Computational protocol: Draft Genome Sequences of Pseudomonas sp. Strain 382 and Pantoea coffeiphila 342, Endophytic Bacteria Isolated from Brazilian Guarana [Paullinia cupana (Mart.) Ducke]

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Protocol publication

[…] We have selected two endophytes, Pseudomonas sp. strain 382 and Pantoea coffeiphila 342, of the seeds of Paullinia cupana (), an Amazonian plant of economic interest.First, the DNA was extracted using a PowerSoil DNA isolation kit, and the libraries were prepared using a Nextera DNA library preparation kit. After quantification by quantitative PCR (qPCR) and size quality control of libraries using the Agilent 1200 Bioanalyzer (Agilent, USA), the DNA samples were sequenced using the HiSeq 4000 sequencer (Illumina, USA) in the 150-bp paired-end mode. Adapters and low-quality sequences were removed using the software Trimmomatic ().The whole-genome sequences of P. coffeiphila 342 and Pseudomonas sp. 382 were de novo assembled using SPAdes (), resulting in 315 and 66 scaffolds, respectively. Their genomes were represented in single linear chromosomes with, respectively, 5,967,657 and 6,385,645 bp, 52% and 62% GC content, and N50 values of 288,204 bp (mean read length, 555,521 bp) and 178,683 bp (mean read length, 585.472 bp). Genome completeness analysis with BUSCO () resulted in 99.5% complete (C) (0.4% duplicated [D]), 0.0% fragmented (F), 0.5% missed (M), and 452 genes (n) for P. coffeiphila 342; and 98% C (2.0% D), 0.2% F, 1.8% M, and 1,452 genes (n) for Pseudomonas sp. 382, indicating that the assembled genome sequences covered most of the coding regions.Annotation of the genome sequence using the Rapid Annotations using Subsystem Technology (RAST) server (), followed by tRNA and rRNA detection using ARAGORN () and RNAmmer (), respectively, identified 5,528 coding sequences, 79 tRNAs, and 9 rRNAs in P. coffeiphila 342 and 5,998 coding sequences, 77 tRNAs, and 11 rRNAs in Pseudomonas sp. 382. […]

Pipeline specifications

Software tools Trimmomatic, SPAdes, BUSCO, RAST, ARAGORN, RNAmmer
Applications Genome annotation, WGS analysis
Organisms Bacteria, Escherichia coli