Members of the actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different families of actinorhizal plants. We report a 5.57-Mbp draft genome sequence for Frankia sp. strain CcI6, a salt-tolerant nitrogen-fixing actinobacterium isolated from root nodules of Casurina cunninghamiana grown in Egyptian soils

Hurst, Sheldon G., IV

Mansour, Samira R.

Morris, Krystalynne

Oshone, Rediet

Thomas, W. Kelley

Tisa, Louis S.

English

PubMed

UNH Scholars' Repository

University of New HampshireUniversity of New Hampshire Scholars' RepositoryMolecular, Cellular and Biomedical SciencesScholarship Molecular, Cellular and Biomedical Sciences1-1-2014Draft Genome Sequence of Frankia sp. Strain CcI6,a Salt-Tolerant Nitrogen-Fixing ActinobacteriumIsolated from the Root Nodule of CasuarinacunninghamianaSamira R. MansourSuez Canal UniversityRediet OshoneUniversity of New Hampshire, DurhamSheldon G. Hurst IVUniversity of New Hampshire, DurhamKrystalynne MorrisUniversity of New Hampshire, DurhamW. Kelley ThomasUniversity of New Hampshire, Durham, Kelley.Thomas@unh.eduSee 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 CitationMansour, S.R, R. Oshone , S. G. Hurst IV, K. Morris, W. K. Thomas, and L. S. Tisa. 2014. Draft Genome Sequence of Frankia sp. strainCcI6, a Salt-tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodule of Casuarina cunninghamiana. GenomeAnnounc. 2(1) e01205-13 (doi:10.1128/genomeA.01205-13).AuthorsSamira R. Mansour, Rediet Oshone, Sheldon G. Hurst IV, Krystalynne Morris, W. Kelley Thomas, and LouisS. TisaThis article is available at University of New Hampshire Scholars' Repository: https://scholars.unh.edu/mcbs_facpub/156Draft Genome Sequence of Frankia sp. Strain CcI6, a Salt-TolerantNitrogen-Fixing Actinobacterium Isolated from the Root Nodule ofCasuarina cunninghamianaSamira R. Mansour,a Rediet Oshone,b Sheldon G. Hurst IV,b Krystalynne Morris,b W. Kelley Thomas,b Louis S. TisabSuez Canal University, Ismailia, Egypta; University of New Hampshire, Durham, New Hampshire, USAbMembers of the actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different families of actinorhizal plants. Wereport a 5.57-Mbp draft genome sequence for Frankia sp. strain CcI6, a salt-tolerant nitrogen-fixing actinobacterium isolatedfrom root nodules of Casurina cunninghamiana grown in Egyptian soils.Received 11 December 2013 Accepted 13 December 2013 Published 16 January 2014CitationMansour SR, Oshone R, Hurst SG, IV, Morris K, Thomas WK, Tisa LS. 2014. Draft genome sequence of Frankia sp. strain CcI6, a salt-tolerant nitrogen-fixingactinobacterium isolated from the root nodule of Casuarina cunninghamiana. Genome Announc. 2(1):e01205-13. doi:10.1128/genomeA.01205-13.Copyright © 2014 Mansour 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.Members of the genus Frankia are well known for their facul-tative lifestyles as free-living soil dwellers and as plant symbi-onts of wood angiosperms termed actinorhizal plants (1–3). Acti-norhizal plants are ecologically important as pioneer communityplants, are distributed worldwide under a broad range of ecologicalconditions, and have economic significance for land reclamation, re-forestation, soil stabilization, landscaping, and fuel. Their symbiosisallows actinorhizal plants to colonize harsh environmental terrainsunder diverse ecological conditions. The genomes for representativesfrom four major lineages have been sequenced (4–9) and have pro-vided vital baseline information for genomic approaches toward un-derstanding these novel bacteria.In arid and semiarid areas, the salinization of soils and ground-water is a serious problem (10). Egypt, which occupies the north-eastern corner of Africa, has arid and semiarid climates and greatlysuffers from high soil salinity. Among the actinorhizal plants, thegenus Casuarina has been shown to have the ability to grow wellunder such conditions, and it is widely distributed in Egyptiansoil. Frankia sp. strain CcI6 was isolated from root nodules ofCasuarina cunninghamiana grown in Egypt and shown to reinfectC. cunninghamiana, Casuarina glauca, and Casuarina equisetifolia(11). This strain showed an increased level of NaCl tolerance (12).Based on 16S phylogenetic analysis, this strain is close to Frankiasp. strain CcI3, another narrow-host range symbiont, whose ge-nome has been sequenced. Frankia sp. CcI6 has the potential to beused as a large-scale inoculum forCasuarina trees involved in landreclamation of Egyptian saline soils. Frankia sp. CcI6 was se-quenced to increase our understanding of its salt tolerance mech-anisms and to provide information about its potential ecologicalroles and interactions with actinorhizal plants.The draft genome of Frankia sp. CcI6 was generated at theHubbard Genome Center (University of New Hampshire, Dur-ham, NH) using Illumina technology (13) techniques. A standardIllumina shotgun library was constructed and sequenced using theIllumina HiSeq 2000 platform, which generated 17,617,450 reads(260-bp insert size) totaling 1,665.7 Mbp. The Illumina sequencedata were assembled using CLC Genomics Workbench (version6.5.1) and AllPaths-LG (version r41043) (14). The final draft as-sembly contains 138 contigs, with an N50 of 103 kb. The total sizeof the genome is 5.6 Mbp, and the final assembly is based on1,243.2 Mb of Illumina draft data, providing an average 222coverage of the genome.The high-quality draft genome ofFrankia sp. CcI6 was resolvedto 138 contigs consisting of 5,565,969 bp, with a GC content of67.6%. The assembled Frankia sp. CcI6 genome was annotated viathe Integrated Microbial Genomes (IMG) platform developed bythe Joint Genome Institute, Walnut Creek, CA (15), and resultedin 4,900 candidate protein-encoding genes, 46 tRNA genes, and 3rRNA regions.Nucleotide sequence accessionnumbers.This whole-genomeshotgun project has been deposited at DDBJ/EMBL/GenBank un-der the accession no. AYTZ00000000. The version described inthis paper is version AYTZ01000000.ACKNOWLEDGMENTSThis work was supported in part by United States-Egypt Joint Researchgrant no. BIO13-001 (to S.R.M. and L.S.T.) and Hatch grant no. NH585(to L.S.T.).REFERENCES1. Benson DR, Silvester WB. 1993. 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Genome characteristics of facultatively symbiotic Frankia sp. strainsreflect host range and host plant biogeography. Genome Res. 17:7–15.Genome AnnouncementsJanuary/February 2014 Volume 2 Issue 1 e01205-13 genomea.asm.org 1 on January 26, 2018 by UNIVERSITY OF NEW HAMPSHIRE LIBRARYhttp://genomea.asm.org/Downloaded from 5. Persson T, Benson DR, Normand P, Vanden Heuvel B, Pujic P, Chert-kov O, Teshima H, Bruce DC, Detter C, Tapia R, Han S, Han J, Woyke,Pitlock S, Pennacchio L, Nolan M, Ivanova N, Pati A, Land ML,Pawlowski K, Berry AM. 2011. Genome sequence of “Candidatus Frankiadatiscae” Dg1, the uncultured microsymbiont from nitrogen-fixing rootnodules of the dicot Datisca glomerata. J. Bacteriol. 193:7017–7018. http://dx.doi.org/10.1128/JB.06208-11.6. 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Draft genome sequence ofFrankia sp. strain QA3, a nitrogen-fixing actinobacterium isolated fromthe root nodule of Alnus nitida. Genome Announc. 1(2):e00103-13. http://dx.doi.org/10.1128/genomeA.00103-13.8. Nouioui I, Beauchemin N, Cantor MN, Chen A, Detter JC, FurnholmT, Ghodhbane-Gtari F, Goodwin L, Gtari M, Han C, Han J, Hunt-emann M, Hua SX, Ivanova N, Kyrpides N, Markowitz V, Mavrom-matis K, Mikhailova N, Nordberg HP, Ovchinnikova G, Pagani I, PatiA, Sen A, Sur S, Szeto E, Thakur S, Wall L, Wei CL, Woyke T, Tisa LS.2013. Draft genome sequence of Frankia sp. strain BMG5.12, a nitrogen-fixing actinobacterium isolated from Tunisian soils. Genome Announc.1(4):e00468-13. http://dx.doi.org/10.1128/genomeA.00468-13.9. 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Nucleic Acids Res. 34:D344 –D348. http://dx.doi.org/10.1093/nar/gkj024.Mansour et al.Genome Announcements2 genomea.asm.org January/February 2014 Volume 2 Issue 1 e01205-13 on January 26, 2018 by UNIVERSITY OF NEW HAMPSHIRE LIBRARYhttp://genomea.asm.org/Downloaded from 

