Frankia strain ACN1ag is a member of Frankia lineage Ia, which are able to re-infect plants of the Betulaceae and Myricaceae families. Here, we report a 7.5-Mbp draft genome sequence with a G+C content of 72.35% and 5,687 candidate protein-encoding genes

Abebe-Akele, Feseha

Morris, Krystalynne

Oshone, Rediet

Simpson, Stephen

Swanson, Erik

Thomas, W. Kelley

Tisa, Louis S.

English

PubMed

Simpson, Stephen D.

Thomas, William Kelley

UNH Scholars' Repository

University of New HampshireUniversity of New Hampshire Scholars' RepositoryNew Hampshire Agricultural Experiment Station Research Institutes, Centers and Programs12-17-2015Permanent draft genome sequence of Frankia sp.strain ACN1ag, a nitrogen-fixing actinobacteriumisolated from the root nodules of Alnus glutinosaErik SwansonUniversity of New Hampshire, DurhamRediet OshoneUniversity of New Hampshire, DurhamStephen D. SimpsonUniversity of New Hampshire, Durham, Stephen.Simpson@unh.eduKrystalynne MorrisUniversity of New Hampshire, Durham, Krystalynne.Morris@unh.eduFeseha Abebe-AkeleUniversity of New Hampshire, DurhamSee next page for additional authorsFollow this and additional works at: https://scholars.unh.edu/nhaesThis Article is brought to you for free and open access by the Research Institutes, Centers and Programs at University of New Hampshire Scholars'Repository. It has been accepted for inclusion in New Hampshire Agricultural Experiment Station by an authorized administrator of University of NewHampshire Scholars' Repository. For more information, please contact nicole.hentz@unh.edu.Recommended CitationSwanson E, Oshone R, Simpson S, Morris K, Abebe-Akele F, Thomas WK, Tisa LS. 2015. Permanent draft genome sequence ofFrankia sp. strain ACN1ag, a nitrogen-fixing actinobacterium isolated from the root nodules of Alnus glutinosa. Genome Announc3(6):e01483-15. https://dx.doi.org/10.1128/genomeA.01483-15AuthorsErik Swanson, Rediet Oshone, Stephen D. Simpson, Krystalynne Morris, Feseha Abebe-Akele, William KelleyThomas, and Louis S. TisaThis article is available at University of New Hampshire Scholars' Repository: https://scholars.unh.edu/nhaes/373Permanent Draft Genome Sequence of Frankia sp. Strain ACN1ag, aNitrogen-Fixing Actinobacterium Isolated from the Root Nodules ofAlnus glutinosaErik Swanson, Rediet Oshone, Stephen Simpson, Krystalynne Morris, Feseha Abebe-Akele, W. Kelley Thomas, Louis S. TisaUniversity of New Hampshire, Durham, New Hampshire, USAFrankia strain ACN1ag is a member of Frankia lineage Ia, which are able to re-infect plants of the Betulaceae andMyricaceaefamilies. Here, we report a 7.5-Mbp draft genome sequence with a GC content of 72.35% and 5,687 candidate protein-encodinggenes.Received 27 October 2015 Accepted 27 October 2015 Published 17 December 2015Citation Swanson E, Oshone R, Simpson S, Morris K, Abebe-Akele F, Thomas WK, Tisa LS. 2015. Permanent draft genome sequence of Frankia sp. strain ACN1ag, a nitrogen-fixing actinobacterium isolated from the root nodules of Alnus glutinosa. Genome Announc 3(6):e01483-15. doi:10.1128/genomeA.01483-15.Copyright © 2015 Swanson 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.Among the Actinobacteria, the genus Frankia is well known forits facultative lifestyle as a plant symbiont of dicotyledonousplants, termed actinorhizal plants, and as a free-living soil dweller(1–3). Actinorhizal plants are ecologically important pioneercommunity plants that are found worldwide in a broad range ofecological and environmental conditions (4). The symbiosis al-lows