Strain HIMB30 was isolated from coastal Hawaii seawater by extinction culturing in seawater-based oligotrophic medium. It is a phylogenetically unique member of the class Gammaproteobacteria that is only distantly related to its closest cultured relatives. Here we present the genome sequence of strain HIMB30, including genes for proteorhodopsin-based phototrophy and the Calvin-Benson-Bassham cycle

Acinas SG

Choi A

Kim H

Poretsky RS

Rappé MS

English

PubMed

Huggett, Megan

Rappe, Michael

Research Online @ ECU

Edith Cowan University Research Online ECU Publications 2012 1-1-2012 Genome sequence of strain HIMB30, a novel member of the marine Gammaproteobacteria Megan Huggett Michael Rappe Follow this and additional works at: https://ro.ecu.edu.au/ecuworks2012  Part of the Genetics and Genomics Commons 10.1128/JB.06506-11 This is an Author's Accepted Manuscript of: Huggett, M. J., & Rappe, M. (2012). Genome sequence of strain HIMB30, a novel member of the marine Gammaproteobacteria . Journal of Bacteriology, 194(3), 732-733. Available here. Copyright © American Society for Microbiology This Journal Article is posted at Research Online. https://ro.ecu.edu.au/ecuworks2012/409   2012, 194(3):732. DOI: 10.1128/JB.06506-11. J. Bacteriol. Megan J. Huggett and Michael S. Rappé GammaproteobacteriaNovel Member of the Marine Genome Sequence of Strain HIMB30, ahttp://jb.asm.org/content/194/3/732Updated information and services can be found at: These include:REFERENCEShttp://jb.asm.org/content/194/3/732#ref-list-1This article cites 11 articles, 6 of which can be accessed free at:CONTENT ALERTS more»articles cite this article), Receive: RSS Feeds, eTOCs, free email alerts (when newhttp://journals.asm.org/site/misc/reprints.xhtmlInformation about commercial reprint orders: http://journals.asm.org/site/subscriptions/To subscribe to to another ASM Journal go to:  on November 17, 2013 by guesthttp://jb.asm.org/Downloaded from  on November 17, 2013 by guesthttp://jb.asm.org/Downloaded from Genome Sequence of Strain HIMB30, a Novel Member of theMarine GammaproteobacteriaMegan J. Huggett and Michael S. RappéHawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, Kaneohe, Hawaii, USAStrain HIMB30 was isolated from coastal Hawaii seawater by extinction culturing in seawater-based oligotrophic medium. It is aphylogenetically unique member of the classGammaproteobacteria that is only distantly related to its closest cultured relatives.Here we present the genome sequence of strain HIMB30, including genes for proteorhodopsin-based phototrophy and theCalvin-Benson-Bassham cycle.Strain HIMB30 was isolated via dilution-to-extinction cultur-ing methods (3) from surface seawater collected off the coastof Oahu, HI, in the subtropical Pacific Ocean. It is of interestbecause it belongs to a novel, previously uncultivated lineage ofGammaproteobacteria that is found in cultivation-independentsurveys of marine bacterioplankton, including coastal picoplank-ton communities from the continental shelf of North Carolina(11), the coast of Sapelo Island in Georgia (10), and Plum IslandSound in Massachusetts (1). The two most closely related de-scribed species, Litoricola lipolytica and L. marina in the familyLitoricolaceae (2, 6), share just 89.9% 16S rRNA gene sequencesimilarity with strain HIMB30. Given the unique phylogeneticstatus of strain HIMB30, it most likely represents a novel familywithin the order Oceanospirillales.The genome of HIMB30 was shotgun sequenced by the J. CraigVenter Institute as part of theMoore FoundationMicrobialGenomeSequencing Project (http://camera.calit2.net/microgenome), result-ing in 629,573 reads of 454 FLX Titanium sequence data. A draft,unclosed genome was assembled to 102 coverage from624,954 reads (254,771,663 bases) of sequence data. Functionalannotation was performed with the Integrated Microbial Ge-nomes Expert Review (IMG-ER) pipeline (9). Genes identifiedusing Prodigal (5) were translated and used to search the NCBInonredundant protein database and the UniProt, TIGRFam,Pfam, PRIAM, KEGG, COG, and InterPro databases. Non-translated genes were predicted using tRNAScanSE (8),RNAmmer (7), and Rfam (4). Additional gene prediction anal-ysis and manual functional annotation were performed withinIMG-ER.The draft genome of HIMB30 consists of 36 contigs rangingin size from 266 to 638,152 bases, resulting in a total genome of2,168,870 bases. The GC content is 49.86%. In