Frankia stains CpI1-S and CpI1-P are members of Frankia lineage Ia that are able to reinfect plants of the Betulaceae and Myricaceae families. Here, we report two 7.6-Mbp draft genome sequences with 6,396 and 6,373 candidate protein-coding genes for CpI1-S and CpI1-P, respectively

Abebe-Akele, Feseha

Hurst, Sheldon G., IV

Morris, Krystalynne

Oshone, Rediet

Simpson, Stephen

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 Programs1-14-2016Permanent draft genome sequences for twovariants of Frankia sp. strain CpI1, the first Frankiastrain isolated from root nodules of ComptoniaperegrinaRediet OshoneUniversity of New Hampshire, DurhamSheldon G. Hurst IVUniversity of New Hampshire, DurhamFeseha Abebe-AkeleUniversity of New Hampshire, DurhamStephen D. SimpsonUniversity of New Hampshire, Durham, Stephen.Simpson@unh.eduKrystalynne MorrisUniversity of New Hampshire, Durham, Krystalynne.Morris@unh.eduSee 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 CitationOshone R, Hurst SG, IV, Abebe-Akele F, Simpson S, Morris K, Thomas WK, Tisa LS. 2016. Permanent draft genome sequences fortwo variants of Frankia sp. strain CpI1, the first Frankia strain isolated from root nodules of Comptonia peregrina. Genome Announc4(1):e01588-15. https://dx.doi.org/10.1128/genomeA.01588-15AuthorsRediet Oshone, Sheldon G. Hurst IV, Feseha Abebe-Akele, Stephen D. Simpson, Krystalynne Morris, WilliamKelley Thomas, and Louis S. TisaThis article is available at University of New Hampshire Scholars' Repository: https://scholars.unh.edu/nhaes/372Permanent Draft Genome Sequences for Two Variants of Frankia sp.Strain CpI1, the First Frankia Strain Isolated from Root Nodules ofComptonia peregrinaRediet Oshone, Sheldon G. Hurst IV, Feseha Abebe-Akele, Stephen Simpson, Krystalynne Morris, W. Kelley Thomas, Louis S. TisaUniversity of New Hampshire, Durham, New Hampshire, USAFrankia stains CpI1-S and CpI1-P are members of Frankia lineage Ia that are able to reinfect plants of the Betulaceae andMyri-caceae families. Here, we report two 7.6-Mbp draft genome sequences with 6,396 and 6,373 candidate protein-coding genes forCpI1-S and CpI1-P, respectively.Received 17 November 2015 Accepted 18 November 2015 Published 14 January 2016Citation Oshone R, Hurst SG, IV, Abebe-Akele F, Simpson S, Morris K, Thomas WK, Tisa LS. 2016. Permanent draft genome sequences for two variants of Frankia sp. strain CpI1,the first Frankia strain isolated from root nodules of Comptonia peregrina. Genome Announc 4(1):e01588-15. doi:10.1128/genomeA.01588-15.Copyright © 2016 Oshone 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.Actinorhizal symbiosis is the association between an actinobac-terium from the genus Frankia and a wide variety of dicoty-ledonous plants representing 8 different families of angiosperms,resulting in the formation of root nodule structure (1–3). Thesymbiosis allows these ecologically important pioneer plants tocolonize harsh environments that are found worldwide (4). Mo-lecular phylogenetic approaches have identified four majorFrankia lineages (5–8). Cluster I contains two subclusters: onesubcluster (cluster Ia) represents Frankia strains with the ability toinfect a wider range of host plants, including members of theBetu-laceae and Myricaceae families, and the other subcluster (clusterIb) contains strains limited to Casuarina and Allocasuarina hostplants. Members of cluster II infect host plants of the subfamilyDryadoideae (Rosaceae), Coriariaceae, and Datiscaceae, and of thegenus Ceanothus (Rhamnaceae). The members of cluster III arethe most promiscuous and infect Elaeagnaceae, Rhamnaceae,Myricaceae,Gymnostoma (Casuarinaceae), and occasionallyAlnusspecies. The fourth Frankia lineage consists of the atypical strains,which are unable to reinfect actinorhizal host plants or form inef-fective root nodule structures that are unable to fix nitrogen. Thegenomes for representatives from each cluster have been se-quenced (9–24).In 1978, the first Frankia isolate, CpI1, was obtained from rootnodules of Comptonia peregrina and fulfilled Koch’s postulates(25). Following this initial success, many other strains