actinorhizal plants to colonize harsh environmental terrains.The genus Frankia has not yet been described to the species level,but it has become an area of greater interest. Four major Frankialineages have been identified (5–8), and genomes for representa-tives from each cluster have been sequenced (9–21).Cluster I contains two subclusters: one subcluster (Cluster Ia)represents Frankia strains with the ability to infect a wider range ofhost plants, including member of the Betulaceae and Myricaceaefamilies, and the other subcluster (Cluster Ib) contains strainslimited to Casuarina and Allocasuarina host plants. As anothermember of Cluster Ia, Frankia sp. strain ACN1ag was chosen forsequencing to provide more information on this lineage and itsinteraction with actinorhizal plants. Frankia sp. strain ACN1ag is are-isolate from root nodules ofAlnus glutinosa inoculated from anisolate of Alnus viridis crispa collected from Atikokan, Ontario,Canada (22, 23).The draft genome of Frankia sp. strain ACN1ag was generatedat the Hubbard Genome Center (University of New Hampshire,Durham, NH, USA) using Illumina technology (24) techniques. Astandard Illumina shotgun library was constructed and sequencedusing the Illumina HiSeq2000 platform, which generated14,474,194 reads (260-bp insert size) totaling 2,127.7 Mbp. TheIllumina sequence data were assembled using CLC GenomicsWorkbench version 8.0.1 and AllPaths-LG version r41043 (25).The final draft assembly contained 108 contigs with an N50 of157.4 kb. The total size of the genome is 7.5 Mbp, and the finalassembly is based on 2,127.17 Mb of Illumina draft data and pro-vided an average 220 coverage of the genome.The high-quality draft genome of Frankia sp. strain ACN1agwas resolved to 108 contigs consisting of 7,505,639 bp with a GCcontent of 72.35%. The assembled Frankia sp. strain ACN1ag ge-nome was annotated via the Integrated Microbial Genomes(IMG) platform developed by the Joint Genome Institute, WalnutCreek, CA, USA (26, 27), and resulted in 5,687 candidate protein-encoding genes, 45 tRNA genes, and 2 rRNA regions.Nucleotide sequence accessionnumbers.This whole-genomeshotgun project has been deposited at DDBJ/EMBL/GenBank un-der the accession number LJPA00000000. The version describedin this paper is the first version, LJPA01000000.ACKNOWLEDGMENTSPartial funding was provided by the New Hampshire Agricultural Exper-iment Station. This is Scientific Contribution Number 2638. This workwas supported by the USDA National Institute of Food and AgricultureHatch 022821 (L.S.T.), Agriculture and Food Research Initiative Grant2015-67014-22849 from the USDA National Institute of Food and Agri-culture (L.S.T.), and the College of Life Science and Agriculture at theUniversity of New Hampshire–Durham. Sequencing was performed onan Illumina HiSeq2500 purchased with NSF MRI Grant DBI-1229361toW.K.T.REFERENCES1. Schwencke J, Carú 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. http://dx.doi.org/10.1080/153249801753127615.2. Chaia EE, Wall LG, Huss-Danell K. 2010. Life in soil by the actinorhizalroot nodule endophyte Frankia. A review. Symbiosis 51:201–226. http://dx.doi.org/10.1007/s13199-010-0086-y.3. Normand P, Benson DR, Berry AM, Tisa LS. 2014. Family Frankiaceae,p 339 –356. