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Genetics and Molecular Biology

versão impressa ISSN 1415-4757versão On-line ISSN 1678-4685

Genet. Mol. Biol., ahead of print  Epub 02-Set-2019

http://dx.doi.org/10.1590/1678-4685-gmb-2018-0314 

Articles

[PROVISIONAL] Genome sequence of Shewanella corallii strain A687 isolated from pufferfish (Sphoeroides spengleri)

Gustavo P. R.  Azevedo1 

Pedro H. C da  Paz1 

Hannah K.  Mattsson1 

Ana Paula B. Moreira1 

Luciana  Leomil1 

Gabriela  Calegário1 

Luciana  Appolinario1 

Lívia  Vidal1 

Bruno S.  Silva1 

Luciane A. Chimetto  Tonon2 

Diogo A.  Tschoeke1 

Gizele D.  Garcia1  3 

Fabiano L.  Thompson1 

Cristiane C.  Thompson1 

1Institute of Biology and SAGE-COPPE. Federal University of Rio de Janeiro, Avenida Carlos Chagas Fo, s/n, Bloco A, Ilha do Fundão, CEP 21941-590, Rio de Janeiro, RJ, Brazil.

2Chemical Institute of São Carlos, São Paulo University (IQSC-USP), São Carlos, SP, Brazil.

3Departamento de Ensino de Graduação - Universidade Federal do Rio de Janeiro - Campus UFRJ - Macaé Professor Aloisio Teixeira, Macaé, 27930-480, Rio de Janeiro, RJ, Brazil.

Abstract

We present here the genome sequence of Shewanella corallii strain A687 isolated from pufferfish Sphoeroides spengleri (Family Tetraodontidae). The assembly consists of 5,215,037 bp and contains 284 contigs, with a G+C content of 50.3%. The genus Shewanella comprises 67 recognized species. These bacteria are Gram-negative, rod-shaped, facultatively anaerobic gammaproteobacteria and frequently isolated from marine environments (MacDonell & Colwell, 1985, Sugimoto et al., 2018). Shewanella species are involved in the production of antimicrobial metabolites and tetrodotoxin, a strong neurotoxin (Simidu et al., 1990, Magarlamov et al., 2017, Matsui et al., 1989). Shewanella corallii was recorded from red sea coral (Shnit-Orland, 2010). The aim of the present study was to determine the genome sequence of Shewanella corallii strain A687. S. corallii A687 was isolated from pufferfish Sphoeroides spengleri (Family Tetraodontidae), in Arraial do Cabo (Brazil) in 2016. Genomic DNA was extracted using according to Pitcher's protocol (Pitcher et al., 1989) and used for 300-bp paired-end library preparation with Nextera XT DNA Sample Preparation Kit. The genome was sequenced using MiSeq (Illumina, San Diego, CA, USA) as previously described (Walter et al., 2016). Sequences obtained were pre-processed using PRINSEQ software to remove reads smaller than 35 bp and low-score sequences (Phred 30) (Schmieder & Edwards, 2011). Sequence reads were assembled using A5-Miseq (Coil et al., 2015) and CAP3 software (Huang & Madan, 1999). The gene prediction and functional annotation were performed using the RAST server (Overbeek et al., 2014). Secondary metabolism was analyzed by antiSMASH (Weber et al., 2015) and clustered regularly interspaced short palindromic repeat (CRISPR) arrays were determined with CRISPRFinder (Grissa et al., 2007). The sequencing generated a total of 4,557,272 reads and 768,079,097 bp that were assembled in 284 contigs (N50=298,540 bp). The estimated genome size is 5,215,037 bp with G+C of 50.3%, and a coverage of 146-fold. RAST predicted 4,555 coding sequences, and 175 RNA sequences (147 tRNAs, 11 16S rRNAs, 6 23S rRNAs, and 11 5S rRNAs). Analyzing the genes predicted by RAST, a total of 74 genes were involved in resistance to antibiotics and toxic compounds including copper homeostasis (N=8); bile hydrolysis (N=2); cobalt-zinc-cadmium resistance (N=20); resistance to fluoroquinolones (N=4); arsenic resistance (N=4); copper homeostasis: copper tolerance (N=6); tetracycline resistance, ribosome protection type II (N=2); beta-lactamase (N=5); multidrug resistance efflux pumps (N=22); resistance to chromium compounds (N=1); 24 genes for the metabolism of aromatic compounds, including salicylate ester, chloroaromatic and quinate degradation. Phage elements sequences (N=44) were found in this genome, and CRISPRs arrays candidates were predicted in four sequences. We searched through subsystems for genes associated to symbiosis. Genes encoding type I, (lapBCDE, lapL, lapP, RTX and TolC) and type II (TadA, TadB, TadC, VirB11, RcpC, CpaB and CpaF) secretion systems were detected. We also identified 16 genes related to vitamin B12 synthesis and four LuxR gene families (Bondarev et al., 2013).

Full text available in PDF.

Recebido: 01 de Novembro de 2018; Aceito: 12 de Março de 2019

Send correspondence to Cristiane C. Thompson. E-mailthompsoncristiane@gmail.com

Creative Commons License License information: This is an open-access article distributed under the terms of the Creative Commons Attribution License (type CC-BY), which permits unrestricted use, distribution and reproduction in any medium, provided the original article is properly cited.