[PMID]: | 29351296 |
[Au] Autor: | Passera A; Marcolungo L; Casati P; Brasca M; Quaglino F; Cantaloni C; Delledonne M |
[Ad] Endereço: | Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy. |
[Ti] Título: | Hybrid genome assembly and annotation of Paenibacillus pasadenensis strain R16 reveals insights on endophytic life style and antifungal activity. |
[So] Source: | PLoS One;13(1):e0189993, 2018. |
[Is] ISSN: | 1932-6203 |
[Cp] País de publicação: | United States |
[La] Idioma: | eng |
[Ab] Resumo: | 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. |
[Mh] Termos MeSH primário: |
Endófitos/genética Fungos/patogenicidade Genoma Bacteriano Paenibacillus/genética Plantas/microbiologia
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[Mh] Termos MeSH secundário: |
Amino Açúcares/metabolismo Metabolismo dos Carboidratos DNA Bacteriano/genética DNA Bacteriano/isolamento & purificação Endófitos/metabolismo Endófitos/fisiologia Sequenciamento de Nucleotídeos em Larga Escala Compostos Orgânicos/metabolismo Paenibacillus/metabolismo Paenibacillus/fisiologia Desenvolvimento Vegetal Sideróforos/biossíntese Esporos Bacterianos
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[Pt] Tipo de publicação: | JOURNAL ARTICLE |
[Nm] Nome de substância:
| 0 (Amino Sugars); 0 (DNA, Bacterial); 0 (Organic Chemicals); 0 (Siderophores) |
[Em] Mês de entrada: | 1802 |
[Cu] Atualização por classe: | 180215 |
[Lr] Data última revisão:
| 180215 |
[Sb] Subgrupo de revista: | IM |
[Da] Data de entrada para processamento: | 180120 |
[St] Status: | MEDLINE |
[do] DOI: | 10.1371/journal.pone.0189993 |
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