baetica strain a390T is the type strain of this recently described species and here we present its high-contiguity draft genome. To celebrate the 16th International Conference on Pseudomonas, the genome of P. baetica strain a390T was sequenced using a unique combination of Ion Torrent semiconductor and Oxford Nanopore methods as part of a collaborative community-led project. The use of high-quality Ion Torrent sequences with long Nanopore reads gave rapid, high-contiguity and -quality, 16-contig genome sequence. Whole genome phylogenetic analysis places P. baetica within the P. koreensis clade of the P. fluorescens group. Comparison of the main genomic features of P. baetica with a variety of other Pseudomonas spp. suggests that it is a highly adaptable organism, typical of the genus. This strain was originally isolated from the liver of a diseased wedge sole fish, and genotypic and phenotypic analyses show that it is tolerant to osmotic stress and to oxytetracycline. Here, we present the high-quality draft genome of Pseudomonas baetica, a bacterial pathogen that has been demonstrated to cause disease in fish cultivated in aquaculture facilities.
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影响因子：
14.8
作者：
Chaturvedi, Kaveri S.;Hung, Chia S.;Crowley, Jan R.;Stapleton, Ann E.;Henderson, Jeffrey P.
通讯作者：
Henderson, Jeffrey P.
Islandviewer 4：扩展了大规模数据集基因组岛的预测。
影响因子：
14.9
作者：
Bertelli C;Laird MR;Williams KP;Simon Fraser University Research Computing Group;Lau BY;Hoad G;Winsor GL;Brinkman FSL
通讯作者：
Brinkman FSL
影响因子：
3.9
作者：
Connor TR;Loman NJ;Thompson S;Smith A;Southgate J;Poplawski R;Bull MJ;Richardson E;Ismail M;Thompson SE;Kitchen C;Guest M;Bakke M;Sheppard SK;Pallen MJ
通讯作者：
Pallen MJ
影响因子：
3.5
作者：
Catel-Ferreira, Manuella;Marti, Sara;De, Emmanuelle
通讯作者：
De, Emmanuelle
影响因子：
16.6
作者：
Butaitė E;Baumgartner M;Wyder S;Kümmerli R
通讯作者：
Kümmerli R