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Comparative Genomic Analysis of Pseudomonas chlororaphis PCL1606 Reveals New Insight into Antifungal Compounds Involved in Biocontrol

March 2015 , Volume 28 , Number  3
Pages  249 - 260

Claudia E. Calderón,1 Cayo Ramos,2 Antonio de Vicente,1 and Francisco M. Cazorla1

1Departamento de Microbiología and 2Área de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, IHSM-UMA-CSIC, Facultad de Ciencias, Campus de Teatinos s/n, 29071 Málaga, España

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Accepted 4 December 2014.

Pseudomonas chlororaphis PCL1606 is a rhizobacterium that has biocontrol activity against many soilborne phytopathogenic fungi. The whole genome sequence of this strain was obtained using the Illumina Hiseq 2000 sequencing platform and was assembled using SOAP denovo software. The resulting 6.66-Mb complete sequence of the PCL1606 genome was further analyzed. A comparative genomic analysis using 10 plant-associated strains within the fluorescent Pseudomonas group, including the complete genome of P. chlororaphis PCL1606, revealed a diverse spectrum of traits involved in multitrophic interactions with plants and microbes as well as biological control. Phylogenetic analysis of these strains using eight housekeeping genes clearly placed strain PCL1606 into the P. chlororaphis group. The genome sequence of P. chlororaphis PCL1606 revealed the presence of sequences that were homologous to biosynthetic genes for the antifungal compounds 2-hexyl, 5-propyl resorcinol (HPR), hydrogen cyanide, and pyrrolnitrin; this is the first report of pyrrolnitrin encoding genes in this P. chlororaphis strain. Single-, double-, and triple-insertional mutants in the biosynthetic genes of each antifungal compound were used to test their roles in the production of these antifungal compounds and in antagonism and biocontrol of two fungal pathogens. The results confirmed the function of HPR in the antagonistic phenotype and in the biocontrol activity of P. chlororaphis PCL1606.

© 2015 The American Phytopathological Society