Frankia forms a nitrogen-fixing symbiosis with actinorhizal plants. We report a draft genome sequence for Frankia sp. strain BCU110501, a nitrogen-fixing actinobacterium isolated from nodules of Discaria trinevis grown in the Patagonia region of Argentina

Beauchemin, Nicholas

Cantor, Michael N.

Chaia, Eugenia

Chen, Amy

Detter, J. Chris

Furnholm, Teal

Ghodhbane-Gtari, Faten

Goodwin, Lynne

Gtari, Maher

Han, Cliff

Han, James

Hua, Susan Xinyu

Huntemann, Marcel

Ivanova, Natalia

Kyrpides, Nikos

Markowitz, Victor

Mavrommatis, Kostas

Mikhailova, Natalia

Nordberg, Henrik P.

Nouioui, Imen

Ovchinnikova, Galina

Pagani, Ioanna

Pati, Amrita

Sen, Arnab

Sur, Saubashya

Szeto, Ernest

Thakur, Subarna

Tisa, Louis S.

Wall, Luis G.

Wei, Chia-Lin

Woyke, Tanja

English

PubMed

Beauchemin, Nicholas J.

Gtari, Mahar

UNH Scholars' Repository

University of New HampshireUniversity of New Hampshire Scholars' RepositoryMolecular, Cellular and Biomedical SciencesScholarship Molecular, Cellular and Biomedical Sciences7-11-2013Draft Genome Sequence of Frankia sp. StrainBCU110501, a Nitrogen-Fixing ActinobacteriumIsolated from Nodules of Discaria trinevisLuis G. WallUniversity of QuilmesNicholas J. BeaucheminUniversity of New Hampshire, DurhamMichael N. CantorLos Alamos National LaboratoryEugenia ChaiaCentro Regional UniversitarioAmy ChenJoint Genome InstituteSee next page for additional authorsFollow this and additional works at: https://scholars.unh.edu/mcbs_facpubThis Article is brought to you for free and open access by the Molecular, Cellular and Biomedical Sciences at University of New Hampshire Scholars'Repository. It has been accepted for inclusion in Molecular, Cellular and Biomedical Sciences Scholarship by an authorized administrator of Universityof New Hampshire Scholars' Repository. For more information, please contact nicole.hentz@unh.edu.Recommended CitationWall L.G., N. Beauchemin, M. N. Cantor, E. Chaia, A. Chen, J. C. Detter, T. Furnholm, F. Ghodhbane-Gtari, L. Goodwin, M. Gtari, C.Han, J. Han, M. Huntemann, S. X. Hua, N. Ivanova, N. Kyrpides, V. Markowitz, K. Mavrommatis, N. Mikhalova, H.P. Nordberg, I.Nouioui, G. Ovchinnikova, I. Pagani, A. Pati, A. Sen, S. Sur, E. Szeto, S. Thakur, C.-L. Wei, T. Woyke, and L.S. Tisa. 2013. DraftGenome sequence of Frankia sp. strain BCU110501, a nitrogen-fixing actinobacterium isolated from nodules of Discaria trinevis.GenomeAnnounc 1(4) e00503-13 (doi:10.1128/genomeA00503-13).AuthorsLuis G. Wall, Nicholas J. Beauchemin, Michael N. Cantor, Eugenia Chaia, Amy Chen, J. Chris Detter, TealFurnholm, Faten Ghodhbane-Gtari, Lynne Goodwin, Mahar Gtari, Cliff Han, James Han, MarcelHuntemann, Susan Xinyu Hua, Natalia Ivanova, Nikos Kyrpides, Victor Markowitz, Kostas Mavrommatis,Natalia Mikhailova, Henrik P. Nordberg, Imen Nouioui, Galina Ovchinnikova, Ioanna Pagani, Amrita Pati,Arnab Sen, Saubashya Sur, Ernest Szeto, Subarna Thakur, and Louis S. TisaThis article is available at University of New Hampshire Scholars' Repository: https://scholars.unh.edu/mcbs_facpub/167Draft Genome Sequence of Frankia sp. Strain BCU110501, a Nitrogen-Fixing Actinobacterium Isolated from Nodules of Discaria trinevisLuis G. Wall,a Nicholas Beauchemin,b Michael N. Cantor,c Eugenia Chaia,d Amy Chen,e J. Chris Detter,c Teal Furnholm,bFaten Ghodhbane-Gtari,b,f Lynne Goodwin,c Maher Gtari,b,f Cliff Han,c James Han,e Marcel Huntemann,e Susan Xinyu Hua,eNatalia Ivanova,e Nikos Kyrpides,e Victor Markowitz,e Kostas Mavrommatis,e Natalia Mikhailova,e Henrik P. Nordberg,c Imen Nouioui,fGalina Ovchinnikova,e Ioanna Pagani,e Amrita Pati,e Arnab Sen,g Saubashya Sur,g Ernest Szeto,e Subarna Thakur,g Chia-Lin Wei,cTanja Woyke,e Louis S. TisabUniversity of Quilmes, Bernal, Argentinaa; University of New Hampshire, Durham, New Hampshire, USAb; Los Alamos National Laboratory, Los Alamos, New Mexico, USAc;Centro Regional Universitario, Bariloche, Argentinad; Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USAe; University of Tunis–El Manar,Tunis, Tunisiaf; University of North Bengal, Siliguri, IndiagFrankia forms a nitrogen-fixing symbiosis with actinorhizal plants. We report a draft genome sequence for Frankia sp. strainBCU110501, a nitrogen-fixing actinobacterium isolated from nodules ofDiscaria trinevis grown in the Patagonia region of Ar-gentina.Received 7 June 2013 Accepted 7 June 2013 Published 11 July 2013CitationWall LG, Beauchemin N, Cantor MN, Chaia E, Chen A, Detter JC, Furnholm T, Ghodhbane-Gtari F, Goodwin L, Gtari M, Han C, Han J, Huntemann M, Hua SX, Ivanova N,Kyrpides N, Markowitz V, Mavrommatis K, Mikhailova N, Nordberg HP, Nouioui I, Ovchinnikova G, Pagani I, Pati A, Sen A, Sur S, Szeto E, Thakur S, Wei C-L, Woyke T, Tisa LS. 2013.Draft genome sequence of Frankia sp. strain BCU110501, a nitrogen-fixing actinobacterium isolated from nodules of Discaria trinevis. Genome Announc. 