# Permanent Draft Genome Sequence for Frankia sp. Strain CeD, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equistifolia Grown in Senegal.

Mariama Ngom, Rediet Oshone, Sheldon G Hurst, Feseha Abebe-Akele, Stephen Simpson, Krystalynne Morris, Mame Ourèye Sy, Antony Champion, W. Kelley Kelley Thomas, Louis S Tisa

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Mariama Ngom, Rediet Oshone, Sheldon G Hurst, Feseha Abebe-Akele, Stephen Simpson, et al. Permanent Draft Genome Sequence for Frankia sp. Strain CeD, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equistifolia Grown in Senegal. Genome Announcements, 2016, 4 (2), pp.e00265-16. 10.1128/genomeA.00265-16. hal-03182868

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# Permanent Draft Genome Sequence for *Frankia* sp. Strain CeD, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of *Casuarina equistifolia* Grown in Senegal

Mariama Ngom,ª,ᵇ,ᶜ,ᵈ Rediet Oshone,ª Sheldon G. Hurst IV,ª Feseha Abebe-Akele,ª Stephen Simpson,ª Krystalynne Morris,ª Mame Ourèye Sy,ᵇ,ᶜ Antony Champion,ᵇ,ᵈ,ᵉ W. Kelley Thomas,ª Louis S. Tisaª

University of New Hampshire, Durham, New Hampshire, USAª; Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégalᵇ; Département de Biologie Végétale, Laboratoire Campus de Biotechnologies Végétales, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Dakar-Fann, Sénégalᶜ; Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Centre de Recherche de Bel Air, Dakar, Sénégalᵈ; Institut de Recherche pour le Développement (IRD), UMR DIADE, Montpellier, Franceᵉ

This article is New Hampshire Agricultural Experiment Station scientific contribution 2656.

*Frankia* strain CeD is a member of *Frankia* lineage Ib that is able to reinfect plants of the *Casuarina* families. Here, we report a 5.0-Mbp draft genome sequence with a G+C content of 70.1% and 3,847 candidate protein-encoding genes.

**Received** 23 February 2016 **Accepted** 24 February 2016 **Published** 7 April 2016

**Citation** Ngom M, Oshone R, Hurst SG, IV, Abebe-Akele F, Simpson S, Morris K, Sy MO, Champion A, Thomas WK, Tisa LS. 2016. Permanent draft genome sequence for *Frankia* sp. strain CeD, a nitrogen-fixing actinobacterium isolated from the root nodules of *Casuarina equistifolia* grown in Senegal. Genome Announc 4(2):e00265-16. doi:10.1128/ genomeA.00265-16.

**Copyright** © 2016 Ngom et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Louis S. Tisa, louis.tisa@unh.edu.

Members of the genus *Frankia* are soil-dwelling actinobacteria that are well known for their facultative lifestyle as a plant symbiont of dicotyledonous plants, termed actinorhizal plants (1–3). As ecologically important pioneer community plants, actinorhizal plants are found worldwide in a broad range of ecological and environmental conditions (4). The symbiosis allows actinorhizal plants to colonize harsh environmental terrains.

Based on molecular phylogenetic analysis, four major clusters within the genus are recognized (5–8) and genomes for representatives from each cluster have been sequenced (9–24). Cluster I contains two subclusters: One subcluster (cluster Ia) represents *Frankia* strains with the ability to infect a wider range of host plants including member of the *Betulaceae* and *Myricaceae* families, and the other subcluster (cluster Ib) contains strains limited to *Casuarina* and *Allocasuarina* host plants. Members of cluster II infect host plants of the subfamily *Dryadoideae* (*Rosaceae*), the families *Coriariaceae* and *Datiscaceae*, and the genus *Ceanothus* (*Rhamnaceae*). Members of cluster III are the most promiscuous and are infective on *Eleagnaceae*, *Rhamnaceae*, *Myricaceae*, *Gynmostoma* (*Casuarinaceae*), and occasionally *Alnus*. The fourth *Frankia* lineage consists of the “atypical” strains which are unable to reinfect actinorhizal host plants or form ineffective root nodule structures that are unable to fix nitrogen.