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thomp-son F (ed), The prokaryote—Actinobacteria, 4th ed. Springer-Verlag, Ber-lin, Germany.4. Benson DR, Dawson JO. 2007. Recent advances in the biogeography andgenecology of symbiotic Frankia and its host plants. Physiol Plant 130:318 –330. http://dx.doi.org/10.1111/j.1399-3054.2007.00934.x.5. Normand P, Orso S, Cournoyer B, Jeannin P, Chapelon C, Dawson J,Evtushenko L, Misra AK. 1996. Molecular phylogeny of the genusFrankia and related genera and emendation of the family Frankiaceae. IntJ Syst Bacteriol 46:1–9. http://dx.doi.org/10.1099/00207713-46-1-1.6. Cournoyer B, Lavire C. 1999. Analysis of Frankia evolution radiationusing glnII sequences. FEMS Microbiol Lett 117:29 –34.crossmarkGenome AnnouncementsNovember/December 2015 Volume 3 Issue 6 e01483-15 genomea.asm.org 17. Nouioui I, Ghodhbane-Gtari F, Beauchemin NJ, Tisa LS, Gtari M. 2011.Phylogeny of members of the Frankia genus based on gyrB, nifH and glnIIsequences. Antonie Van Leeuwenhoek 100:579 –587. http://dx.doi.org/10.1007/s10482-011-9613-y.8. Ghodhbane-Gtari F, Nouioui I, Chair M, Boudabous A, Gtari M 2010.16S-23S rRNA intergenic spacer region variability in the genus Frankia.Microb Ecol 60:487– 495. http://dx.doi.org/10.1007/s00248-010-9641-6.9. Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E,Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, CournoyerB, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E,Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J,Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawns-ley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP,Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C, Benson DR.2007. Genome characteristics of facultatively symbiotic Frankia sp. strainsreflect host range and host plant biogeography. Genome Res 17:7–15.http://dx.doi.org/10.1101/gr.5798407.10. Normand P, Queiroux C, Tisa LS, Benson DR, Rouy Z, Cruveiller S,Médigue C. 2007. Exploring the genomes of Frankia. Physiol Plant 130:331–343. http://dx.doi.org/10.1111/j.1399-3054.2007.00918.x.11. 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, WoykeT, Pitluck 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.06208-11.12. Ghodhbane-Gtari F, Beauchemin N, Bruce D, Chain P, Chen A, Wal-ston Davenport K, Deshpande S, Detter C, Furnholm T, Goodwin L,Gtari M, Han C, Han J, Huntemann M, Ivanova N, Kyrpides N, LandML, Markowitz V, Mavrommatis K, Nolan M, Nouioui I, Pagani I, PatiA, Pitluck S, Santos CL, Sen A, Sur S, Szeto E, Tavares F, Teshima H,Thakur S, Wall L, Woyke T, Tisa LS. 2013. Draft genome sequence ofFrankia sp. strain CN3, an atypical, noninfective (Nod) ineffective(Fix) isolate from Coriaria nepalensis. Genome Announc 1(2):e00085-13. http://dx.doi.org/10.1128/genomeA.00085-13.13. Sen A, Beauchemin N, Bruce D, Chain P, Chen A, Walston DavenportK, Deshpande S, Detter C, Furnholm T, Ghodbhane-Gtari F, GoodwinL, Gtari M, Han C, Han J, Huntemann M, Ivanova N, Kyrpides N, LandML, Markowitz V, Mavrommatis K, Nolan M, Nouioui I, Pagani I, PatiA, Pitluck S, Santos CL, Sur S, Szeto E, Tavares F, Teshima H, ThakurS, Wall L, Wishart J, Woyke T, Tisa LS. 2013. Draft genome sequence ofFrankia sp. strain QA3, a nitrogen-fixing actinobacterium isolated fromthe root nodule ofAlnus nitida. Genome Announc 1(2):e00103-13. http://dx.doi.org/10.1128/genomeA.00103-13.14. 