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Hybrid genome assembly and annotation of Paenibacillus pasadenensis strain R16 reveals insights on endophytic life style and antifungal activity

机译：Paasadenensis Paenidenillus paasadenensis R16菌株的杂种基因组组装和注释揭示了对内生生活方式和抗真菌活性的见解

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Bacteria of the Paenibacillus genus are becoming important in many fields of science, including agriculture, for their positive effects on the health of plants. However, there are little information available on this genus compared to other bacteria (such as Bacillus or Pseudomonas), especially when considering genomic information. Sequencing the genomes of plant-beneficial bacteria is a crucial step to identify the genetic elements underlying the adaptation to life inside a plant host and, in particular, which of these features determine the differences between a helpful microorganism and a pathogenic one. In this study, we have characterized the genome of Paenibacillus pasadenensis, strain R16, recently investigated for its antifungal activities and plant-associated features. An hybrid assembly approach was used integrating the very precise reads obtained by Illumina technology and long fragments acquired with Oxford Nanopore Technology (ONT) sequencing. De novo genome assembly based solely on Illumina reads generated a relatively fragmented assembly of 5.72 Mbp in 99 ungapped sequences with an N50 length of 544 Kbp; hybrid assembly, integrating Illumina and ONT reads, improved the assembly quality, generating a genome of 5.75 Mbp, organized in 6 contigs with an N50 length of 3.4 Mbp. Annotation of the latter genome identified 4987 coding sequences, of which 1610 are hypothetical proteins. Enrichment analysis identified pathways of particular interest for the endophyte biology, including the chitin-utilization pathway and the incomplete siderophore pathway which hints at siderophore parasitism. In addition the analysis led to the identification of genes for the production of terpenes, as for example farnesol, that was hypothesized as the main antifungal molecule produced by the strain. The functional analysis on the genome confirmed several plant-associated, plant-growth promotion, and biocontrol traits of strain R16, thus adding insights in the genetic bases of these complex features, and of the Paenibacillus genus in general.
机译：芽孢杆菌属细菌由于其对植物健康的积极影响，在包括农业在内的许多科学领域中都变得越来越重要。但是，与其他细菌（如芽孢杆菌或假单胞菌）相比，有关该属的信息很少，尤其是在考虑基因组信息时。对植物有益细菌的基因组进行测序是确定植物宿主内部适应生命的遗传因素的关键步骤，尤其是这些特征中的哪些决定了有用微生物与致病微生物之间的差异。在这项研究中，我们已经表征了Paenidenillus paasadenensis R16菌株的基因组，最近对其抗真菌活性和与植物相关的特征进行了研究。使用混合组装方法，将通过Illumina技术获得的非常精确的读数与通过牛津纳米孔技术（ONT）测序获得的长片段整合在一起。仅基于Illumina读数的从头基因组组装产生了相对片段化的5.72 Mbp的组装，排列成99个无缺口序列，N50长度为544 Kbp；整合了Illumina和ONT读段的杂交装配提高了装配质量，生成了5.75 Mbp的基因组，该基因组分为6个重叠群，N50长度为3.4 Mbp。后一个基因组的注释确定了4987个编码序列，其中1610个是假设的蛋白质。富集分析确定了内生菌生物学特别感兴趣的途径，包括几丁质利用途径和不完整的铁载体途径，这暗示了铁载体的寄生性。另外，该分析导致鉴定了用于产生萜烯的基因，例如法尼醇，其被假定为由菌株产生的主要抗真菌分子。对基因组的功能分析证实了菌株R16的几种与植物相关，促进植物生长和生物防治的特性，从而增加了这些复杂特征以及Paenibacillus属的遗传基础的见识。

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