Comparative Genomics of Pseudoalteromonas Reveals a Genetic Lineage Including Proficient Producers of Natural Products

R. Gavilan, J. Sanchez, L. Atencio, P. Charusanti, P. C. Dorrestein, M. Gutierrez


The genus Pseudoalteromonas is a diverse group of marine bacteria, and most species have shown to be a rich source of bioactive compounds. To search for the presence of natural products biosynthetic gene clusters inPseudoalteromonas associated with octocorals, we sequenced and analyzed the draft genome of two strains that produced antibacterial and antifungal compounds. The selected strains OT59 and 04M1 were recovered from two different octocorals collected at Otoque and Coiba Islands, in the Pacific of Panama. The genomes of these isolates were sequenced using Illumina approaches and the obtained reads of each isolate were filtered, trimmed, and de novo assembled using Velvet package and CLC Genomics Software in order to maximize contig assembling and coverage. The resulting draft genome of strain OT59 (~5.29 Mb), and strain 04M1 (about 6.43 Mb) were annotated using RAST server. A total of 4,666 protein-encoding genes were predicted for OT59 and 5,573 for 04M1. Preliminary phylogenomic analysis based on orthologous genes between OT59 and 04M1, and other 22Pseudoalteromonas genomes retrieved from public databases, indicated that Panamanian strains were most closely related to P. piscicida JCM 20779, P. flavipulchra JG1, and Pseudoalteromonas sp. NJ631. A comprehensive comparison between Pseudoalteromonas genomes and genome mining was performed in order to identify genomic variation and potential natural products biosynthetic clusters. Based on this analysis, we identified 7 hybrid gene clusters coding for non-ribosomal peptide synthetases and polyketide synthases (NRPS-PKS) for the strain OT59 and 8 hybrid NRPS-PKS gene clusters for the strain 04M1. This comparative analysis revealed a novel bioactive-genetic lineage including two Panamanian isolates and three public Pseudoalteromonas genomes, as well as the promising biosynthetic potential of Panamanian isolates that will allow further analysis focused on identifying novel natural products biosynthetic gene clusters using the abundant coral-associated microbial diversity in Panama.

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American Society for Microbiology General Meeting
    • ASM 113th (2013)