from dif-ferent host plants have been isolated, including the recent isola-tion of a member of cluster II (20). Two variants of Frankia sp.strain CpI1 were identified that had different carbon source re-quirements for growth. The Frankia sp. strain CpI1 succinate vari-ant (CpI1-S) will use succinate and other dicarboxylic acids forgrowth, while the Frankia sp. strain CpI1 propionate variant(CpI1-P) will not (26). These two variants also show differences intheir heavy metal tolerances and antibiotic resistance patterns (27,28). Frankia sp. strains CpI1-S and CpI1-P were chosen for se-quencing to provide more information on the differences betweenthese two variants.The draft genome sequences of Frankia sp. strains CpI1-S andCpI1-P were generated at the Hubbard Genome Center (Univer-sity of New Hampshire, Durham, NH) using Illumina technologytechniques (29). A standard Illumina shotgun library was con-structed and sequenced using the Illumina HiSeq 2000 platform,which generated 10,867,000 reads (260-bp insert size) totaling1,628.6 Mbp for CpI1-S and 20,978,588 reads (260-bp insert size)totaling 3,146.7 Mbp for CpI1-P. The Illumina sequence data wereassembled using CLC Genomics Workbench (version 8.0.1) andAllPaths-LG (version r41043) (30). The final draft assembly forFrankia sp. CpI1-S consisted of 153 contigs containing a totalsequence of 7,614,630 bp, with an N50 contig size of 99.4 kb and206.3 coverage of the genome. For Frankia sp. CpI1-P, the finaldraft assembly consisted of 181 contigs containing 7,593,325 bp,with an N50 contig size of 98.1 kb and 287 coverage of the ge-nome.The assembled Frankia sp. CpI1-S and CpI1-P genomes wereannotated via the Integrated Microbial Genomes (IMG) platformdeveloped by the Joint Genome Institute, Walnut Creek, CA, USA(31, 32), and resulted in 6,396 and 6,373 candidate protein-codinggenes for strains CpI1-S and CpI1-P, respectively.Nucleotide sequence accessionnumbers.This whole-genomeshotgun project has been deposited at DDBJ/EMBL/GenBank un-der the accession numbers JYFN00000000 (CpI1-S) andLJJX00000000 (CpI1-P). The versions described in this paper areversions JYFN01000000 and LJJX01000000, respectively.ACKNOWLEDGMENTSPartial funding was provided by the New Hampshire Agricultural Exper-iment Station. This is Scientific Contribution no. 2641. This work wassupported by the USDA National Institute of Food and Agriculture Hatch022821 (to L.S.T.), Agriculture and Food Research Initiative grant 2015-67014-22849 from the USDA National Institute of Food and Agriculture(to L.S.T.), and the College of Life Science and Agriculture at the Univer-sity of New Hampshire-Durham. Sequencing was performed on an Illu-mina HiSeq 2500 purchased with an NSF MRI grant DBI-1229361toW.K.T.crossmarkGenome AnnouncementsJanuary/February 2016 Volume 4 Issue 1 e01588-15 genomea.asm.org 1 on January 26, 2016 by UNIV OF NEW HAMPSHIRE LIBRARYhttp://genomea.asm.org/Downloaded from FUNDING INFORMATIONThe National Science Foundation (NSF) provided funding to W. KelleyThomas under grant number DBI-122936. USDA | The National Instituteof Food and Agriculture (NIFA) provided funding to Louis S. Tisa undergrant numbers Hatch 02281 and 2015-67014-22849.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 prokaryotes—Actinobacteria, 4th ed. Springer-Verlag,Berlin, 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 –34.7. 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– 495.9. 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, WoykeI, 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 LG, Woyke T, Tisa LS. 2013. Draft genome sequence ofFrankia sp. strain CN3, an atypical, non-infective (Nod-) ineffective (Fix-)isolate from Coriaria nepalensis. Genome Announc 1(2):00085-13. 