1(4):e00503-13. doi:10.1128/genomeA.00503-13.Copyright © 2013 Wall et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Louis S. Tisa, louis.tisa@unh.edu.The genus Frankia forms a symbiotic nitrogen-fixing associa-tion with woody trees and shrubs, resulting in a root noduleformation (1–3). Frankia exists either in a free-living state in thesoil or in symbiosis with actinorhizal plants. These actinorhizalplants comprise over 200 different plant species belonging to 8distinct plant families. Because of symbiosis, these globally distrib-uted actinorhizal plants are able to colonize harsh environmentalterrains under diverse ecological conditions. Phylogenetic studieshave shown that Frankia has four major lineages or clusters thatcan also be defined by physiology, host specificity, and mode ofinfection of the host plant (4–7). Genomes for representativesfrom each of these clusters have been sequenced (8–13) and haveprovided essential baseline information for genomic approachestoward understanding these novel bacteria.Frankia strains from cluster III have the greatestmetabolic ver-satility, are known to associate with five plant families (Betulaceae,Myricaceae, Elaeagnaceae, Rhamnaceae, and Casuarinaceae), andare considered broad-host-range symbionts.Many of these strainshave adapted to harsh environmental conditions. Frankia sp.strain BCU110501 (also called Dtl1 and T1) was isolated from afield nodule of Discaria trinevis growing wild in a semiarid steppe(40°41=S, 71°10=W) of the Argentinian Reserve and National Park“Parque Nacional Nahuel Huapi,” located in the northwest ofPatagonia (14). The physiology and infectivity of this strain havebeen well studied (15–20), and it uses an intercellular route ofplant infection (18). Frankia sp. strain BCU110501was chosen forsequencing as another cluster III representative with broad-host-range properties and an intercellular infection route. StrainBCU110501 was sequenced to provide information about the po-tential ecological roles of the Frankia strains and their interactionswith actinorhizal plants.The draft genome of Frankia sp. strain BCU110501 was gener-ated at the Department of Energy (DOE) Joint Genome Institute(JGI) using Illumina technology (21). An Illumina standard shot-gun library was constructed and sequenced using the IlluminaHiSeq 2000 platform, which generated 12,553,550 reads totaling1,883.0 Mbp. All techniques for DNA isolation, library construc-tion, and sequencing were performed according to JGI standardsand protocols (http://www.jgi.doe.gov). The Illumina sequencedata were assembled using Velvet (version 1.1.04) (22) andAllpaths-LG (version r41043) (23). The final draft assembly con-tained 207 contigs in 207 scaffolds. The total size of the genome is7.9Mbp and the final assembly is based on 950.8Mbp of Illuminadata, which provides an average 120.4 coverage of the genome.The draft genome of Frankia BCU110501 was resolved to 207scaffolds consisting of 7,891,711 bp with a GC content of72.39%, 6,742 candidate protein-encoding genes, 47 tRNA genes,and 2 rRNA regions.Nucleotide sequence accession numbers. The Frankia sp.strain BCU110501 genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession number ARDT00000000.The version described in this paper is the first version,ARDT01000000.ACKNOWLEDGMENTSThe work conducted by the U.S. Department of Energy Joint GenomeInstitute is supported by the Office of Science of the U.S. Department ofEnergy under contract no. DE-AC02-05CH11231. This project (L.S.T.)was supported in part by Agriculture and Food Research Initiative grant2010-65108-20581 from the USDA National Institute of Food and Agri-culture, Hatch grant NH530, and the College of Life Sciences and Agri-culture at the University of New Hampshire, Durham, NH. M.G. andGenome AnnouncementsJuly/August 2013 Volume 1 Issue 4 e00503-13 genomea.asm.org 1 on January 26, 2018 by UNIVERSITY OF NEW HAMPSHIRE LIBRARYhttp://genomea.asm.org/Downloaded from F.G.-G. were supported in part by a Visiting Scientist and PostdoctoralScientist Program administered by the NH AES at the University of NewHampshire.REFERENCES1. Benson DR, Silvester WB. 1993. Biology of Frankia strains, actinomycetesymbionts of actinorhizal plants. Microbiol. Rev. 57:293–319.2. Schwencke J, Caru M. 2001. Advances in actinorhizal symbiosis: hostplant-Frankia interactions, biology, and applications in arid land reclama-tion. A review. Arid Land Res. Manag. 15:285–327.3. 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Draft Genome Sequence of Frankia sp. Strain BCU110501, a Nitrogen-Fixing Actinobacterium Isolated from Nodules of Discaria trinevis

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Draft Genome Sequence of Frankia sp. Strain BCU110501, a Nitrogen-Fixing Actinobacterium Isolated from Nodules of Discaria trinevis

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