Computational protocol: Draft Genome Sequence of Beneficial Rice Rhizosphere Isolate Pseudomonas aeruginosa PUPa3

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Protocol publication

[…] Pseudomonas aeruginosa is a metabolically versatile Gram-negative bacterium that is mostly studied as an opportunistic human pathogen causing chronic infections in the lungs of cystic fibrosis patients (, ). P. aeruginosa is thought to be ubiquitous in nature and can be found in aquatic sediments, water-exposed surfaces, soil, plant roots and leaves, and also on human and animal surfaces (, ). This bacterium has numerous signaling regulatory pathways responsible for sensing, responding, and adapting to many different environmental conditions (). It remains unclear whether there are significant genomic differences between environmental and clinical P. aeruginosa isolates. Plant environments are believed to be reservoirs for several human opportunistic pathogens including P. aeruginosa ().P. aeruginosa strain PUPa3 is a plant growth-promoting strain with a broad spectrum of antifungal activity and was isolated from the rhizosphere of rice in India (). PUPa3, like P. aeruginosa PAO1, was reported to have two different N-acyl homoserine lactone (AHL)-dependent quorum-sensing (QS) systems, namely, the LasI/R and RhlI/R systems. Strain PUPa3 has been shown to be virulent in the Caenorhabditis elegans and the wax moth Galleria mellonella infection models, and the two AHL systems are required for full virulence. Interestingly, unlike what occurs in strain PAO1, the two QS systems are not hierarchically arranged and do not cross-regulate each other and thus act independently ().Here we announce the draft genome sequence of beneficial rhizosphere-colonizing P. aeruginosa PUPa3. The genome sequence of P. aeruginosa PUPa3 was determined using a 150-bp paired-end library with the Illumina Hi Seq 2500 system. The total number of pairs of reads was 5,748,337, representing approximately 135-fold coverage of the genome. We performed the de novo assembly using Velvet 1.2.09 (), generating 138 contigs with a maximum length of 723 kbp. The total length of the contig assembly was 6.3 Mbp, and the N50 length was 208 kbp, assuming a genome size of 6.3 Mbp. The G+C content was 65.8%, similar to that of other Pseudomonas sequenced genomes. Automated annotation of the P. aeruginosa PUPa3 draft genome sequence using Prokka 1.7 () assigned a total of 5,838 candidate protein-coding genes. A total of 4 rRNA and 59 tRNA genes were identified by the Prokka annotation system. Comparative genome analysis was performed on the P. aeruginosa PAO1 genome (GenBank accession no. NC_002516.2) using MUMmer () and it was found that 96% of PAO1 is aligned with PUPa3 with an average of 99% identity. […]

Pipeline specifications

Software tools Velvet, Prokka, MUMmer
Application Nucleotide sequence alignment
Organisms Pseudomonas aeruginosa, Oryza sativa