Under tropic and subtropic conditions, fast growing and highly tolerant trees from the family *Casuarinaceae* have been used as windbreaks, dune stabilizers, fuel wood, and soil regeneration and these actinorhizal plants grow well under the harsh conditions including high salinity (25). *Frankia* sp. strain CeD was isolated from root nodules of *Casuarina equistifolia* growing in Senegal and effectively reinfects its original host plant, *Casuarina* spp. (26). *Frankia* sp. strain CeD has been used extensively in

infection studies and is well characterized for its host plant interactions (27).

The draft genome of *Frankia* sp. strain CeD was generated at the Hubbard Genome Center (University of New Hampshire, Durham, NH, USA) using Illumina technology (28) techniques. A standard Illumina shotgun library was constructed and sequenced using the Illumina HiSeq2000 platform, which generated 29,802,574 reads (260 bp insert size) totaling 4,381.0 Mbp. The Illumina sequence data were assembled using CLC Genomics Workbench (8.0.1) and AllPaths-LG (version r41043) (29). The final draft assembly for *Frankia* CeD consisted of 154 contigs in 120 scaffolds containing a total sequence of 5,004,600 bp with an N<sub>50</sub> contig size of 73.6 kb and G+C content of 70.1%. This assembled draft resulted in 703× coverage of the genome.

The assembled *Frankia* sp. strain CeD genome was annotated via the Integrated Microbial Genomes (IMG) platform developed by the Joint Genome Institute, Walnut Creek, CA, USA (30, 31) and resulted in 3,847 candidate protein-encoding genes, 45 tRNA, and 2 rRNA regions.

**Nucleotide sequence accession numbers.** This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number *JPGU00000000*. The version described in this paper is version *JPGU01000000*.

## ACKNOWLEDGMENTS

Partial funding was provided by the New Hampshire Agricultural Experiment Station. This work was also supported by the USDA National Institute of Food and Agriculture Hatch 022821 (L.S.T.), Agriculture and Food Research Initiative Grant 2015-67014-22849 from the USDA National Institute of Food and Agriculture (L.S.T.), and the College of Life Science and Agriculture at the University of New Hampshire–Durham. M.N. was supported by an ARTS (Allocation de Recherche pour une
Thèse au Sud) Ph.D. grant from the IRD (Institut de recherche pour le développement). Sequencing was performed on an Illumina HiSeq2500 purchased with NSF MRI grant DBI-1229361to W.K.T.

## FUNDING INFORMATION

This work, including the efforts of Mariama Ngom, was funded by Institut de Recherche pour le Developpement (ARTS [Allocation de Recherche pour une Thèse au Sud]). This work, including the efforts of W. Kelley Thomas, was funded by National Science Foundation (NSF) (DBI-1229361). This work, including the efforts of Louis S. Tisa, was funded by USDA | National Institute of Food and Agriculture (NIFA) (Hatch 022821 and 2015-67014-22849).

## REFERENCES

1. Chaia EE, Wall LG, Huss-Danell K. 2010. Life in soil by actinorhizal root nodule endophyte *Frankia*. A review. Symbiosis 51:201-226. http://dx.doi.org/10.1007/s13199-010-0086-y.

2. Normand P, Benson DR, Berry AM, Tisa LS. 2014. Family *Frankiaceae*, p. 339-356. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (ed), The prokaryote—Actinobacteria, 4th ed. Springer-Verlag Berlin Heidelberg.

3. Schwencke J, Carú M. 2001. Advances in actinorhizal symbiosis: host plant-*Frankia* interactions, biology, and applications in arid land reclamation. A review. Arid Land Res Manag 15:285-327. http://dx.doi.org/10.1080/153249801753127615.

4. Benson DR, Dawson JO. 2007. Recent advances in the biogeography and genealogy 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 JO, Evtushenko L, Misra AK. 1996. Molecular phylogeny of the genus *Frankia* and related genera and emendation of the family *Frankiaceae*. Int J 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 radiation using *glnII* sequences. FEMS Microbiol Lett 177:29-34.