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 C-L, Woyke T, Tisa LS.2013. Draft genome sequence of Frankia sp. strain BMG5.12, a nitrogen-fixing actinobacterium isolated from Tunisian soils. Genome Announc1(4):e00468-13. http://dx.doi.org/10.1128/genomeA.00468-13.15. Wall 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, Mav-rommatis 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, anitrogen-fixing actinobacterium isolated from nodules of Discaria trin-evis. Genome Announc 1(4):e00503-13. http://dx.doi.org/10.1128/genomeA.00503-13.16. Mansour SR, Oshone R, Hurst IV SG, Morris K, Thomas WK, Tisa LS.2014. Draft genome sequence of Frankia sp. strain cci6, a Salt-tolerantnitrogen-fixing actinobacterium isolated from the root nodule of Casu-arina cunninghamiana. Genome Announc 2(1):e01205-13. http://dx.doi.org/10.1128/genomeA.01205-13.17. Hurst IV SG, Oshone R, Ghodhbane-Gtari F, Morris K, Abebe-Akele F,Thomas WK, Ktari A, Salem K, Mansour S, Gtari M, Tisa LS. 2014.Draft genome sequence of Frankia sp. strain Thr, a nitrogen-fixing acti-nobacterium isolated from the root nodules of Casuarina cunninghami-ana grown in Egypt. Genome Announc 2(3):e00493-14. http://dx.doi.org/10.1128/genomeA.00493-14.18. Ghodhbane-Gtari F, Hurst IV SG, Oshone R, Morris K, Abebe-Akele F,Thomas WK, Ktari A, Salem K, Gtari M, Tisa LS. 2014. Draft genomesequence of Frankia sp. strain BMG5.23, a salt-tolerant nitrogen-fixingactinobacterium isolated from the root nodules of Casuarina glaucagrown in Tunisia. Genome Announc 2(3):e00520-14. http://dx.doi.org/10.1128/genomeA.00520-14.19. Tisa LS, Beauchemin N, Gtari M, Sen A, Wall LG. 2013. What stories canthe Frankia genomes start to tell us? J Biosci 38:719 –726. http://dx.doi.org/10.1007/s12038-013-9364-1.20. Gtari M, Ghodhbane-Gtari F, Nouioui I, Ktari A, Hezbri K, MimouniW, Sbissi I, Ayari A, Yamanaka T, Normand P, Tisa LS, Boudabous A.2015. Cultivating the uncultured: growing the recalcitrant cluster-2Frankia strains. Sci Rep 5:13112. http://dx.doi.org/10.1038/srep13112.21. Tisa LS, Beauchemin N, Cantor MN, Furnholm T, Ghodhbane-Gtari F,Goodwin L, Copeland A, Gtari M, Huntemann M, Ivanova N, KyrpidesN, Markowitz V, Mavrommatis K, Mikhailova N, Nouioui I, Oshone R,Ovchinnikova G, Pagani I, Palaniappan K, Pati A. 2015. Draft genomesequence of Frankia sp. strain DC12, an atypical, noninfective, ineffectiveisolate fromDatisca cannabina. Genome Announc 3(4):e00889-15. http://dx.doi.org/10.1128/genomeA.00889-15.22. Baker D, Torrey JG, Kidd GH. 1979. Isolation by sucrose-density frac-tionation and cultivation in vitro of actinomycetes from nitrogen-fixingroot nodules. Nature 281:76 –78. http://dx.doi.org/10.1038/281076a0.23. Lalonde M, Calvert HE, Pine S. 1981. Isolation and use of Frankia strainsin actinorhizae formation, p 296 –299. In Gibson AH, Newton WE (ed),Current perspectives in nitrogen fixation. Australian Academy of Science,Canberra, Australia.24. Bennett S. 2004. Solexa Ltd. Pharmacogenomics 5:433– 438. http://dx.doi.org/10.1517/14622416.5.4.433.25. Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, WalkerBJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M,Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, JaffeDB. 2011. High-quality draft assemblies of mammalian genomes frommassively parallel sequence data. Proc Natl Acad Sci USA 108:1513–1518.http://dx.doi.org/10.1073/pnas.1017351108.26. Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G,Padki A, Zhao XL, Dubchak I, Hugenholtz P, Anderson I, Lykidis A,Mavromatis K, Ivanova N, Kyrpides NC. 2006. The integrated microbialgenomes (IMG) system. Nucleic Acids Res 34:D344 –D348. http://dx.doi.org/10.1093/nar/gkj024.27. Markowitz VM, Mavromatis K, Ivanova NN, Chen IA, Chu K, KyrpidesNC. 2009. IMG ER: a system for microbial genome annotation expertreview and curation. Bioinformatics 25:2271–2278. http://dx.doi.org/10.1093/bioinformatics/btp393.Swanson et al.Genome Announcements2 genomea.asm.org November/December 2015 Volume 3 Issue 6 e01483-15

