An improved, high-quality draft genome sequence of the Germination-Arrest Factor-producing Pseudomonas fluorescens WH6.
An improved, high-quality draft genome sequence of the Germination-Arrest Factor-producing Pseudomonas fluorescens WH6.
复制标题
DOI：
10.1186/1471-2164-11-522
复制
发表时间：
2010-09-28
期刊：
影响因子：
4.4
通讯作者：
Chang JH
中科院分区：
文献类型：
--
作者：
Kimbrel JA;Givan SA;Halgren AB;Creason AL;Mills DI;Banowetz GM;Armstrong DJ;Chang JH
荧光假单胞菌是一种遗传和生理上多样化的细菌，存在于许多栖息地并与植物相关。这种细菌产生大量具有天然产物潜力的次生代谢物。荧光假单胞菌分离株 WH6 产生萌发阻止因子 (GAF)，这是一种预测的小肽或氨基酸类似物，具有除草活性，可特异性抑制禾本科物种种子的萌发。我们使用混合下一代测序方法来开发荧光假单胞菌 WH6 的高质量基因组序列草案。我们采用自动化、手动和实验方法来进一步改进基因组序列草案。从这个 6.27 个兆碱基的组装中，我们预测了 5876 个基因，其中 3115 个是荧光假单胞菌的核心基因，1567 个是 WH6 特有的基因。 WH6 的比较基因组研究揭示了与荧光假单胞菌 SBW25 基因的同线性和直系同源性高度相似性。系统发育基因组研究也将 WH6 与 SBW25 属于同一谱系。在之前的非饱和诱变筛选中，我们鉴定了 WH6 中 GAF 活性必需的两个基因。对它们侧翼序列的作图揭示了编码候选抗西格玛因子和转氨酶的基因。最后，我们发现了几种候选毒力和宿主关联机制，其中之一似乎是完整的 III 型分泌系统。改进后的 WH6 高质量基因组序列草案有助于解析荧光假单胞菌物种，为建立荧光假单胞菌两个独立的谱系提供了额外的动力。尽管与 SBW25 具有高水平的直系同源性和同线性性，WH6 仍然具有大量独特基因，并且代表了发现影响植物生长和健康的基因的另一个来源。两个基因显然是 GAF 所必需的，其蛋白质的进一步表征对于开发天然产品作为针对禾本科杂草的控制措施非常重要。最后，WH6 是第一个据报道编码完整 T3SS 的荧光假单胞菌分离株。这使我们有机会探索传统上被认为是与植物非致病性相互作用的毒力机制的作用。
Pseudomonas fluorescens is a genetically and physiologically diverse species of bacteria present in many habitats and in association with plants. This species of bacteria produces a large array of secondary metabolites with potential as natural products. P. fluorescens isolate WH6 produces Germination-Arrest Factor (GAF), a predicted small peptide or amino acid analog with herbicidal activity that specifically inhibits germination of seeds of graminaceous species. We used a hybrid next-generation sequencing approach to develop a high-quality draft genome sequence for P. fluorescens WH6. We employed automated, manual, and experimental methods to further improve the draft genome sequence. From this assembly of 6.27 megabases, we predicted 5876 genes, of which 3115 were core to P. fluorescens and 1567 were unique to WH6. Comparative genomic studies of WH6 revealed high similarity in synteny and orthology of genes with P. fluorescens SBW25. A phylogenomic study also placed WH6 in the same lineage as SBW25. In a previous non-saturating mutagenesis screen we identified two genes necessary for GAF activity in WH6. Mapping of their flanking sequences revealed genes that encode a candidate anti-sigma factor and an aminotransferase. Finally, we discovered several candidate virulence and host-association mechanisms, one of which appears to be a complete type III secretion system. The improved high-quality draft genome sequence of WH6 contributes towards resolving the P. fluorescens species, providing additional impetus for establishing two separate lineages in P. fluorescens. Despite the high levels of orthology and synteny to SBW25, WH6 still had a substantial number of unique genes and represents another source for the discovery of genes with implications in affecting plant growth and health. Two genes are demonstrably necessary for GAF and further characterization of their proteins is important for developing natural products as control measure against grassy weeds. Finally, WH6 is the first isolate of P. fluorescens reported to encode a complete T3SS. This gives us the opportunity to explore the role of what has traditionally been thought of as a virulence mechanism for non-pathogenic interactions with plants.
登录
查看更多内容
影响因子：
3.5
作者：
Caldelari, I;Mann, S;Palmer, T
通讯作者：
Palmer, T
影响因子：
3.7
作者：
Blanvillain S;Meyer D;Boulanger A;Lautier M;Guynet C;Denancé N;Vasse J;Lauber E;Arlat M
通讯作者：
Arlat M
影响因子：
4
作者：
Flores-Vargas, R. D.;O'Hara, G. W.
通讯作者：
O'Hara, G. W.
DOI：
10.1073/pnas.0409660102
发表时间：
2005-02-15
影响因子：
11.1
作者：
Chang, JH;Urbach, JM;Dangl, JL
通讯作者：
Dangl, JL
DOI：
10.1073/pnas.1731982100
发表时间：
2003-09-02
影响因子：
11.1
作者：
Buell, CR;Joardar, V;Collmer, A
通讯作者：
Collmer, A