Statistics of <i>P</i>. <i>lycopersici</i> ER1518 gene prediction.

<p>Statistics of <i>P</i>. <i>lycopersici</i> ER1518 gene prediction.</p

Heatmap of OrthoMCL orthologous groups for the most interesting Pfam protein and CAZymes domains identified in <i>P</i>. <i>lycopersici</i> ER1518 (PLY ER1518) and ten other fungal pathogens.

<p>The heatmap represents the type and the number of domains (rows) for each fungus (columns). The Z-score indicates that the values have been centred and scaled by rows (domains), so that negative z-scores are more likely coloured in red and high z-scores in white. Abbreviations: PLY ER1211, <i>P</i>. <i>lycopersici</i> ER1211; AN, <i>Aspergillus nidulans</i>; BG, <i>Blumeria graminis</i>; CH, <i>Colletotrichum higgisinianum</i>; FO, <i>Fusarium oxysporum</i>; LM, <i>Leptosphaeria maculans</i>; NC, <i>Neurospora crassa</i>; PTT, <i>Pyrenophora teres</i>; PTR, <i>Pyrenophora tritici-repentis</i>; PN, <i>Phaeospheria nodorum</i>. CMB, Carbohydrate-Binding Modules; CE, carbohydrate esterases; GH, Glycoside Hydrolases; GT, Glycosyl-Transferases; PL, Polysaccharide Lyases; HET, HETerokaryon Incompatibility-related domains, NB-ARC, Nucleotide-Binding Adaptor shared by APAF-1, R proteins, and CED-4 domain; NACHT, Neuronal Apoptosis inhibitor; ANK, ankyrin; TPR, tetratricopeptide; ABC, ATP-Binding Cassette transporters; MFS, Major Facilitator domains.</p

The genome assembly of the fungal pathogen <i>Pyrenochaeta lycopersici</i> from Single-Molecule Real-Time sequencing sheds new light on its biological complexity

<div><p>The first draft genome sequencing of the non-model fungal pathogen <i>Pyrenochaeta lycopersici</i> showed an expansion of gene families associated with heterokaryon incompatibility and lacking of mating-type genes, providing insights into the genetic basis of this “imperfect” fungus which lost the ability to produce the sexual stage. However, due to the Illumina short-read technology, the draft genome was too fragmented to allow a comprehensive characterization of the genome, especially of the repetitive sequence fraction. In this work, the sequencing of another <i>P</i>. <i>lycopersici</i> isolate using long-read Single Molecule Real-Time sequencing technology was performed with the aim of obtaining a gapless genome. Indeed, a gapless genome assembly of 62.7 Mb was obtained, with a fraction of repetitive sequences representing 30% of the total bases. The gene content of the two <i>P</i>. <i>lycopersici</i> isolates was very similar, and the large difference in genome size (about 8 Mb) might be attributable to the high fraction of repetitive sequences detected for the new sequenced isolate. The role of repetitive elements, including transposable elements, in modulating virulence effectors is well established in fungal plant pathogens. Moreover, transposable elements are of fundamental importance in creating and re-modelling genes, especially in imperfect fungi. Their abundance in <i>P</i>. <i>lycopersici</i>, together with the large expansion of heterokaryon incompatibility genes in both sequenced isolates, suggest the presence of possible mechanisms alternative to gene re-assorting mediated by sexual recombination. A quite large fraction (~9%) of repetitive elements in <i>P</i>. <i>lycopersici</i>, has no homology with known classes, strengthening this hypothesis. The availability of a gapless genome of <i>P</i>. <i>lycopersici</i> allowed the in-depth analysis of its genome content, by annotating functional genes and TEs. This goal will be an important resource for shedding light on the evolution of the reproductive and pathogenic behaviour of this soilborne pathogen and the onset of a possible speciation within this species.</p></div

Circular representation of genomic features.

<p>Circular representation of the assembled sequences (length > 10Kb) of <i>P</i>. <i>lycopersici</i> ER1518 genome reporting the distribution of the following features: A) Repetitive elements count (blue); B) Gene density (green); C) Sequence identity percentage (red) of <i>P</i>. <i>lycopersici</i> ER1211 genomic sequences based on pairwise alignment between genome assemblies performed with MUMmer.</p

Phylogenetic tree of RPB2 protein of <i>P</i>. <i>lycopersici</i> ER1518 and other ten ascomycetes obtained with PhyML 3.0 and drawn with MEGA7.

<p>The tree is drawn to scale, with bootstrap values on branches and branch lengths measured in the number of substitutions per site.</p

Repeat content comparative analysis among <i>P</i>. <i>lycopersici</i> ER1518 and other five ascomycetes.

<p>Histogram of percentages of different TE categories respect to the total annotated TEs reported for each species.</p

Statistics of repeat annotation and masking of <i>P</i>. <i>lycopersici</i>.

<p>TE classes have been reported according to Wicker classification [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0200217#pone.0200217.ref010" target="_blank">10</a>].</p

Statistics of orthologous analysis performed with OrthoMCL.

<p>Statistics of orthologous analysis performed with OrthoMCL.</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

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