Permanent draft genome sequence of Frankia sp. strain ACN1ag, a nitrogen-fixing actinobacterium isolated from the root nodules of Alnus glutinosa

ABSTRACT
 
 Frankia
 strain ACN1
 ag
 is a member of
 Frankia
 lineage Ia, which are able to re-infect plants of the
 Betulaceae
 and
 Myricaceae
 families. Here, we report a 7.5-Mbp draft genome sequence with a G+C content of 72.35% and 5,687 candidate protein-encoding genes.
 </jats:p

Erik Swanson

Rediet Oshone

Stephen Simpson

Krystalynne Morris

Feseha Abebe-Akele

W. Kelley Thomas

Louis S. Tisa

Crossref

Genome Announcements

Permanent Draft Genome Sequence of
 Frankia
 sp. Strain ACN1
 ag
 , a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of
 Alnus glutinosa

University of New HampshireUniversity of New Hampshire Scholars' RepositoryMolecular, Cellular and Biomedical SciencesScholarship Molecular, Cellular and Biomedical Sciences12-17-2015Permanent Draft Genome Sequence of Frankia sp.Strain ACN1ag, a Nitrogen-FixingActinobacterium Isolated from the Root Nodulesof Alnus glutinosaErik SwansonUniversity of New Hampshire, DurhamRediet OshoneUniversity of New Hampshire, DurhamStephen SimpsonUniversity of New Hampshire, DurhamKrystalynne MorrisUniversity of New Hampshire, DurhamFeseha Abebe-AkeleUniversity of New Hampshire, DurhamSee 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 CitationSwanson, E., R. Oshone, K. Morris, F. Abebe-Akele, S. Simpson, W. K. Thomas, and L. S. Tisa. 2015. Draft Genome sequence ofFrankia sp. strain ACN1ag, a nitrogen-fixing actinobacterium isolated from the root nodule of Alnus glutinosa. Genome Announc3(6):e01483-15. doi:10.1128/genomeA.01483-15.AuthorsErik Swanson, Rediet Oshone, Stephen Simpson, Krystalynne Morris, Feseha Abebe-Akele, W. KelleyThomas, and Louis S. TisaThis article is available at University of New Hampshire Scholars' Repository: https://scholars.unh.edu/mcbs_facpub/160Permanent Draft Genome Sequence of Frankia sp. Strain ACN1ag, aNitrogen-Fixing Actinobacterium Isolated from the Root Nodules ofAlnus glutinosaErik Swanson, Rediet Oshone, Stephen Simpson, Krystalynne Morris, Feseha Abebe-Akele, W. Kelley Thomas, Louis S. TisaUniversity of New Hampshire, Durham, New Hampshire, USAFrankia strain ACN1ag is a member of Frankia lineage Ia, which are able to re-infect plants of the Betulaceae andMyricaceaefamilies. Here, we report a 7.5-Mbp draft genome sequence with a GC content of 72.35% and 5,687 candidate protein-encodinggenes.Received 27 October 2015 Accepted 27 October 2015 Published 17 December 2015Citation Swanson E, Oshone R, Simpson S, Morris K, Abebe-Akele F, Thomas WK, Tisa LS. 2015. Permanent draft genome sequence of Frankia sp. strain ACN1ag, a nitrogen-fixing actinobacterium isolated from the root nodules of Alnus glutinosa. Genome Announc 3(6):e01483-15. doi:10.1128/genomeA.01483-15.Copyright © 2015 Swanson 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.Among the Actinobacteria, the genus Frankia is well known forits facultative lifestyle as a plant symbiont of dicotyledonousplants, termed actinorhizal plants, and as a free-living soil dweller(1–3). Actinorhizal plants are ecologically important pioneercommunity plants that are found worldwide in a broad range ofecological and environmental conditions (4). The symbiosis al-lows actinorhizal plants to colonize harsh environmental terrains.The genus Frankia has not yet been described to the species level,but it has become an area of greater interest. Four major Frankialineages have been identified (5–8), and genomes for representa-tives from each cluster have been sequenced (9–21).Cluster I contains two