Abstract
Using a pyrosequencing-based custom-made sequencer BIGIS-4, we sequenced a Gram-negative bacterium Glaciecola mesophila sp. nov. (Gmn) isolated from marine invertebrate specimens. We generated 152043 sequencing reads with a mean high-quality length of 406 bp, and assembled them using the BIGIS-4 post-processing module. No systematic low-quality data was detected beyond expected homopolymer-derived errors. The assembled Gmn genome is 5144318 bp in length and harbors 4303 annotated genes. A large number of metabolic genes correspond to various nutrients from surface marine invertebrates. Its abundant cold-tolerant and cellular signaling and related genes reveal a fundamental adaptation to low-temperature marine environment.
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Romanenko L A, Zhukova N V, Rohde M, et al. Glaciecola mesophila sp. nov., a novel marine agar-digesting bacterium. Int J Syst Evol Microbiol, 2003, 53: 647–651 12807181, 10.1099/ijs.0.02469-0, 1:CAS:528:DC%2BD3sXkvFOjur8%3D
Zhang D C, Yu Y, Chen B, et al. Glaciecola psychrophila sp. nov., a novel psychrophilic bacterium isolated from the Arctic. Int J Syst Evol Microbiol, 2006, 56: 2867–2869 17158989, 10.1099/ijs.0.64575-0, 1:CAS:528:DC%2BD2sXhtVWmtrg%3D
Van Trappen S, Tan T L, Yang J, et al. Glaciecola polaris sp. nov., a novel budding and prosthecate bacterium from the Arctic Ocean, and emended description of the genus Glaciecola. Int J Syst Evol Microbiol, 2004, 54: 1765–1771 15388742, 10.1099/ijs.0.63123-0
Baik K S, Park Y D, Seong C N, et al. Glaciecola nitratireducens sp. nov., isolated from seawater. Int J Syst Evol Microbiol, 2006, 56: 2185–2188 16957118, 10.1099/ijs.0.64330-0, 1:CAS:528:DC%2BD28XhtFektL%2FI
Chen L P, Xu H Y, Fu S Z, et al. Glaciecola lipolytica sp. nov., isolated from seawater near Tianjin city, China. Int J Syst Evol Microbiol, 2009, 59: 73–76 19126727, 10.1099/ijs.0.000489-0, 1:CAS:528:DC%2BD1MXisVCmtLk%3D
Matsuyama H, Hirabayashi T, Kasahara H, et al. Glaciecola chathamensis sp. nov., a novel marine polysaccharide-producing bacterium. Int J Syst Evol Microbiol, 2006, 56: 2883–2886 17158992, 10.1099/ijs.0.64413-0, 1:CAS:528:DC%2BD2sXhtVWmtrc%3D
Zhang Y J, Zhang X Y, Mi Z H, et al. Glaciecola arctica sp. nov., isolated from Arctic marine sediment. Int J Syst Evol Microbiol, 2010
Yong J J, Park S J, Kim H J, et al. Glaciecola agarilytica sp. nov., an agar-digesting marine bacterium from the East Sea, Korea. Int J Syst Evol Microbiol, 2007, 57: 951–953 17473239, 10.1099/ijs.0.64723-0, 1:CAS:528:DC%2BD2sXntVCgs74%3D
Prabagaran S R, Manorama R, Delille D, et al. Predominance of Roseobacter, Sulfitobacter, Glaciecola and Psychrobacter in seawater collected off Ushuaia, Argentina, Sub-Antarctica. FEMS Microbiol Ecol, 2007, 59: 342–355 17026513, 10.1111/j.1574-6941.2006.00213.x, 1:CAS:528:DC%2BD2sXhslGrs78%3D
Guo B, Chen X L, Sun C Y, et al. Gene cloning, expression and characterization of a new cold-active and salt-tolerant endo-beta-1,4-xylanase from marine Glaciecola mesophila KMM 241. Appl Microbiol Biotechnol, 2009, 84: 1107–1115 19506861, 10.1007/s00253-009-2056-y, 1:CAS:528:DC%2BD1MXht1Sqs7jM
Ronaghi M, Uhlen M, Nyren P. A sequencing method based on real-time pyrophosphate. Science, 1998, 281: 363–365 9705713, 10.1126/science.281.5375.363, 1:CAS:528:DyaK1cXkslagtL4%3D
