Sequencing the genome of Janthinobacterium sp. RA13 from Lake Washington sediment is announced. From the genome content, a versatile life-style is predicted, but not bona fide methylotrophy. With the availability of its genomic sequence, Janthinobacterium sp. RA13 presents a prospective model for studying microbial communities in lake sediments

Chistoserdova, Ludmila

McTaggart, Tami L

Shapiro, Nicole

Woyke, Tanja

English

PubMed

eScholarship - University of California

UC IrvineUC Irvine Previously Published WorksTitleDraft Genome of Janthinobacterium sp. RA13 Isolated from Lake Washington SedimentPermalinkhttps://escholarship.org/uc/item/70h985pjJournalMicrobiology Resource Announcements, 3(1)ISSN2576-098XAuthorsMcTaggart, Tami LShapiro, NicoleWoyke, Tanjaet al.Publication Date2015-02-26DOI10.1128/genomea.01588-14 Peer reviewedeScholarship.org Powered by the California Digital LibraryUniversity of CaliforniaDraft Genome of Janthinobacterium sp. RA13 Isolated from LakeWashington SedimentTami L. McTaggart,a* Nicole Shapiro,b Tanja Woyke,b Ludmila ChistoserdovaaDepartment of Chemical Engineering, University of Washington, Seattle, Washington, USAa; DOE Joint Genome Institute, Walnut Creek, California, USAb* Present address: Tami L. McTaggart, University of California, Irvine, Irvine, California, USA.Sequencing the genome of Janthinobacterium sp. RA13 from Lake Washington sediment is announced. From the genome con-tent, a versatile life-style is predicted, but not bona fide methylotrophy. With the availability of its genomic sequence, Janthino-bacterium sp. RA13 presents a prospective model for studying microbial communities in lake sediments.Received 29 December 2014 Accepted 5 January 2015 Published 12 February 2015Citation McTaggart TL, Shapiro N, Woyke T, Chistoserdova L. 2015. Draft genome of Janthinobacterium sp. RA13 isolated from Lake Washington sediment. Genome Announc3(1):e01588-14. doi:10.1128/genomeA.01588-14.Copyright © 2015 McTaggart et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Ludmila Chistoserdova, milachis@u.washington.edu.When natural microbial communities from Lake Washingtonsediment are incubated under the atmosphere of methane,simple, semi-stable communities are formed, consisting of bonafide methanotroph species and of nonmethanotrophic satellitespecies. One of the types found to persist in such methane-fedmicrocosms is the Janthinobacterium species (1). Strain Janthino-bacterium sp. RA13 was isolated from such an enrichment culturethat was incubated at 10°C in a minimal salts medium, with mul-tiple transfers and dilutions, for approximately 18 months (1), byplating onto Nutrient Broth (NB) agar medium (Difco). Axenicculture was obtained by selecting a single colony, followed by mul-tiple re-streaking onto fresh NB plates. The culture features a typ-ical violet color caused by violacein (2).The draft genome of Janthinobacterium sp. RA13 was gener-ated at the DOE Joint genome Institute (JGI), Walnut Creek, CA,USA using Pacific Biosciences (PacBio) sequencing technology(3). All general aspects of library construction and sequencingperformed at the JGI can be found at http://www.jgi.doe.gov. Theraw reads were assembled using HGAP (version 2.2.0.p1) (4). Thefinal draft assembly contains one contig, totaling 6,421,258 bp insize. Genes were identified using Prodigal (5), followed by a roundof manual curation using GenePRIMP (6). The predicted codingsequences (CDSs) were translated and used to search the NationalCenter for Biotechnology Information (NCBI) nonredundant da-tabase, UniProt, TIGRFam, Pfam, KEGG, COG, and InterPro da-tabases. The tRNAScanSE tool (7) was used to find tRNA genes,whereas rRNA genes were found by searches against models of therRNA genes built from SILVA (8). Other noncoding RNAs such asthe RNA components of the protein secretion complex and theRNase P were identified by searching the genome for the correspond-ing Rfam profiles using Infernal (http://infernal.janelia.org). Addi-tional gene prediction analysis and manual functional annotationwas performed within the Integrated Microbial Genomes (IMG)platform (http://img.jgi.doe.gov) developed by the JGI (9).From