Comparative genomic and functional analysis reveal conservation of plant growth promoting traits in Paenibacillus polymyxa and its closely related species.
Comparative genomic and functional analysis reveal conservation of plant growth promoting traits in Paenibacillus polymyxa and its closely related species.
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比较基因组和功能分析揭示多粘类芽孢杆菌及其密切相关物种的植物生长促进性状的保守性
DOI：
10.1038/srep21329
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发表时间：
2016-02-09
影响因子：
4.6
通讯作者：
Chen S
中科院分区：
文献类型：
--
作者：
Xie J;Shi H;Du Z;Wang T;Liu X;Chen S
多粘类芽孢杆菌作为促进植物根际细菌（PGPR）的模型已被广泛研究。在这里，对 9 个多粘类芽孢杆菌菌株以及其他 26 个已测序的类芽孢杆菌属物种的基因组序列进行了比较研究。对串联的 244 个单拷贝核心基因的系统发育分析表明，从不同地理区域和生态位中分离出来的 9 种多粘类芽孢杆菌菌株和其他 5 种类芽孢杆菌形成了一个密切相关的进化枝（此处称为 Poly-clade）。单核苷酸多态性 (SNP) 分析揭示了 14 个 Poly-clade 基因组的局部多样化。 SNP在14个基因组中分布不均匀，SNP密度高的区域包含与次生代谢相关的基因，包括编码聚酮化合物的基因。重组在该进化枝的遗传多样性中发挥了重要作用，尽管重组率明显低于突变率。一些与植物生长促进性状相关的基因，即解磷和 IAA 产生，得到了很好的保守，而一些与固氮和抗生素合成相关的基因在这个多进化枝中进化得具有多样性。这项研究表明，多粘多粘菌及其近缘物种都具有促进植物生长的特性，它们与PGPR一样在农业和园艺中具有巨大的潜在用途。
Paenibacillus polymyxa has widely been studied as a model of plant-growth promoting rhizobacteria (PGPR). Here, the genome sequences of 9 P. polymyxa strains, together with 26 other sequenced Paenibacillus spp., were comparatively studied. Phylogenetic analysis of the concatenated 244 single-copy core genes suggests that the 9 P. polymyxa strains and 5 other Paenibacillus spp., isolated from diverse geographic regions and ecological niches, formed a closely related clade (here it is called Poly-clade). Analysis of single nucleotide polymorphisms (SNPs) reveals local diversification of the 14 Poly-clade genomes. SNPs were not evenly distributed throughout the 14 genomes and the regions with high SNP density contain the genes related to secondary metabolism, including genes coding for polyketide. Recombination played an important role in the genetic diversity of this clade, although the rate of recombination was clearly lower than mutation. Some genes relevant to plant-growth promoting traits, i.e. phosphate solubilization and IAA production, are well conserved, while some genes relevant to nitrogen fixation and antibiotics synthesis are evolved with diversity in this Poly-clade. This study reveals that both P. polymyxa and its closely related species have plant growth promoting traits and they have great potential uses in agriculture and horticulture as PGPR.