Gordon D. Viewing and editing assembled sequences using Consed. Curr Protoc Bioinformatics, 2003, Chapter 11: Unit11.2
Delcher A L, Bratke K A, Powers E C, et al. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics, 2007, 23: 673–679 17237039, 10.1093/bioinformatics/btm009, 1:CAS:528:DC%2BD2sXkt1GhtL8%3D
Zdobnov E M, Apweiler R. InterProScan—an integration platform for the signature-recognition methods in InterPro. Bioinformatics (Oxford, England), 2001, 17: 847–848 10.1093/bioinformatics/17.9.847, 1:CAS:528:DC%2BD3MXotFehsro%3D
Schattner P, Brooks A N, Lowe T M. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res, 2005, 33: W686–W689 15980563, 10.1093/nar/gki366, 1:CAS:528:DC%2BD2MXlslyrt7c%3D
Siguier P, Perochon J, Lestrade L, et al. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res, 2006, 34: D32–D36 16381877, 10.1093/nar/gkj014, 1:CAS:528:DC%2BD28XisFOhug%3D%3D
Kurtz S, Phillippy A, Delcher A L, et al. Versatile and open software for comparing large genomes. Genome Biol, 2004, 5: R12 14759262, 10.1186/gb-2004-5-2-r12
Bott O J, Bergmann J, Hoffmann I, et al. Analysis and specification of telemedical systems using modelling and simulation: the MOSAIK-M approach. Stud Health Technol Inform, 2005, 116: 503–508 16160307, 1:STN:280:DC%2BD2MvptVSlsg%3D%3D
Ivars-Martinez E, Martin-Cuadrado A B, D’Auria G, et al. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. ISME J, 2008, 2: 1194–1212 18670397, 10.1038/ismej.2008.74, 1:CAS:528:DC%2BD1MXhtVKitb0%3D
Collins T, Gerday C, Feller G. Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiol Rev, 2005, 29: 3–23 15652973, 10.1016/j.femsre.2004.06.005, 1:CAS:528:DC%2BD2MXkvFeiug%3D%3D
Tosco A, Birolo L, Madonna S, et al. GroEL from the psychrophilic bacterium Pseudoalteromonas haloplanktis TAC 125: molecular characterization and gene cloning. Extremophiles, 2003, 7: 17–28 12579376, 1:CAS:528:DC%2BD3sXhtVKktbw%3D
Yamauchi S, Okuyama H, Morita E H, et al. Gene structure and transcriptional regulation specific to the groESL operon from the psychrophilic bacterium Colwellia maris. Arch Microbiol, 2003, 180: 272–278 12898133, 10.1007/s00203-003-0587-7, 1:CAS:528:DC%2BD3sXnslSntbY%3D
Xu K, Ma B G. Comparative analysis of predicted gene expression among deep-sea genomes. Gene, 2007, 397: 136–142 17544603, 10.1016/j.gene.2007.04.023, 1:CAS:528:DC%2BD2sXntFaqt7o%3D
Lopez-Lopez A, Bartual S G, Stal L, et al. Genetic analysis of house-keeping genes reveals a deep-sea ecotype of Alteromonas macleodii in the Mediterranean Sea. Environ Microbiol, 2005, 7: 649–659 15819847, 10.1111/j.1462-2920.2005.00733.x, 1:CAS:528:DC%2BD2MXksFCgsLg%3D
Gauthier G, Gauthier M, Christen R. Phylogenetic analysis of the genera Alteromonas, Shewanella, and Moritella using genes coding for small-subunit rRNA sequences and division of the genus Alteromonas into two genera, Alteromonas (emended) and Pseudoalteromonas gen. nov., and proposal of twelve new species combinations. Int J Syst Bacteriol, 1995, 45: 755–761 7547295, 10.1099/00207713-45-4-755, 1:CAS:528:DyaK28XivFGl
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Yuan, L., Ren, L., Li, Y. et al. A complete genome assembly of Glaciecola mesophila sp. nov. sequenced by using BIGIS-4 sequencer system. Sci. China Life Sci. 54, 835–840 (2011). https://doi.org/10.1007/s11427-011-4211-9
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DOI: https://doi.org/10.1007/s11427-011-4211-9