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Draft Genome Sequence of Halomonas sp. HG01, a Polyhydroxyalkanoate-Accumulating Strain Isolated from Peru Juliana Cardinali-Rezende,a Rafael Augusto Teodoro Pereira de Souza Nahat,a César Wilber Guzmán Moreno,a Carmen Rosa Carreño Farfán,b Luiziana Ferreira Silva,a Marilda Keico Taciro,a José Gregório Cabrera Gomeza Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazila; Facultad de Ciencias Biológicas, Universidad Nacional Pedro Ruiz Gallo, Lambayeque, Perub

Halomonas sp. strain HG01, isolated from a salt mine in Peru, is a halophilic aerobic heterotrophic bacterium accumulating poly-3-hydroxybutyrate and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) from different carbon sources. Here, we report the draft genome sequence of this isolate, which was found to be 3,665,487 bp long, with a GⴙC content of 68%. Received 19 November 2015 Accepted 20 November 2015 Published 21 January 2016 Citation Cardinali-Rezende J, Nahat RATPDS, Guzmán Moreno CW, Carreño Farfán CR, Silva LF, Taciro MK, Gomez JGC. 2016. Draft genome sequence of Halomonas sp. HG01, a polyhydroxyalkanoate-accumulating strain isolated from Peru. Genome Announc 4(1):e01598-15. doi:10.1128/genomeA.01598-15. Copyright © 2016 Cardinali-Rezende et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to José Gregório Cabrera Gomez, [email protected].

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he gammaproteobacterium Halomonas sp. strain HG01, belonging to the order Oceanospirillales, is a moderate halophilic aerobic and heterotrophic bacterium isolated in medium containing 10% NaCl from a salt mine located in San José, Lambayeque, Peru (6°46=8.26⬙S and 79°56=56.78⬙W) (1). This strain presented a great potential for poly-3-hydroxybutyrate (P3HB) production from different carbon sources, such as glucose, sucrose, and fructose, under high concentrations of salt. Furthermore, Halomonas sp. HG01 presented poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (P3HBco-3HV) production when propionic and valeric acids precursors were added to the culture medium (2). Whole genomic DNA of the strain was extracted using a DNeasy blood and tissue kit (Qiagen, Valencia, CA, USA) and quantified using a Qubit 2.0 fluorometer (Life Technologies, USA). We obtained 550-bp DNA fragments using a Covaris S2 ultrasonicator (Covaris, Inc.), which were subsequently visualized on agarose gel electrophoresis and quantified using a Qubit 2.0 fluorometer. A paired-end sequencing library was constructed using a TruSeq DNA PCR-free LT sample preparation kit (Illumina, San Diego, CA, USA). The library insert size was verified using a 2100 Bioanalyzer (Agilent Technologies, USA) and quantified by real-time PCR (qPCR) using a library quantification kit for the Illumina genome analyzer (Kapa Biosystems, MA). The sequencing library was prepared according to the manufacturer’s protocols and sequenced on an Illumina MiSeq. A total of 2,743,560 reads were generated, decreasing to 1,414,506 reads after quality control was performed using the Galaxy software (https://usegalaxy.org/). De novo genome assembly was performed with Velvet assembler 1.2.10 (3) (considering k-mer ⫽ 71, cov k-mer ⫽ 21, and reads ⬎200 bp), and contig annotation was carried out using the Rapid Annotations using Subsystems Technology (RAST) server (4). A draft genome composed of 42 contigs and an N50 contig of 2,184,772 bp were obtained. The Halomonas sp. HG01 genome was found to be 3,665,487 bp long, with 30-fold coverage and a G⫹C content of 68%. A total of 3,362 coding sequences and 67 RNAs were annotated. Three hundred sixty-seven genes were related to carbohydrate transport and me-

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tabolism, with 153 belonging to central carbohydrate metabolism organized as methylglyoxal metabolism (21 genes); pyruvate metabolism II: acetyl-coenzyme A (CoA) and acetogenesis from pyruvate (19 genes); pyruvate-alanine-serine interconversions (12 genes); glyoxylate bypass (6 genes); glycolysis and gluconeogenesis (17 genes); the Entner-Doudoroff pathway (20 genes); dehydrogenase complexes (9 genes); the tricarboxylic acid (TCA) cycle (15 genes); pyruvate metabolism I: anaplerotic reactions and phosphoenolpyruvate (PEP) (15 genes); the pentose phosphate pathway (9 genes); and glycolate-glyoxylate interconversions (9 genes). A deeper study of some of the genes will be performed, emphasizing those genes related to carbohydrate metabolism, P3HB and P3HB-co-3HV production, and cell resistance, such as PHB polymerases, PHB depolymerases, and ectoine synthesis. Sequencing of the Halomonas sp. HG01 genome and annotation of the specific genes are first efforts at understanding and improving the performance of P3HB and P3HB-co-3HV production using different carbon sources and cultured under different conditions. Nucleotide sequence accession numbers. The contig sequences generated from the whole-genome sequence of Halomonas sp. HG01 were deposited in the DDBJ/EMBL/GenBank database under the accession numbers LAEZ00000000. The version described here is the first version, LAEZ01000000. ACKNOWLEDGMENTS Financial support was provided by the São Paulo Research Foundation (FAPESP 2010/51692-1 and 2014/08061-1).

FUNDING INFORMATION Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) provided funding to Marilda Keico Taciro under grant number FAPESP 2010/51692-1.

REFERENCES 1. Guzmán CM, Hurtado AM. 2011. Producción de polihidroxialcanoatos por bacterias halófilas nativas en diferentes concentraciones de almidón contenido en cáscaras de Solanum tuberosum L. Tesis de Licenciatura. Universidad Nacional Pedro Ruiz Gallo, Lambayeque, Perú.

Genome Announcements

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2. Guzmán CWM. 2015. Production of polyhydroxyalkanoates (PHA) by Halomonas sp. HG01. MSc dissertation. University of São Paulo, São Paulo, Brazil. 3. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821– 829. http:// dx.doi.org/10.1101/gr.074492.107.

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4. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/1471-2164-9-75.

Genome Announcements

January/February 2016 Volume 4 Issue 1 e01598-15

Draft Genome Sequence of Halomonas sp. HG01, a Polyhydroxyalkanoate-Accumulating Strain Isolated from Peru.

Halomonas sp. strain HG01, isolated from a salt mine in Peru, is a halophilic aerobic heterotrophic bacterium accumulating poly-3-hydroxybutyrate and ...
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