the genome content, a versatile lifestyle can be predictedfor Janthinobacterium sp. RA13, including the potential for anaer-obic metabolism linked to denitrification. However, with the ex-ception of the C1 transfer pathway linked to tetrahydrofolate, notraditional methylotrophy pathways (10) are identifiable. Withthe availability of its genomic sequence, Janthinobacterium sp.RA13 presents a prospective model for studying microbial com-munities in lake sediments.Nucleotide sequence accession number. The genome se-quence has been deposited in GenBank under the accession no.JQNP01000001.ACKNOWLEDGMENTSThis material is based upon work supported by the National Science Foun-dation (grant MCB-0950183) and by the U.S. Department of Energy, Officeof Science, Office of Biological and Environmental Research under awardDE-SC-0010556. The work conducted by the U.S. Department of EnergyJoint Genome Institute was supported by the Office of Science of the U.S.Department of Energy under contract DE-AC02-05CH11231.REFERENCES1. Oshkin IY, Beck DA, Lamb AE, Tchesnokova V, Benuska G, McTaggartTL, Kalyuzhnaya MG, Dedysh SN, Lidstrom ME, Chistoserdova L. 21October 2014. Methane-fed microbial microcosms show differential com-munity dynamics and pinpoint taxa involved in communal response.ISME J. http://dx.doi.org/10.1038/ismej.2014.203.2. Pantanella F, Berlutti F, Passariello C, Sarli S, Morea C, Schippa S.2007. Violacein and biofilm production in Janthinobacterium lividum. JAppl Microbiol 102:992–999. http://dx.doi.org/10.1111/j.1365-2672.2006.03155.x.3. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D,Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Chris-tians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M,Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G,Kong X, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma C, Marks P,Maxham M, Murphy D, Park I, Pham T, Phillips M, Roy J, Sebra R,Shen G, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J,Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J,Turner S. 2009. Real-time DNA sequencing from single polymerase mol-ecules. Science 323:133–138. http://dx.doi.org/10.1126/science.1162986.4. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C,Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J.2013. Nonhybrid, finished microbial genome assemblies from long-readSMRT sequencing data. Nat Methods 10:563–569. http://dx.doi.org/10.1038/nmeth.2474.crossmarkGenome AnnouncementsJanuary/February 2015 Volume 3 Issue 1 e01588-14 genomea.asm.org 15. Hyatt D, Chen GL, LaCascio PF, Land ML, Larimer FW, Hauser LJ.2010. Prodigal: prokaryotic gene recognition and translation initiationsite identification. BMC Bioinformatics 11:119. http://dx.doi.org/10.1186/1471-2105-11-119.6. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD,Lykidis A, Kyrpides NC. 2010. GenePRIMP: a gene prediction improve-ment pipeline for prokaryotic genomes. Nat Methods 7:455– 457. http://dx.doi.org/10.1038/nmeth.1457.7. Lowe TM, Eddy SR. 1997. tRNAscan–SE: a program for improved detec-tion of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. http://dx.doi.org/10.1093/nar/25.5.0955.8. Pruesse E, Quast C, Knittel, Fuchs BM, Ludwig W, Peplies J, GlöcknerFO. 2007. Silva: a comprehensive online resource forquality checked andaligned ribosomal RNA sequence data compatible with ARB. Nucleic Ac-ids Res 35:2188 –7196. http://dx.doi.org/10.1093/nar/gkm864.9. Markowitz VM, Mavromatis K, Ivanova NN, Chen IMA, Chu K,Kyrpides NC. 2009. IMG ER: a system for microbial genome annotationexpert review and curation. BioInformatics 25:2271–2278. http://dx.doi.org/10.1093/bioinformatics/btp393.10. Chistoserdova L. 2011. Modularity of methylotrophy, revisited. EnvironMicrobiol 13:2603–2622. http : / /dx.doi .org/10.1111/ j .1462-2920.2011.02464.x.McTaggart et al.Genome Announcements2 genomea.asm.org January/February 2015 Volume 3 Issue 1 e01588-14

Draft Genome of Janthinobacterium sp. RA13 Isolated from Lake Washington Sediment

http://dx.doi.org/10.1128/genomeA.01588-14

Draft Genome of Janthinobacterium sp. RA13 Isolated from Lake Washington Sediment.

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