Abstract
Organisms in the Haloferax genus are extreme halophiles that grow in environments with pH values between 4 and 12, and temperatures between 0°C and 60°C. In the present study, a draft of the first Haloferax sp. strain ATB1 genome isolated from the region of Cariri (in Paraíba State, Brazil) is presented.
GENOME ANNOUNCEMENT
Organisms in the Haloferax genus, which belong to the Archaea domain, characteristically inhabit extreme environments. In particular, these organisms can grow in locations with salinities ranging from 10% to 37%, pH values between 4 and 12, and temperatures between 0°C and 60°C (1). For instance, H. chudinovii grows at a pH of 6.8, 42°C, and 16% salinity (2). Halophilic species, which are resistant to dehydration, exhibit low levels of cellular macromolecule denaturation and high thermal stability (3). Moreover, these species are resistant to ultraviolet (UV) light because they contain light-driven proton pumps and produce high levels of carotenoids (4). Thus, halophilic organisms can be used as models to help understand the fundamental limits of life (5) and to identify proteins with biotechnological potential.
The Haloferax sp. ATB1 specimen examined in the present study was isolated from the soil of the Cariri complex (in Paraíba, Brazil), a portion of the Caatinga biome that is affected by the desertification processes. The isolate was cultured at a pH of 7.4, temperatures ranging from 37°C to 50°C, and a salinity of approximately 25%. The genome was sequenced with the Ion Torrent PGM platform using a mate-paired library (6). A crude data quality analysis was performed using the FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The data was submitted to quality filter to remove the reads with quality values less than Phred 20.
This approach resulted in 8,480.874 reads, which corresponded to a genomic coverage of 224× based on the size of the reference genome, H. volcanni DS2 (4.1 Mb, including the main chromosome [CP001956] and the plasmids pHV1 [CP001957], pHV2 [CP001954], pHV3 [CP001953], and pHV4 [CP001955]).
A hybrid approach that utilized the four assemblers MIRA (7), CLC Genomics Workbench (http://www.clcbio.com/), SeqMan (http://www.dnastar.com), and SPAdes (8) was adopted for assembly; these assemblers produced 20,586, 14,800, 2,455, and 10,475 contigs, respectively. These results were integrated to generate a single set of sequences. This sequence set was subsequently processed using the CISA program (9) to finalize gaps, producing a total of only 120 contigs with an N50 of 36,538 that totaled 4.1 Mb.
The contigs were subjected to an automatic annotation process using the RAST software (10). This process identified 4,517 coding sequences (CDSs) and 33 RNAs, which had a G+C content of 61%. The examined Haloferax sp. ATB1 genome contains 4,223,705 bp.
Nucleotide sequence accession number.
The genomic sequence obtained in this study has been deposited in the DDBJ/EMBL/GenBank database under accession number JPES00000000.
ACKNOWLEDGMENTS
This study was performed by the Paraense Network of Genomics and Proteomics (Rede Paraense de Genômica e Proteômica), with support from the Brazilian National Council for Scientific and Technological Development (Conselho Nacional de Desenvolvimento Científico e Tecnológico—CNPq), the Coordination of Improvement of Higher Education Personnel (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—CAPES), and the Research Support Foundation of the State of Pará (Fundação de Amparo a Pesquisa do Estado do Pará—FAPESPA).
Footnotes
Citation Castro WD, Torres-Ballesteros AM, Nakayama CR, Melo IS, Pellizari VH, Silva A, Ramos RTJ. 2014. Draft genome sequence of Haloferax sp. strain ATB1, isolated from a semi-arid region in the Brazilian Caatinga. Genome Announc. 2(4):e00812-14. doi:10.1128/genomeA.00812-14.
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