The complete genome of hydrocarbon-degrading <i>Pseudoal-teromonas</i> sp. NJ289 and its phylogenetic relationship

LIU Fangming; WANG Yibin; QU Changfeng; ZHENG Zhou; MIAO Jinlai; XU Hua; XIAO Tian

doi:10.1007/s13131-017-0979-1

Volume 36 Issue 2

Turn off MathJax

Article Contents

Abstract

References

Article Navigation > Acta Oceanologica Sinica > 2017 > 36(2): 88-93

LIU Fangming, WANG Yibin, QU Changfeng, ZHENG Zhou, MIAO Jinlai, XU Hua, XIAO Tian. The complete genome of hydrocarbon-degrading Pseudoal-teromonas sp. NJ289 and its phylogenetic relationship[J]. Acta Oceanologica Sinica, 2017, 36(2): 88-93. doi: 10.1007/s13131-017-0979-1

Citation:

LIU Fangming, WANG Yibin, QU Changfeng, ZHENG Zhou, MIAO Jinlai, XU Hua, XIAO Tian. The complete genome of hydrocarbon-degrading Pseudoal-teromonas sp. NJ289 and its phylogenetic relationship[J]. Acta Oceanologica Sinica, 2017, 36(2): 88-93. doi: 10.1007/s13131-017-0979-1

Citation:

PDF( 3302 KB)

The complete genome of hydrocarbon-degrading Pseudoal-teromonas sp. NJ289 and its phylogenetic relationship

doi: 10.1007/s13131-017-0979-1

1.
Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;University of Chinese Academy of Sciences, Beijing 100049, China;The First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, China
2.
The First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, China
3.
Key Laboratory of Sustainable Development of Marine Fisheries of Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
4.
Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China

Received Date: 2015-11-01
Rev Recd Date: 2016-02-18

Abstract

Abstract

Genus Pseudoalteromonas belongs to Family Pseudoalteromonadaceae in Gammaproteobacteria. A cold-adapted gram-negative bacterium, hydrocarbon-degrading Pseudoalteromonas sp. NJ289, was isolated from sea-ice of the Antarctica region, and sequenced the whole genome through the next generation sequencing platform. The assembly yielded three contigs representing two chromosomes and one plasmid with the sizes of 3.2 Mb, 636 kb and 1.8 kb, respectively. The G+C contents of genome were 40.83% and included 3 589 ORFs. Functional annotation indicated some potential roles in enzymatic activity and environmental adaptability. This study may help for understanding the population diverse, evolutionary ecology and the microbial interaction.
- Pseudoalteromonas,
- low temperature,
- environmental adaptability,
- sequencing,
- phylogenetic tree

FullText(HTML)

References(22)

References

Altschul S F, Gish W, Miller W, et al. 1990. Basic local alignment search tool. Journal of Molecular Biology, 215(3):403-410

Bankevich A, Nurk S, Antipov D, et al. 2012. SPAdes:a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19(5):455-477

Bland C, Ramsey T L, Sabree F, et al. 2007. CRISPR Recognition Tool (CRT):a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics, 8(1):209

Chen X L, Xie B B, Lu J T, et al. 2007. A novel type of subtilase from the psychrotolerant bacterium Pseudoalteromonas sp. SM9913:catalytic and structural properties of deseasin MCP-01. Microbiology, 153:2116-2125

Delcher A L, Harmon D, Kasif S, et al. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Research, 27(23):4636-4641

Huston A L, Methe B, Deming J W. 2004. Purification, characterization, and sequencing of an extracellular cold-active aminopeptidase produced by marine Psychrophile Colwellia psychrerythraea Strain 34H. Applied and Environmental Microbiology, 70(6):3321-3328

Ivanova E P, Gorshkova N M, Zhukova N V, et al. 2004. Characterization of Pseudoalteromonas distincta-like sea-water isolates and description of Pseudoalteromonas aliena sp. nov. Int J Syst Evol Microbiol, 54:1431-1437

Kallmeyer J, Pockalny R, Adhikari R R, et al. 2012. Global distribution of microbial abundance and biomass in subseafloor sediment. Proceedings of the National Academy of Sciences of the United States of America, 109(40):16213-16216

Keane T M, Creevey C J, Pentony M M, et al. 2006. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol, 6:29

Lagesen K, Hallin P, Rødland E A, et al. 2007. RNAmmer:consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Research, 35(9):3100-3108

Li Chunyang, Chen Xiulan, Qin Qilong, et al. 2015. Structural insights into the multispecific recognition of dipeptides of deep-sea gram-negative bacterium Pseudoalteromonas sp. strain SM9913. Journal of Bacteriology, 197(6):1125-1134

Liu Shengbo, Chen Xiulan, He Hailun, et al. 2013. Structure and ecological roles of a novel exopolysaccharide from the Arctic sea ice bacterium Pseudoalteromonas sp. strain SM20310. Applied and Environmental Microbiology, 79(1):224-230

Lloyd K G, Schreiber L, Petersen D G, et al. 2013. Predominant archaea in marine sediments degrade detrital proteins. Nature, 496(7444):215-218

Lobry J R, Louarn J M. 2003. Polarisation of prokaryotic chromosomes. Current Opinion in Microbiology, 6(2):101-108

Lowe T M, Eddy S R. 1997. tRNAscan-SE:a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research, 25(5):955-964

Marraffini L A. 2015. CRISPR-Cas immunity in prokaryotes. Nature, 526(7571):55-61

Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. European Molecular Biology Network Journal, 17(1):10-12

Médigue C, Krin E, Pascal G, et al. 2005. Coping with cold:the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Research, 15(10):1325-1335

Petersen T N, Brunak S, von Heijne G, et al. 2011. SignalP 4.0:discriminating signal peptides from transmembrane regions. Nature Methods, 8(10):785-786

Ribeiro F J, Przybylski D, Yin Shuangye, et al. 2012. Finished bacterial genomes from shotgun sequence data. Genome Research, 22(11):2270-2277

Stothard P, Wishart D S. 2005. Circular genome visualization and exploration using CGView. Bioinformatics, 21(4):537-539

Zhao Huilin, Chen Xiulan, Xie Binbin, et al. 2012. Elastolytic mechanism of a novel M23 metalloprotease pseudoalterin from deep-sea Pseudoalteromonas sp. CF6-2:cleaving not only glycyl bonds in the hydrophobic regions but also peptide bonds in the hydrophilic regions involved in cross-linking. Journal of Biological Chemistry, 287(47):39710-39720

Relative Articles

Relative Articles

Supplements(0)

Cited By

Cited by

Periodical cited type(3)

1.	Desy Putri Handayani, Alim Isnansetyo, Indah Istiqomah, et al. New Report: Genome Mining Untaps the Antibiotics Biosynthetic Gene Cluster of Pseudoalteromonas xiamenensis STKMTI.2 from a Mangrove Soil Sediment. Marine Biotechnology, 2022. doi:10.1007/s10126-022-10096-1
2.	Qingqing Zhao, Haixiao Zhao, Yongchao Gao, et al. Alterations of bacterial and archaeal communities by freshwater input in coastal wetlands of the Yellow River Delta, China. Applied Soil Ecology, 2020, 153: 103581. doi:10.1016/j.apsoil.2020.103581
3.	Ermenegilda Parrilli, Pietro Tedesco, Marco Fondi, et al. The art of adapting to extreme environments: The model system Pseudoalteromonas. Physics of Life Reviews, 2019. doi:10.1016/j.plrev.2019.04.003