subclusters: one subcluster (Cluster Ia)represents Frankia strains with the ability to infect a wider range ofhost plants, including member of the Betulaceae and Myricaceaefamilies, and the other subcluster (Cluster Ib) contains strainslimited to Casuarina and Allocasuarina host plants. As anothermember of Cluster Ia, Frankia sp. strain ACN1ag was chosen forsequencing to provide more information on this lineage and itsinteraction with actinorhizal plants. Frankia sp. strain ACN1ag is are-isolate from root nodules ofAlnus glutinosa inoculated from anisolate of Alnus viridis crispa collected from Atikokan, Ontario,Canada (22, 23).The draft genome of Frankia sp. strain ACN1ag was generatedat the Hubbard Genome Center (University of New Hampshire,Durham, NH, USA) using Illumina technology (24) techniques. Astandard Illumina shotgun library was constructed and sequencedusing the Illumina HiSeq2000 platform, which generated14,474,194 reads (260-bp insert size) totaling 2,127.7 Mbp. TheIllumina sequence data were assembled using CLC GenomicsWorkbench version 8.0.1 and AllPaths-LG version r41043 (25).The final draft assembly contained 108 contigs with an N50 of157.4 kb. The total size of the genome is 7.5 Mbp, and the finalassembly is based on 2,127.17 Mb of Illumina draft data and pro-vided an average 220 coverage of the genome.The high-quality draft genome of Frankia sp. strain ACN1agwas resolved to 108 contigs consisting of 7,505,639 bp with a GCcontent of 72.35%. The assembled Frankia sp. strain ACN1ag ge-nome was annotated via the Integrated Microbial Genomes(IMG) platform developed by the Joint Genome Institute, WalnutCreek, CA, USA (26, 27), and resulted in 5,687 candidate protein-encoding genes, 45 tRNA genes, and 2 rRNA regions.Nucleotide sequence accessionnumbers.This whole-genomeshotgun project has been deposited at DDBJ/EMBL/GenBank un-der the accession number LJPA00000000. The version describedin this paper is the first version, LJPA01000000.ACKNOWLEDGMENTSPartial funding was provided by the New Hampshire Agricultural Exper-iment Station. This is Scientific Contribution Number 2638. This workwas supported by the USDA National Institute of Food and AgricultureHatch 022821 (L.S.T.), Agriculture and Food Research Initiative Grant2015-67014-22849 from the USDA National Institute of Food and Agri-culture (L.S.T.), and the College of Life Science and Agriculture at theUniversity of New Hampshire–Durham. Sequencing was performed onan Illumina HiSeq2500 purchased with NSF MRI Grant DBI-1229361toW.K.T.REFERENCES1. Schwencke J, Carú 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. http://dx.doi.org/10.1080/153249801753127615.2. Chaia EE, Wall LG, Huss-Danell K. 2010. Life in soil by the actinorhizalroot nodule endophyte Frankia. A review. Symbiosis 51:201–226. http://dx.doi.org/10.1007/s13199-010-0086-y.3. Normand P, Benson DR, Berry AM, Tisa LS. 2014. Family Frankiaceae,p 339 –356. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thomp-son F (ed), The prokaryote—Actinobacteria, 4th ed. Springer-Verlag, Ber-lin, Germany.4. Benson DR, Dawson JO. 2007. Recent advances in the biogeography andgenecology of symbiotic Frankia and its host plants. Physiol Plant 130:318 –330. http://dx.doi.org/10.1111/j.1399-3054.2007.00934.x.5. Normand P, Orso S, Cournoyer B, Jeannin P, Chapelon C, Dawson J,Evtushenko L, Misra AK. 1996. Molecular phylogeny of the genusFrankia and related genera and emendation of the family Frankiaceae. IntJ Syst Bacteriol 46:1–9. http://dx.doi.org/10.1099/00207713-46-1-1.6. Cournoyer B, Lavire C. 1999. Analysis of Frankia evolution radiationusing glnII sequences. FEMS