Abstract
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.
Highlights
The genus Paenibacillus was proposed by Ash and colleagues in 1993 [1]
In comparison with previous literature, the R16 draft genome obtained with the hybrid approach constitutes a significant technical improvement over the only other available genome for this species, belonging to strain DSM 19293 (Accession Number NZ_AULW01000001 in NCBI: Nucleotide), which consisted of 85 contigs assembled in 49 scaffolds, having N50 length of approximately 125 Kbp
The total length of this genome and its GC content percentage are similar to the genome of P. pasadenensis described in this study
Summary
Despite being constituted by very varied organisms, found in the most diverse environments and with a great potential for scientific research [2], there is little information available on bacteria belonging to this genus. Several strains of Paenibacillus spp. are known to produce effective lytic enzymes that are studied for biotechnological applications [3, 4]. Other strains are known to be associated with plants, some even to the point of becoming endophytes, to which they offer protection against pathogens as well as a general positive effect on growth [5]. Despite the great potential for applications in agriculture, there are not many resources and information available on the bacteria of this genus, especially when compared to better studied plant-associated bacteria such as those belonging to the genera Bacillus and Pseudomonas. Genetic information in particular is lacking, with only a handful of sequenced genomes available for plant-growth promoting bacteria, all belonging to just two species: P. polymyxa and P. terrae [6]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