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, Goodwin L, Gtari M, Han C,Han J, Huntemann M, Ivanova N, Kyrpides N, Land ML, Markowitz V,Mavrommatis K, Nolan M, Nouioui I, Pagani I, Pati A, Pitluck S,Santos CL, Sur S, Szeto E, Tavares F, Teshima H, Thakur S, Wall LG,Woyke T, Tisa LS. 2013. Draft genome sequence of Frankia sp. strainQA3, a nitrogen-fixing actinobacterium isolated from the 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 Announc 1: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, HanJ, Huntemann M, Hua SX, Ivanova N, Kyrpides N, Markowitz V,Mavrommatis K, Mikhailova N, Nordberg HP, Nouioui I, Ovchin-nikova 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. strainBCU110501, a nitrogen-fixing actinobacterium isolated from nodulesof Discaria trinevis. Genome Announc 1(4): http://dx.doi.org/10.1128/genomeA.00503-13.16. Mansour SR, Oshone R, Hurst SG, IV, 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 SG, IV, 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): http://dx.doi.org/10.1128/genomeA.00493-14.18. Ghodhbane-Gtari F, Hurst SG, IV, 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, Mi-mouni W, Sbissi I, Ayari A, Yamanaka T, Normand P, Tisa LS,Boudabous A. 2015. Cultivating the uncultured: growing the recalci-trant cluster-2 Frankia 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 LL, Copeland A, Gtari M, Huntemann M, Ivanova N, Kyrpi-des N, Markowitz V, Mavrommatis K, Mikhailova N, Nouioui I, Os-hone R, Ovchinnikova G, Pagani I, Palaniappan K, Pati A, Sen A,Shapiro N, Szeto E, Wall LG, Wishart J, Woyke T. 2015. Draft genomesequence of Frankia sp. strain DC12, an atypical, non-infective, ineffectiveisolate fromDatisca cannabina. Genome Announc 3(4):e00889-15. http://dx.doi.org/10.1128/genomeA.00889-15.22. Swanson E, Oshone R, Simpson S, Morris K, Abebe-Akele F, ThomasWK, Tisa TLS. 2015. Draft genome sequence of Frankia sp. strainACN1ag, a nitrogen-fixing actinobacterium isolated from the root noduleof Alnus glutinosa. Genome Announc 3:e01483-15. http://dx.doi.org/10.1128/genomeA.01483-15.23. Swanson E, Oshone R, Simpson S, Morris K, Abebe-Akele F, ThomasWK, Tisa TLS. 2015. Permanent draft genome sequence of Frankia sp.strain avci1, a nitrogen-fixing actinobacterium isolated from the rootnodule of Alnus viridis ssp. crispa grown in Canada. Genome Announc3:. http://dx.doi.org/10.1128/genomeA.01511-15.24. Pujic P, Bolotin A, Fournier P, Sorokin A, Lapidus A, Richau KH,Briolay J, Mebarki F, Normand P, Sellstedt A. 2015. Genome sequenceof the atypical symbiotic Frankia R43 strain, a nitrogen-fixing andhydrogen-evolving actinobacterium. Genome Announc 3:e01387-15.http://dx.doi.org/10.1128/genomeA.01387-15.25. Callaham D, Deltredici P, Torrey JG. 1978. Isolation and cultivation invitro of the actinomycete causing root nodulation in Comptonia. Science199:899 –902. http://dx.doi.org/10.1126/science.199.4331.899.26. Tisa L, McBride M, Ensign JC. 1983. Studies of growth and morphologyof Frankia strains EAN1pec, EuI1c, CpI1 and ACN1AG. Can J Bot 61:2768 –2773. http://dx.doi.org/10.1139/b83-306.27. Tisa LS, Chval MS, Krumholz GD, Richards J. 1999. Antibiotic resis-tance patterns of Frankia strains. Can J Bot 77:1257–1260.Oshone et al.Genome Announcements2 genomea.asm.org January/February 2016 Volume 4 Issue 1 e01588-15 on January 26, 2016 by UNIV OF NEW HAMPSHIRE LIBRARYhttp://genomea.asm.org/Downloaded from 28. Richards JW, Krumholz GD, Chval MS, Tisa LS. 2002. Heavy metalresistance patterns of Frankia strains. Appl Environ Microbiol 68:923–927.29. Bennett S. 2004. Solexa Ltd. Pharmacogenomics 5:433– 438. http://dx.doi.org/10.1517/14622416.5.4.433.30. Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, WalkerBJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, CostelloM, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES,Jaffe DB. 2011. High– quality draft assemblies of mammalian genomesfrom massively parallel sequence data. Proc Natl Acad Sci USA 108:1513–1518. http://dx.doi.org/10.1073/pnas.1017351108.31. 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/gkj024.32. Markowitz VM, Mavromatis K, Ivanova NN, Chen IA, Chu K, KyrpidesNC. 2009. IMG er: a system for microbial genome annotation expert re-view and curation. Bioinformatics 25:2271–2278. http://dx.doi.org/10.1093/bioinformatics/btp393.Genome AnnouncementGenome AnnouncementsJanuary/February 2016 Volume 4 Issue 1 e01588-15 genomea.asm.org 3 on January 26, 2016 by UNIV OF NEW HAMPSHIRE LIBRARYhttp://genomea.asm.org/Downloaded from 