Microbiol Lett 117:29 –34.crossmarkGenome AnnouncementsNovember/December 2015 Volume 3 Issue 6 e01483-15 genomea.asm.org 1 on January 29, 2018 by UNIVERSITY OF NEW HAMPSHIRE LIBRARYhttp://genomea.asm.org/Downloaded from 7. Nouioui I, Ghodhbane-Gtari F, Beauchemin NJ, Tisa LS, Gtari M. 2011.Phylogeny of members of the Frankia genus based on gyrB, nifH and glnIIsequences. Antonie Van Leeuwenhoek 100:579 –587. http://dx.doi.org/10.1007/s10482-011-9613-y.8. Ghodhbane-Gtari F, Nouioui I, Chair M, Boudabous A, Gtari M 2010.16S-23S rRNA intergenic spacer region variability in the genus Frankia.Microb Ecol 60:487– 495. http://dx.doi.org/10.1007/s00248-010-9641-6.9. Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E,Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, CournoyerB, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E,Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J,Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawns-ley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP,Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C, Benson DR.2007. Genome characteristics of facultatively symbiotic Frankia sp. strainsreflect host range and host plant biogeography. Genome Res 17:7–15.http://dx.doi.org/10.1101/gr.5798407.10. Normand P, Queiroux C, Tisa LS, Benson DR, Rouy Z, Cruveiller S,Médigue C. 2007. Exploring the genomes of Frankia. Physiol Plant 130:331–343. http://dx.doi.org/10.1111/j.1399-3054.2007.00918.x.11. 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, WoykeT, Pitluck 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.06208-11.12. Ghodhbane-Gtari F, Beauchemin N, Bruce D, Chain P, Chen A, Wal-ston Davenport K, Deshpande S, Detter C, Furnholm T, Goodwin L,Gtari M, Han C, Han J, Huntemann M, Ivanova N, Kyrpides N, LandML, Markowitz V, Mavrommatis K, Nolan M, Nouioui I, Pagani I, PatiA, Pitluck S, Santos CL, Sen A, Sur S, Szeto E, Tavares F, Teshima H,Thakur S, Wall L, Woyke T, Tisa LS. 2013. Draft genome sequence ofFrankia sp. strain CN3, an atypical, noninfective (Nod) ineffective(Fix) isolate from Coriaria nepalensis. Genome Announc 1(2):e00085-13. http://dx.doi.org/10.1128/genomeA.00085-13.13. Sen A, Beauchemin N, Bruce D, Chain P, Chen A, Walston DavenportK, Deshpande S, Detter C, Furnholm T, Ghodbhane-Gtari F, GoodwinL, Gtari M, Han C, Han J, Huntemann M, Ivanova N, Kyrpides N, LandML, Markowitz V, Mavrommatis K, Nolan M, Nouioui I, Pagani I, PatiA, Pitluck S, Santos CL, Sur S, Szeto E, Tavares F, Teshima H, ThakurS, Wall L, Wishart J, Woyke T, Tisa LS. 2013. Draft genome sequence ofFrankia sp. strain QA3, a nitrogen-fixing actinobacterium isolated fromthe root nodule ofAlnus nitida. Genome Announc 1(2):e00103-13. http://dx.doi.org/10.1128/genomeA.00103-13.14. 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 C-L, Woyke T, Tisa LS.2013. Draft genome sequence of Frankia sp. strain BMG5.12, a nitrogen-fixing actinobacterium isolated from Tunisian soils. Genome Announc1(4):e00468-13. http://dx.doi.org/10.1128/genomeA.00468-13.15. Wall 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, Mav-rommatis 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, anitrogen-fixing actinobacterium isolated from nodules of Discaria trin-evis. Genome Announc 1(4):e00503-13. http://dx.doi.org/10.1128/genomeA.00503-13.16. Mansour SR, Oshone R, Hurst IV SG, Morris K, Thomas WK, Tisa LS.2014. Draft genome sequence of Frankia sp. strain cci6, a Salt-tolerantnitrogen-fixing actinobacterium isolated from the root nodule of Casu-arina cunninghamiana. Genome Announc 2(1):e01205-13. http://dx.doi.org/10.1128/genomeA.01205-13.17. Hurst IV SG, Oshone