Draft Genome Sequence of Frankia sp. Strain CcI6, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodule of Casuarina cunninghamiana

ABSTRACT
          
            Members of the actinomycete genus
            Frankia
            form a nitrogen-fixing symbiosis with 8 different families of actinorhizal plants. We report a 5.57-Mbp draft genome sequence for
            Frankia
            sp. strain CcI6, a salt-tolerant nitrogen-fixing actinobacterium isolated from root nodules of
            Casurina cunninghamiana
            grown in Egyptian soils
            .
          </jats:p

Samira R. Mansour

Rediet Oshone

Sheldon G. Hurst

Krystalynne Morris

W. Kelley Thomas

Louis S. Tisa

Crossref

Genome Announcements

Draft Genome Sequence of
            <i>Frankia</i>
            sp. Strain CcI6, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodule of
            <i>Casuarina cunninghamiana</i>

Advances in actinorhizal symbiosis: host plant-Frankiainteractions,biology,andapplicationsinaridlandreclamation. A review. Arid Land Res.

Biology of Frankia strains, actinomycete symbionts of actinorhizal plants.

Draft genome sequence of Frankia sp. strain BMG5.12, a nitrogenﬁxing actinobacterium isolated from Tunisian soils. Genome Announc.

Draft genome sequence of Frankia sp. strain QA3, a nitrogen-ﬁxing actinobacterium isolated from the root nodule of Alnus nitida.

Draft genome sequence of Frankiasp.strainCN3,anatypical,non-infective(nod-)ineffective(Fix-) isolate from Coriaria nepalensis.

Effect of salt stress on the physiology of Frankia sp. strain CcI6.

GenomecharacteristicsoffacultativelysymbioticFrankiasp.strains reﬂect host range and host plant biogeography. Genome Res. 17:7–15. Genome Announcements January/February

High–quality draft assemblies of mammalian genomes from massively parallel sequence data.

Role of gamma-radiation on spore germination and infectivity of Frankia strains

TisaLS.2013.DraftgenomesequenceofFrankiasp.strainBCU110501,a nitrogen-ﬁxing actinobacterium isolated from nodules of Discaria trinevis.

World salinization with emphasis on

http://dx.doi.org/10.1128/genomeA.01205-13

Draft Genome Sequence of Frankia sp. Strain CcI6, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodule of Casuarina cunninghamiana

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