Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
Facultad de Ciencias Exactas, Departamento de Ciencias Biologicas, IBBM, Universidad Nacional de La Plata, Calle 115 y 47, 1900 La Plata, Argentina.
Genes (Basel). 2019 Aug 9;10(8):601. doi: 10.3390/genes10080601.
The genus comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain 3Re2-7, formerly known as and , elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known biocontrol agents. The 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of . Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, subsp. NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol () and hydrogen cyanide () were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in species, towards a sustainable and safe application of biocontrol agents.
该属包含许多已知的与植物相关的微生物，具有促进植物生长和抑制疾病的特性。基于基因组的研究允许使用基因组挖掘工具预测潜在机制，并通过实施比较基因组学分析菌株特有的基因来分析。在这里，我们提供了菌株 3Re2-7 的基因组序列，该菌株以前被称为 和 ，阐明了其修订后的分类学分类，通过转录组测序实验验证了基因预测，描述了其遗传生物防治潜力，并将其与其他已知的 生物防治剂联系起来。3Re2-7 基因组由一个大小为 6738544 bp 的圆形染色体组成，GC 含量为 60.83%。注释了 6267 个基因，其中 6113 个基因在丰富培养基中和/或存在 时被转录。基因组挖掘鉴定了与生物防治特性相关的基因，如次生代谢物和铁载体生物合成、植物生长促进、无机磷酸盐溶解、脂多糖和胞外多糖合成、外蛋白酶、挥发物和解毒。核心基因组分析表明，3Re2-7 基因组与代表种的代表基因组 subsp. NFM421 具有高度的共线性。比较基因组学允许鉴定 105 个特定基因，并揭示了可能编码菌株 3Re2-7 特定生物防治机制的基因簇。此外，我们捕获了 3Re2-7 的转录组，证实了预测的生物防治相关基因的转录。编码 2,4-二乙酰基间苯三酚（）和氢氰酸（）的基因簇被证明高度转录。进一步预测编码可能的褐藻酸盐产生酶、吡咯喹啉醌前体肽 PqqA 和基质金属蛋白酶家族金属蛋白酶的基因也被发现高度转录。通过这项研究，我们为进一步研究 种生物防治机制提供了基础，以期实现 生物防治剂的可持续和安全应用。