R, Ghodhbane-Gtari F, Morris K, Abebe-Akele F,Thomas WK, Ktari A, Salem K, Mansour S, Gtari M, Tisa LS. 2014.Draft genome sequence of Frankia sp. strain Thr, a nitrogen-fixing acti-nobacterium isolated from the root nodules of Casuarina cunninghami-ana grown in Egypt. Genome Announc 2(3):e00493-14. http://dx.doi.org/10.1128/genomeA.00493-14.18. Ghodhbane-Gtari F, Hurst IV SG, Oshone R, Morris K, Abebe-Akele F,Thomas WK, Ktari A, Salem K, Gtari M, Tisa LS. 2014. Draft genomesequence of Frankia sp. strain BMG5.23, a salt-tolerant nitrogen-fixingactinobacterium isolated from the root nodules of Casuarina glaucagrown in Tunisia. Genome Announc 2(3):e00520-14. http://dx.doi.org/10.1128/genomeA.00520-14.19. Tisa LS, Beauchemin N, Gtari M, Sen A, Wall LG. 2013. What stories canthe Frankia genomes start to tell us? J Biosci 38:719 –726. http://dx.doi.org/10.1007/s12038-013-9364-1.20. Gtari M, Ghodhbane-Gtari F, Nouioui I, Ktari A, Hezbri K, MimouniW, Sbissi I, Ayari A, Yamanaka T, Normand P, Tisa LS, Boudabous A.2015. Cultivating the uncultured: growing the recalcitrant cluster-2Frankia strains. Sci Rep 5:13112. http://dx.doi.org/10.1038/srep13112.21. Tisa LS, Beauchemin N, Cantor MN, Furnholm T, Ghodhbane-Gtari F,Goodwin L, Copeland A, Gtari M, Huntemann M, Ivanova N, KyrpidesN, Markowitz V, Mavrommatis K, Mikhailova N, Nouioui I, Oshone R,Ovchinnikova G, Pagani I, Palaniappan K, Pati A. 2015. Draft genomesequence of Frankia sp. strain DC12, an atypical, noninfective, ineffectiveisolate fromDatisca cannabina. Genome Announc 3(4):e00889-15. http://dx.doi.org/10.1128/genomeA.00889-15.22. Baker D, Torrey JG, Kidd GH. 1979. Isolation by sucrose-density frac-tionation and cultivation in vitro of actinomycetes from nitrogen-fixingroot nodules. Nature 281:76 –78. http://dx.doi.org/10.1038/281076a0.23. Lalonde M, Calvert HE, Pine S. 1981. Isolation and use of Frankia strainsin actinorhizae formation, p 296 –299. In Gibson AH, Newton WE (ed),Current perspectives in nitrogen fixation. Australian Academy of Science,Canberra, Australia.24. Bennett S. 2004. Solexa Ltd. Pharmacogenomics 5:433– 438. http://dx.doi.org/10.1517/14622416.5.4.433.25. Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, WalkerBJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M,Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, JaffeDB. 2011. High-quality draft assemblies of mammalian genomes frommassively parallel sequence data. Proc Natl Acad Sci USA 108:1513–1518.http://dx.doi.org/10.1073/pnas.1017351108.26. Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G,Padki A, Zhao XL, Dubchak I, Hugenholtz P, Anderson I, Lykidis A,Mavromatis K, Ivanova N, Kyrpides NC. 2006. The integrated microbialgenomes (IMG) system. Nucleic Acids Res 34:D344 –D348. http://dx.doi.org/10.1093/nar/gkj024.27. Markowitz VM, Mavromatis K, Ivanova NN, Chen IA, Chu K, KyrpidesNC. 2009. IMG ER: a system for microbial genome annotation expertreview and curation. Bioinformatics 25:2271–2278. http://dx.doi.org/10.1093/bioinformatics/btp393.Swanson et al.Genome Announcements2 genomea.asm.org November/December 2015 Volume 3 Issue 6 e01483-15 on January 29, 2018 by UNIVERSITY OF NEW HAMPSHIRE LIBRARYhttp://genomea.asm.org/Downloaded from 

Permanent Draft Genome Sequence of Frankia sp. Strain ACN1ag, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Alnus glutinosa

http://dx.doi.org/10.1128/genomeA.01483-15

Permanent Draft Genome Sequence of Frankia sp. Strain ACN1ag, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Alnus glutinosa

Abstract

Similar works

Full text

Available Versions

UNH Scholars' Repository

Crossref

UNH Scholars' Repository