Computational protocol: Whole-Genome Sequence of Francisella noatunensis subsp. orientalis Strain FNO01 Isolated from Diseased Nile Tilapia in Brazil

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Protocol publication

[…] Francisella noatunensis subsp. orientalis () is recognized as one of the most important pathogens of cultured Nile tilapia (Oreochromis niloticus) (). F. noatunensis subsp. orientalis is the etiologic agent of pyogranulomatous and granulomatous infections in fish. In the last few years, F. noatunensis subsp. orientalis has been responsible for a large number of deaths of tilapia and other freshwater fish species cultured in the United States, United Kingdom, Japan, Taiwan, Jamaica, Costa Rica, and some other Latin American countries (, ). This species is a Gram-negative pleomorphic bacterium and is strictly aerobic and nonmotile. This sequencing initiative is a part of a large study on the molecular epidemiology of F. noatunensis subsp. orientalis in Brazil.DNA from F. noatunensis subsp. orientalis strain FNO01 was isolated from overnight culture with the Maxwell 16 tissue DNA purification kit using the Maxwell 16 system (both from Promega, USA). The genome was sequenced with the Ion Torrent PGM sequencing system (Life Technologies, USA) using a 200-bp-fragment library kit, according to the manufacturer’s recommendations. The obtained depth coverage of ~381-fold was assembled using Newbler 2.9 (Roche, USA), with the recommended parameters. These processes resulted in assembly with 14 contigs and an N50 of 303,981 bp. These contigs were scaffolded through the CONTIGuator 2.0 software (), using F. noatunensis subsp. orientalis strain FNO12 (accession no. CP011921) as a reference. In-house scripts were used to evaluate overlapped contigs, and remaining gaps were closed with CLC Genomics Workbench version 7.0 (CLC bio, Germantown, MD) by filling with successive mappings in the gap flanks, until the overlaps were found.Strain FNO01 is composed of a circular chromosome with a length of 1,859,830 bp and a G+C content of 32.30%. The genome was annotated using an in-house transfer script, using the FNO12 strain as a reference. […]

Pipeline specifications

Software tools Newbler, CONTIGuator, CLC Genomics Workbench
Application De novo sequencing analysis
Organisms Francisella noatunensis, Oreochromis niloticus