Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens.
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens.
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DOI：
10.1186/gb-2009-10-5-r51
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发表时间：
2009
期刊：
影响因子：
12.3
通讯作者：
Thomson NR
中科院分区：
文献类型：
--
作者：
Silby MW;Cerdeño-Tárraga AM;Vernikos GS;Giddens SR;Jackson RW;Preston GM;Zhang XX;Moon CD;Gehrig SM;Godfrey SA;Knight CG;Malone JG;Robinson Z;Spiers AJ;Harris S;Challis GL;Yaxley AM;Harris D;Seeger K;Murphy L;Rutter S;Squares R;Quail MA;Saunders E;Mavromatis K;Brettin TS;Bentley SD;Hothersall J;Stephens E;Thomas CM;Parkhill J;Levy SB;Rainey PB;Thomson NR
三种荧光假单胞菌菌株的基因组序列比较揭示了一种异质性，让人想起物种复合体而不是单一物种荧光假单胞菌是常见的土壤细菌，可以通过营养循环、病原体拮抗和诱导植物防御来改善植物健康。测定菌株SBW 25和Pf 0 -1的基因组序列，并相互比较，并与荧光假单胞菌Pf-5比较。功能性基因组体内表达技术（IVET）筛选提供了对荧光假单胞菌在其自然环境中使用的基因的深入了解，并提高了对该物种多样性生态意义的理解。三种荧光假单胞菌基因组（SBW 25，Pf 0 -1，Pf-5）的比较显示出相当大的差异：61%的基因是共享的，大多数位于复制起点附近。系统发育和平均氨基酸同一性分析表明，低的整体关系。SBW 25的功能筛选定义了125个植物诱导基因，包括一系列特定于植物环境的功能。其中83个的直系同源物存在于Pf 0 -1和Pf-5中，两种菌株共有73个。荧光假单胞菌基因组携带许多复杂的重复DNA序列，其中一些类似于微型反向重复转座元件（MITE）。在SBW 25中，重复密度和分布揭示了缺乏重复的“重复沙漠”，覆盖了大约40%的基因组。荧光假单胞菌基因组高度多样。复制末端周围的菌株特异性区域表明基因组区室化。三个菌株之间的基因组异质性让人想起一个物种复合体，而不是一个单一的物种。42%的植物诱导基因并不是所有菌株都共有的，这进一步证实了这一结论，并表明生态成功需要专门的核心功能。多样性还表明泛假单胞菌基因组内遗传信息的显著大小。
Comparison of the genome sequences of three Pseudomonas fluorescens strains reveals a heterogeneity reminiscent of a species complex rather than a single species Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
7.2
作者：
Howden, Andrew J. M.;Jill Harrison, C.;Preston, Gail M.
通讯作者：
Preston, Gail M.
影响因子：
--
作者：
El-Sayed, AK;Hothersall, J;Thomas, CM
通讯作者：
Thomas, CM
DOI：
10.1073/pnas.0706739104
发表时间：
2007-11-13
影响因子：
11.1
作者：
Giddens, Stephen R.;Jackson, Robert W.;Rainey, Paul B.
通讯作者：
Rainey, Paul B.
影响因子：
64.8
作者：
Bentley, SD;Chater, KF;Hopwood, DA
通讯作者：
Hopwood, DA