7. Nououi I, Ghodbane-Gtari F, Beauchemin NJ, Tisa LS, Gtari M. 2011. Phylogeny of members of the *Frankia* genus based on gyrB, nifH and *glnII* sequences. Ant Van Leeuw 100:579-587. http://dx.doi.org/10.1007/s10482-011-9613-y.

8. Ghodbane-Gtari F, Nououi 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. Ghodbane-Gtari F, Beauchemin N, Bruce D, Chain P, Chen A, Walston Davenport K, 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, Nououi I, Pagani I, Pati A, 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 of *Frankia* sp. strain CN3, an atypical, noninfective (nod⁻) ineffective (fix⁻) isolate from *Coriaria nepalensis*. Genome Announc 1(2):00085-13. http://dx.doi.org/10.1128/genomeA.00085-13.

10. Ghodbane-Gtari F, Hurst SG, IV, Oshone R, Morris K, Abebe-Akele F, Thomas WK, Ktari A, Salem K, Gtari M, Tisa LS. 2014. Draft genome sequence of *Frankia* sp. strain BMG5.23, a salt-tolerant nitrogen-fixing actinobacterium isolated from the root nodules of *Casuarina glauca* grown in Tunisia. Genome Announc 2(3):e00520-14. http://dx.doi.org/10.1128/genomeA.00520-14.

11. Gtari M, Ghodbane-Gtari F, Nououi I, Ktari A, Hezbri K, Minouni W, Sbissi I, Ayari A, Sghaier H, Normand P, Tisa LS, Yamanaka T, Boudabous A. 2015. Cultivating the uncultured: growing the recalcitrant cluster-2 *Frankia* strains. Sci Rep 5:13112. http://dx.doi.org/10.1038/srep13112.

12. Hurst SG, IV, Ghodbane-Gtari F, Oshone R, 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 actinobacterium isolated from the root nodules of *Casuarina cunninghamiana* grown in Egypt. Genome Announc 2(3): http://dx.doi.org/10.1128/genomeA.00493-14.

13. Mansour SR, Oshone R, Hurst SG, IV, Morris K, Thomas WK, Tisa LS. 2014. Draft genome sequence of *Frankia* sp. strain Ccl6, a salt-tolerant nitrogen-fixing actinobacterium isolated from the root nodule of *Casuarina cunninghamiana*. Genome Announc 2(1): http://dx.doi.org/10.1128/genomeA.01205-13.

14. Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, Cournoyer B, 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, Rawnsley 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. strains reflect host range and host plant biogeography. Genome Res 17:7-15.

15. Nououi I, Beauchemin N, Cantor MN, Chen A, Detter JC, Furnholm T, Ghodbane-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, Ovchinnikova G. 2013. Draft genome sequence of *Frankia* sp. strain BMG5.12, a nitrogen-fixing actinobacterium isolated from Tunisian soils. Genome Announc 1(4): http://dx.doi.org/10.1128/genomeA.00468-13.

16. Oshone R, Hurst SG, IV, Abebe-Akele F, Simpson S, Morris K, Thomas WK, Tisa LS. 2016. Permeant draft genome sequences for two variants of *Frankia* sp. strain Cp11, the first *Frankia* strain isolated from the root nodule of *Comptonia peregrina*. Genome Announc 4(1):e01588-15. http://dx.doi.org/10.1128/genomeA.01588-15.

17. Persson T, Benson DR, Normand P, Vanden Heuvel B, Pujic P, Chertkov O, Teshima H, Bruce DC, Detter C, Tapia R, Han S, Han J, Woyke T, Pitlock S, Pennacchio L, Nolan M, Ivanova N, Pati A, Land ML, Pawlowski K, Berry AM. 2011. Genome sequence of "Candidatus Frankia datiscae" Dg1, the uncultured microsymbiont from nitrogen-fixing root nodules of the dicot *Datisca glomerata*. J Bacteriol 193:7017-7018. http://dx.doi.org/10.1128/JB.06208-11.

18. Pujic P, Bolotin A, Fournier P, Sorokin A, Lapidus A, Richau KH, Briolay J, Mebarki F, Normand P, Sellstedt A. 2105. Genome sequence of the atypical symbiotic *Frankia* R43 strain, a nitrogen-fixing and hydrogen-evolving actinobacterium. Genome Announc 3(6):e01387-15. http://dx.doi.org/10.1128/genomeA.01387-15.