Permanent draft genome sequences for two variants of Frankia sp. strain CpI1, the first Frankia strain isolated from root nodules of Comptonia peregrina

ABSTRACT
 
 Frankia
 stains CpI1-S and CpI1-P are members of
 Frankia
 lineage Ia that are able to reinfect plants of the
 Betulaceae
 and
 Myricaceae
 families. Here, we report two 7.6-Mbp draft genome sequences with 6,396 and 6,373 candidate protein-coding genes for CpI1-S and CpI1-P, respectively.
 </jats:p

Rediet Oshone

Sheldon G. Hurst

Feseha Abebe-Akele

Stephen Simpson

Krystalynne Morris

W. Kelley Thomas

Louis S. Tisa

Crossref

Genome Announcements

Permanent Draft Genome Sequences for Two Variants of
 Frankia
 sp. Strain CpI1, the First
 Frankia
 Strain Isolated from Root Nodules of
 Comptonia peregrina

University of New HampshireUniversity of New Hampshire Scholars' RepositoryMolecular, Cellular and Biomedical SciencesScholarship Molecular, Cellular and Biomedical Sciences1-14-2016Permanent Draft Genome Sequences for TwoVariants of Frankia sp. Strain CpI1, the First FrankiaStrain Isolated from Root Nodules of ComptoniaperegrinaRediet OshoneUniversity of New Hampshire, DurhamSheldon G. Hurst IVUniversity of New Hampshire, DurhamFeseha Abebe-AkeleUniversity of New Hampshire, DurhamStephen SimpsonUniversity of New Hampshire, DurhamKrystalynne MorrisUniversity 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 CitationOshone, R. S. Hurst IV, F. Abebe-Akele, S. Simpson, K. Morris, W. K. Thomas, and L. S. Tisa. 2016. Permeant draft genome sequencesfor two variants of Frankia sp. strain CpI1, the first Frankia strain isolated from the root nodule of Comptonia peregrina. GenomeAnnounc. 4(1):e01588-15 (doi: 10.1128/genomeA.01588-15).AuthorsRediet Oshone, Sheldon G. Hurst IV, Feseha Abebe-Akele, Stephen Simpson, Krystalynne Morris, W. KelleyThomas, and Louis S. TisaThis article is available at University of New Hampshire Scholars' Repository: https://scholars.unh.edu/mcbs_facpub/162Permanent Draft Genome Sequences for Two Variants of Frankia sp.Strain CpI1, the First Frankia Strain Isolated from Root Nodules ofComptonia peregrinaRediet Oshone, Sheldon G. Hurst IV, Feseha Abebe-Akele, Stephen Simpson, Krystalynne Morris, W. Kelley Thomas, Louis S. TisaUniversity of New Hampshire, Durham, New Hampshire, USAFrankia stains CpI1-S and CpI1-P are members of Frankia lineage Ia that are able to reinfect plants of the Betulaceae andMyri-caceae families. Here, we report two 7.6-Mbp draft genome sequences with 6,396 and 6,373 candidate protein-coding genes forCpI1-S and CpI1-P, respectively.Received 17 November 2015 Accepted 18 November 2015 Published 14 January 2016Citation Oshone R, Hurst SG, IV, Abebe-Akele F, Simpson S, Morris K, Thomas WK, Tisa LS. 2016. Permanent draft genome sequences for two variants of Frankia sp. strain CpI1,the first Frankia strain isolated from root nodules of Comptonia peregrina. Genome Announc 4(1):e01588-15. doi:10.1128/genomeA.01588-15.Copyright © 2016 Oshone 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.Actinorhizal symbiosis is the association between an actinobac-terium from the genus Frankia and a wide variety of dicoty-ledonous plants representing 8 different families of angiosperms,resulting in the formation of root nodule structure (1–3). Thesymbiosis allows these ecologically important pioneer plants tocolonize harsh environments that are found worldwide (4). Mo-lecular phylogenetic approaches have identified four majorFrankia lineages (5–8). Cluster I contains two subclusters: onesubcluster (cluster Ia) represents Frankia strains with the ability toinfect a wider range of host plants, including members of theBetu-laceae and Myricaceae families, and the other subcluster (clusterIb) contains strains limited to Casuarina and Allocasuarina hostplants. Members of cluster II infect host plants of the subfamilyDryadoideae (Rosaceae), Coriariaceae, and Datiscaceae, and of thegenus Ceanothus (Rhamnaceae). The members of cluster III arethe most promiscuous and infect