Abstract
Halomonas axialensis ACH-L-8, a deep-sea strain isolated from the South China Sea, has the ability to degrade aldehydes. Here, we present an annotated draft genome sequence of this species, which could provide fundamental molecular information on the aldehydes-degrading mechanism.
GENOME ANNOUNCEMENT
Halomonas axialensis was first isolated by Kaye et al. (1) from low-temperature hydrothermal fluid (Cloud Vent) at 1530-m depth. They are rod-shaped with rounded ends and grow in psychrotolerant and moderately halophilic environments. Gutierrez et al. (2) found Halomonas sp. strain MCTG39a can degrade hydrocarbon. On 12 March 2014, we isolated H. axialensis ACH-L-8 from deep sea water (2000-m depth) from the South China Sea that can grow with acetaldehyde as the sole carbon source and degrade aldehydes. This strain has been deposited in the Marine Culture Collection of China (accession number MCCC 1A10756). The 16S rRNA sequence of ACH-L-8 available in the GenBank database (accession number KP689598) showed 99.44% identity with H. axialensis Althf1T (accession number NR_027219.1) (1).
Whole-genome sequencing was performed using Illumina HiSeq 2000 technology by generating Illumina paired-end (PE) libraries (300 bp length) at the Shanghai Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China). Approximately 4,423,238 × 2 Clean data pair reads with 94.84% Q20, which provided a 239-fold depth of coverage, were first assembled using SOAPdenovo version 2.04 (http://soap.genomics.org.cn). The coding sequences (CDS) were predicted using Glimmer version 3.0.2 (http://ccb.jhu.edu/software/glimmer/index.shtml). Homologous comparison of all the genes was performed by BLAST against the NCBI nonredundant public database and KEGG database (3). The rRNAs and tRNAs were identified using Barrnap version 0.4.2 (http://www.vicbioinformatics.com/software.barrnap.shtml) and tRNAscan-SE v1.3.1 (http://lowelab.ucsc.edu/tRNAscan-SE/).
The genome of H. axialensis ACH-L-8 consists of 122 contigs (>1000 bp), with a total length of 3592820 bp and a G+C content of 56.85%; the largest contig length is 164679 bp; the N50 contig length is 70749 bp. There are 3352 predicted open reading frames (ORFs), 51 tRNA genes, and 3 rRNA clusters. The results based on KEGG database analysis predicted that H. axialensis ACH-L-8 contains 20 ALDH (aldehyde dehydrogenase) encoding genes that are involved in 14 metabolic pathways associated with aldehydes degradation. ALDH activity plays an important role in the process of degrading aldehydes. ALDHs are NAD(P)+-dependent enzymes, which catalyze the oxidation of a broad variety of aldehydes to their corresponding acids (4). Although aldehydes could be formed endogenously during the metabolism of amino acids, vitamins, lipids, and carbohydrates (5), they are cytotoxic and mutagenic compounds in the environments as a by-product of industrial activities (6). The H. axialensis genome sequence may provide fundamental molecular information on the aldehydes-degrading mechanism. It is important to further study ALDH genes in strain H. axialensis ACH-L-8, in order to promote its application in the treatment of aldehyde-polluted environments.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JYFV00000000. The version described in this paper is version JYFV01000000.
ACKNOWLEDGMENTS
This work was financially supported by China Ocean Mineral Resources R&D Association (DY125-15-T-06), Hi-Tech Research and Development Program of China (863 program of China; 2012AA092103, 2012AA092101), and Fujian Science & Technology Program (2013N0018).
Footnotes
Citation Ye J, Ren C, Shan X, Zeng R. 2016. Draft genome sequence of aldehyde-degrading strain Halomonas axialensis ACH-L-8. Genome Announc 4(2):e00287-16. doi:10.1128/genomeA.00287-16.
REFERENCES
- 1.Kaye JZ, Márquez MC, Ventosa A, Baross JA. 2004. Halomonas neptuniae sp. nov., Halomonas sulfidaeris sp. nov., Halomonas axialensis sp. nov. and Halomonas hydrothermalis sp. nov.: halophilic bacteria isolated from deep-sea hydrothermal-vent environments. Int J Syst Evol Microbiol 54:499–511. doi: 10.1099/ijs.0.02799-0. [DOI] [PubMed] [Google Scholar]
- 2.Gutierrez T, Whitman WB, Huntemann M, Copeland A, Chen A, Kyrpides N, Markowitz V, Pillay M, Ivanova N, Mikhailova N, Ovchinnikova G, Evan Andersen E, Pati A, Stamatis D, Reddy TBK, Ngan CY, Chovatia M, Daum C, Shapiro N, Cantor MN, Woykec T. 2015. Genome sequence of Halomonas sp. strain MCTG39a, a hydrocarbon-degrading and exopolymeric substance-producing bacterium. Genome Announc 3(4):e00793-15. doi: 10.1128/genomeA.00793-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280. doi: 10.1093/nar/gkh063. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Poels PA, Duine JA. 1989. NAD-linked GSH- and factor-independent aldehyde dehydrogenase of the methylotrophic bacterium, Hyphomicrobium X. Arch Biochem Biophys 271:240–245. doi: 10.1016/0003-9861(89)90274-9. [DOI] [PubMed] [Google Scholar]
- 5.Seto M, Kimbara K, Shimura M, Hatta T, Fukuda M, Yano K. 1995. A novel transformation of polychlorinated biphenyls by Rhodococcus sp. strain RHA1. Appl Environ Microbiol 61:3353–3358. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Vasiliou V, Pappa A, Petersen DR. 2000. Role of aldehyde dehydrogenase in endogenous and xenobiotic metabolism. Chem Biol Interact 129:1–19. doi: 10.1016/S0009-2797(00)00211-8. [DOI] [PubMed] [Google Scholar]