Additional file 1 of Statistical analysis of a Bayesian classifier based on the expression of miRNAs

The datasets are available as Supplementary Material. (TXT 12.8 KB

Transport genes.

<p>Genes related to transport identified in the genome of <i>Paenibacillus pasadenensis</i> strain R16. In normal text are reported the main categories and, when appropriate, the subcategories are indicated in italic.</p

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

<div><p>Bacteria of the <i>Paenibacillus</i> 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 <i>Bacillus</i> or <i>Pseudomonas</i>), 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 <i>Paenibacillus pasadenensis</i>, 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. <i>De novo</i> 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 <i>Paenibacillus</i> genus in general.</p></div

Genome comparison.

<p>Genome comparison.</p

Fructose metabolic pathway.

<p>KEGG map of genes involved in the metabolism of fructose identified in <i>Paenibacillus pasadenensis</i> strain R16. Colored elements highlight genes present in the genome of strain R16.</p

Genome annotation.

<p>Genome annotation.</p

Sporulation genes.

<p>Sporulation genes.</p

Active biocontrol and growth promotion genes.

<p>Active biocontrol and growth promotion genes.</p

Isoprenoids metabolic pathway.

<p>KEGG map of genes involved in the synthesis of isoprenoids identified in <i>Paenibacillus pasadenensis</i> strain R16. Colored elements highlight genes present in the genome of strain R16.</p

ONT read-length distribution.

<p>Histograms of 2D read lengths from the 277,279 2D reads generated from the R16 genome.</p