Elaeagnaceae, Rhamnaceae,Myricaceae,Gymnostoma (Casuarinaceae), and occasionallyAlnusspecies. The fourth Frankia lineage consists of the atypical strains,which are unable to reinfect actinorhizal host plants or form inef-fective root nodule structures that are unable to fix nitrogen. Thegenomes for representatives from each cluster have been se-quenced (9–24).In 1978, the first Frankia isolate, CpI1, was obtained from rootnodules of Comptonia peregrina and fulfilled Koch’s postulates(25). Following this initial success, many other strains from dif-ferent host plants have been isolated, including the recent isola-tion of a member of cluster II (20). Two variants of Frankia sp.strain CpI1 were identified that had different carbon source re-quirements for growth. The Frankia sp. strain CpI1 succinate vari-ant (CpI1-S) will use succinate and other dicarboxylic acids forgrowth, while the Frankia sp. strain CpI1 propionate variant(CpI1-P) will not (26). These two variants also show differences intheir heavy metal tolerances and antibiotic resistance patterns (27,28). Frankia sp. strains CpI1-S and CpI1-P were chosen for se-quencing to provide more information on the differences betweenthese two variants.The draft genome sequences of Frankia sp. strains CpI1-S andCpI1-P were generated at the Hubbard Genome Center (Univer-sity of New Hampshire, Durham, NH) using Illumina technologytechniques (29). A standard Illumina shotgun library was con-structed and sequenced using the Illumina HiSeq 2000 platform,which generated 10,867,000 reads (260-bp insert size) totaling1,628.6 Mbp for CpI1-S and 20,978,588 reads (260-bp insert size)totaling 3,146.7 Mbp for CpI1-P. The Illumina sequence data wereassembled using CLC Genomics Workbench (version 8.0.1) andAllPaths-LG (version r41043) (30). The final draft assembly forFrankia sp. CpI1-S consisted of 153 contigs containing a totalsequence of 7,614,630 bp, with an N50 contig size of 99.4 kb and206.3 coverage of the genome. For Frankia sp. CpI1-P, the finaldraft assembly consisted of 181 contigs containing 7,593,325 bp,with an N50 contig size of 98.1 kb and 287 coverage of the ge-nome.The assembled Frankia sp. CpI1-S and CpI1-P genomes wereannotated via the Integrated Microbial Genomes (IMG) platformdeveloped by the Joint Genome Institute, Walnut Creek, CA, USA(31, 32), and resulted in 6,396 and 6,373 candidate protein-codinggenes for strains CpI1-S and CpI1-P, respectively.Nucleotide sequence accessionnumbers.This whole-genomeshotgun project has been deposited at DDBJ/EMBL/GenBank un-der the accession numbers JYFN00000000 (CpI1-S) andLJJX00000000 (CpI1-P). The versions described in this paper areversions JYFN01000000 and LJJX01000000, respectively.ACKNOWLEDGMENTSPartial funding was provided by the New Hampshire Agricultural Exper-iment Station. This is Scientific Contribution no. 2641. This work wassupported by the USDA National Institute of Food and Agriculture Hatch022821 (to L.S.T.), Agriculture and Food Research Initiative grant 2015-67014-22849 from the USDA National Institute of Food and Agriculture(to L.S.T.), and the College of Life Science and Agriculture at the Univer-sity of New Hampshire-Durham. Sequencing was performed on an Illu-mina HiSeq 2500 purchased with an NSF MRI grant DBI-1229361toW.K.T.crossmarkGenome AnnouncementsJanuary/February 2016 Volume 4 Issue 1 e01588-15 genomea.asm.org 1 on January 29, 2018 by UNIVERSITY OF NEW HAMPSHIRE LIBRARYhttp://genomea.asm.org/Downloaded from FUNDING INFORMATIONThe National Science Foundation (NSF) provided funding to W. KelleyThomas under grant number DBI-122936. 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Permanent Draft Genome Sequences for Two Variants of Frankia sp. Strain CpI1, the First Frankia Strain Isolated from Root Nodules of Comptonia peregrina

http://dx.doi.org/10.1128/genomeA.01588-15

Permanent Draft Genome Sequences for Two Variants of Frankia sp. Strain CpI1, the First Frankia Strain Isolated from Root Nodules of Comptonia peregrina

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