Genome sequencing and analysis of two novel Pseudomonas strains, antagonistic to Rhizoctonia solani

Some Pseudomonas species are effective biocontrol agents while others are phytopathogens. Comparative genomics has become a reliable tool for differentiation of beneficial and pathogenic strains of Pseudomonas. In this study, we report the draft genome sequences and analysis of two Pseudomonas strains (S1E40 and S3E12) that are antagonistic to Rhizoctonia solani. Illumina MiSeq Technology (Génome Québec, Montréal, Canada) was used for genome sequencing, yielding about 8 million paired-end reads (250 bp long). De novo assemblies were performed using ABySS platform at k-mer values of 76-125. K-mer values of 85 and 95 gave the best assembly, generating 49 and 38 contigs for strains S1E40 and S3E12 respectively. The annotation of the draft genomes was performed with RAST and PGAAP automated servers. The size of the draft genomes is 6.98 Mb or 7.06 Mb with a G+C content of 61.6% or 60.9% ; and the number of rRNAs is 12 or 34 with 61 or 79 tRNAs for S1E40 or S3E12 respectively. Similar numbers of protein-coding sequences were predicted using RAST (6218 and 6190); PGAAP (6148 and 6127) and PATRIC (6470 and 6384) for strains S1E40 and S3E12 respectively. Proteome comparison using PATRIC revealed that the strains share 4,484 protein families. Multilocus Sequence Analysis (MLSA) and comparative genomics data especially proteome BLAST and subsystem features of strains S1E40 and S3E12 compared with 11 type strains of known Pseudomonas species highlighted key genetic differences, suggesting that the two strains studied here could be authentic novel species.