Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios.
Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios.
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比较基因组分析揭示弧菌的进化和环境适应策略
DOI：
10.1186/s12864-018-4531-2
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发表时间：
2018-02-13
期刊：
影响因子：
4.4
通讯作者：
Zhang XH
中科院分区：
文献类型：
--
作者：
Lin H;Yu M;Wang X;Zhang XH
研究背景弧菌是最具多样性和生态重要性的海洋细菌之一，它们进化出许多特征和生活方式，占据着各种生态位。弧菌基因组特征与环境适应策略之间的关系是了解海洋系统中弧菌生态功能的重要组成部分。全基因组测序技术的出现为在基因组水平上研究弧菌的遗传特性提供了重要的手段。比较基因组学分析发现，弧菌具有稳定的核心基因组和巨大的泛基因组，在进化过程中发生了大量的基因获得和水平基因转移事件。基于核心基因组树的进化分析表明V. fischeri出现在约3.85亿年前，沿着头足类动物的出现和鱼类的繁荣。相对较大的基因组，大量的16 S rRNA基因拷贝，以及R-M系统和CRISPR系统的存在有助于弧菌在各种海洋环境中生活。几乎所有的弧菌基因组中都含有几丁质降解相关基因。与该属的最新祖先相比，弧菌中几丁质酶基因的数量已大大增加。几丁质酶A基因估计已经进化沿着与属，并经历了显着的纯化选择力，以保护祖先state.ConclusionsVibrios经历了极端的基因组扩增事件在其进化史上，使他们能够开发各种功能，全球范围内传播。尽管它们的系统发育关系密切，但弧菌被发现具有巨大的泛基因组和稳定的核心基因组，这表明该属的基因组具有高度可塑性。此外，多种几丁质降解相关基因的存在和几丁质酶A在该属中的扩增表明了弧菌利用几丁质的重要性。弧菌基因组中的防御系统可以保护它们免受外部DNA的入侵。这些基因组特征的研究提供了一个更好的知识，进化过程中如何foredVibriogenomes占据各种生态位。
BackgroundVibrios are among the most diverse and ecologically important marine bacteria, which have evolved many characteristics and lifestyles to occupy various niches. The relationship between genome features and environmental adaptation strategies is an essential part for understanding the ecological functions of vibrios in the marine system. The advent of complete genome sequencing technology has provided an important method of examining the genetic characteristics of vibrios on the genomic level.ResultsTwoVibriogenomes were sequenced and found to occupy many unique orthologues families which absent from the previously genes pool of the complete genomes of vibrios. Comparative genomics analysis found vibrios encompass a steady core-genome and tremendous pan-genome with substantial gene gain and horizontal gene transfer events in the evolutionary history. Evolutionary analysis based on the core-genome tree suggested thatV. fischeriemerged ~ 385 million years ago, along with the occurrence of cephalopods and the flourish of fish. The relatively large genomes, the high number of 16S rRNA gene copies, and the presence of R-M systems and CRISPR system help vibrios live in various marine environments. Chitin-degrading related genes are carried in nearly all theVibriogenomes. The number of chitinase genes in vibrios has been extremely expanded compared to which in the most recent ancestor of the genus. The chitinase A genes were estimated to have evolved along with the genus, and have undergone significant purifying selective force to conserve the ancestral state.ConclusionsVibrios have experienced extremely genome expansion events during their evolutionary history, allowing them to develop various functions to spread globally. Despite their close phylogenetic relationships, vibrios were found to have a tremendous pan-genome with a steady core-genome, which indicates the highly plastic genome of the genus. Additionally, the existence of various chitin-degrading related genes and the expansion of chitinase A in the genus demonstrate the importance of the chitin utilization for vibrios. Defensive systems in theVibriogenomes may protect them from the invasion of external DNA. These genomic features investigated here provide a better knowledge of how the evolutionary process has forgedVibriogenomes to occupy various niches.
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影响因子：
14.9
作者：
Grissa, Ibtissem;Vergnaud, Gilles;Pourcel, Christine
通讯作者：
Pourcel, Christine
DOI：
10.1099/00207713-45-1-139
发表时间：
1995-01-01
期刊：
INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY
影响因子：
--
作者：
GAUTHIER, G;LAFAY, B;CHRISTEN, R
通讯作者：
CHRISTEN, R
影响因子：
11
作者：
Falcon, Luisa I.;Magallon, Susana;Castillo, Amanda
通讯作者：
Castillo, Amanda
影响因子：
3.3
作者：
Defoirdt, Tom;Ruwandeepika, H. A. Darshanee;Bossier, Peter
通讯作者：
Bossier, Peter
影响因子：
2.7
作者：
Allison, DG
通讯作者：
Allison, DG