all, 2,295 pre-dicted open reading frames and 2,249 predicted protein-coding genes were identified, of which 1,874 have a predictedfunction. There are predicted single copies of the 5S, 16S, and23S rRNA genes and 36 predicted tRNAs. Genes for a completetricarboxylic acid cycle are present in the genome of HIMB30,but it possesses lesions in both the Embden-Meyerhoff-Parnaspathway and the oxidative portion of the pentose phos-phate pathway. Genes for two key enzymes of the Entner-Doudoroff pathway, phosphogluconate dehydratase and2-keto-3-deoxyphosphogluconate aldolase, were found. Thegenome contains putative genes for the synthesis of all of theessential amino acids and a number of vitamins, includingpara-aminobenzoic acid, lipoic acid, pyridoxine (vitamin B6),riboflavin, pantothenic acid, and coenzyme A. In addition togenes for carbon monoxide and sulfur oxidation, genes forproteorhodopsin-based phototrophy and CO2 fixation via theCalvin-Benson-Bassham cycle were found.Nucleotide sequence accession numbers. This Whole Ge-nome Shotgun project has been deposited in GenBank under ac-cession no. AGIG00000000. The version described in this paper isthe first version, AGIG01000000. The genome project was alsodeposited in the Genomes OnLine Database as project Gi03571,and the NCBI taxonomy identification number is 751994.ACKNOWLEDGEMENTSWe thank Steve Ferriera, Justin Johnson, and other J. Craig Venter Insti-tute scientists for performing the sequencing and assembly of this ge-nome, with support provided by the Gordon and Betty Moore Founda-tion Microbial Genome Sequencing Project (http://www.moore.org/marinemicro). Strain preparation, genomic DNA extraction, andannotation were supported by the Center for Microbial Oceanography:Research and Education (NSF Science and Technology Center award EF-0424599).REFERENCES1. Acinas SG, et al. 2004. Fine-scale phylogenetic architecture of a complexbacterial community. Nature 430:551–554.2. Choi A, Lee K, Oh H-M, Feng J, Cho J-C. 2010. Litoricola marina sp. nov.Int. J. Syst. Evol. Microbiol. 60:1303–1306.3. Connon SA, Giovannoni SJ. 2002. High-throughput methods for cultur-ing microorganisms in very-low-nutrient media yield diverse newmarineisolates. Appl. Environ. Microbiol. 68:3878–3885.4. Griffiths-Jones S, et al. 2005. Rfam: annotating non-coding RNAs incomplete genomes. Nucleic Acids Res. 33:D121–D124.5. Hyatt D, et al. 2010. Prodigal: prokaryotic gene recognition and transla-tion initiation site identification. BMC Bioinformatics 11:119.6. Kim H, Choo Y-J, Cho J-C. 2007. Litoricolaceae fam. nov., to includeLitoricola lipolytica gen. nov., sp. nov., a marine bacterium belonging tothe order Oceanospirillales. Int. J. Syst. Evol. Microbiol. 57:1793–1798.7. Lagesen K, et al. 2007. RNAmmer: consistent and rapid annotation ofribosomal RNA genes. Nucleic Acids Res. 35:3100–3108.8. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detec-Received 10 November 2011 Accepted 11 November 2011Address correspondence to Michael S. Rappé, rappe@hawaii.edu.Copyright © 2012, American Society for Microbiology. All Rights Reserved.doi:10.1128/JB.06506-11GENOME ANNOUNCEMENT732 jb.asm.org 0021-9193/12/$12.00 Journal of Bacteriology p. 732–733 on November 17, 2013 by guesthttp://jb.asm.org/Downloaded from tion of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955–964.9. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. 2009.IMG ER: a system for microbial genome annotation expert review andcuration. Bioinformatics 25:2271–2278.10. Poretsky RS, Sun S, Mou X, Moran MA. 2010. Transporter genesexpressed by coastal bacterioplankton in response to dissolved organiccarbon. Environ. Microbiol. 12:616–627.11. Rappé MS, Kemp PF, Giovannoni SJ. 1997. Phylogenetic diversity ofmarine coastal picoplankton 16S rRNA genes cloned from the conti-nental shelf off Cape Hatteras, North Carolina. Limnol. Oceanogr.42:811–826.Genome AnnouncementFebruary 2012 Volume 194 Number 3 jb.asm.org 733 on November 17, 2013 by guesthttp://jb.asm.org/Downloaded from 

Genome sequence of strain HIMB30, a novel member of the marine Gammaproteobacteria

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Genome Sequence of Strain HIMB30, a Novel Member of the Marine Gammaproteobacteria

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Genome sequence of strain HIMB30, a novel member of the marine Gammaproteobacteria

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