19. Sen A, Beauchemin N, Bruce D, Chain P, Chen A, Walston Davenport K, Deshpande S, Detter C, Furnholm T, Ghodbane-Gtari F, Goodwin L, Gtari M, Han C, Han J, Huntemann M, Ivanova N, Kyrpides N, Land ML, Markowitz V, Mavrommatis K, Nolan M, Nououi I, Pagani I, Pati A, Pitluck S, Santos CL, Sur S, Szeto E, Tavares F, Teshima H, Thakur S, Wall L, Wishart J, Woyke T, Tisa LS. 2013. Draft genome sequence of *Frankia* sp. strain QA3, a nitrogen-fixing actinobacterium isolated from the root nodule of *Alnus nitida*. Genome Announc 1(2):e00103-13. http://dx.doi.org/10.1128/genomeA.00103-13.

20. Swanson E, Oshone R, Simpson S, Morris K, Abebe-Akele F, Thomas WK, Tisa TLS. 2015. Draft genome sequence of *Frankia* sp. strain ACN1ag, a nitrogen-fixing actinobacterium isolated from the root nodule of *Alnus glutinosa*. Genome Announc 3(6):e01483-15. http://dx.doi.org/10.1128/genomeA.01483-15.

21. Swanson E, Oshone R, Simpson S, Morris K, Abebe-Akele F, Thomas WK, Tisa LS. 2015. Permeant draft genome sequence of *Frankia* sp. strain Avc11, a nitrogen-fixing actinobacterium isolated from the root nodule of *Alnus viridis* ssp. crispa grown in Canada. Genome Announc 3(6):e01511-15. http://dx.doi.org/10.1128/genomeA.01511-15.

22. Tisa LS, Beauchemin N, Gtari M, Sen A, Wall LG. 2013. What stories can the *Frankia* genomes start to tell us? J Biosci 38:719-726. http://dx.doi.org/10.1007/s12038-013-9364-1.

23. Tisa LS, Beauchemin N, Cantor MN, Furnholm T, Ghodbane-Gtari F, Goodwin L, Copeland A, Gtari M, Huntemann M, Ivanova N, Kyrpides N, Markowitz V, Mavrommatis K, Mikhailova N, Nououi I, Oshone R, Ovchinnikova G, Pagani I, Palaniappan K, Pati A. 2015. Draft genome sequence of *Frankia* sp. strain DC12, an atypical, noninfective, ineffective isolate from *Datisca cannabina*. Genome Announc 3(4):e00889-15. http://dx.doi.org/10.1128/genomeA.00889-15.

24. Wall LG, Beauchemin N, Cantor MN, Chaia E, Chen A, Detter JC, Furnholm T, Ghodbane-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, Nououi 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): http://dx.doi.org/10.1128/genomeA.00503-13.
25. Dommergues YR. 1997. Contribution of actinorhizal plants to tropical soil productivity and rehabilitation. Soil Biol Biochem 29:931-947. http://dx.doi.org/10.1016/S0038-0717(96)00227-1.

26. Diem HG, Dommergues Y. 1983. The isolation of *Frankia* from nodules of *Casuarina*. Can J Bot 61:2822-2825.

27. Ngom M, Diagne N, Laplaze L, Champion A, Sy MO. 2 December 2015. Symbiotic ability of diverse *Frankia* strains on Casuarina glauca plants in hydroponic conditions. Symbiosis. http://dx.doi.org/10.1007/s13199-015-0366-7.

28. Bennett S. 2004. Solexa Ltd. Pharmacogenomics 5:433-438. http://dx.doi.org/10.1517/14622416.5.4.433.

29. Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, 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, Jaffe DB. 2011. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA 108:1513-1518. http://dx.doi.org/10.1073/pnas.1017351108.

30. 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 microbial genomes (IMG) system. Nucleic Acids Res 34:D344–D348. http://dx.doi.org/10.1093/nar/gkj024.

31. Markowitz VM, Mavromatis K, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. 2009. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25:2271-2278. http://dx.doi.org/10.1093/bioinformatics/btp393.