Skip to main content
NCBI home page
Genome Announcements logoLink to Genome Announcements
. 2016 Jul 7;4(4):e00660-16. doi: 10.1128/genomeA.00660-16

Permanent Draft Genome Sequence for Frankia sp. Strain EI5c, a Single-Spore Isolate of a Nitrogen-Fixing Actinobacterium, Isolated from the Root Nodules of Elaeagnus angustifolia

Timothy D’Angelo 1, Rediet Oshone 1, Feseha Abebe-Akele 1, Stephen Simpson 1, Krystalynne Morris 1, W Kelley Thomas 1, Louis S Tisa 1,✉
PMCID: PMC4939792  PMID: 27389275

Abstract

Frankia sp. strain EI5c is a member of Frankia lineage III, which is able to reinfect plants of the Eleagnaceae, Rhamnaceae, Myricaceae, and Gymnostoma, as well as the genus Alnus. Here, we report the 6.6-Mbp draft genome sequence of Frankia sp. strain EI5c with a G+C content of 72.14 % and 5,458 candidate protein-encoding genes.

GENOME ANNOUNCEMENT

Actinorhizal plants form a nitrogen-fixing symbiosis with the genus Frankia that results in the ability of these plants to colonize harsh environments (1–3). These important pioneer community plants are found worldwide under a wide range of ecological and environmental conditions, especially in poor and marginal fertile soils (3,4). Actinorhizal plants represent 8 different families of angiosperms and over 200 species of woody dicotyledonous plants.

Based on phylogenetic markers, four major clusters are recognized within the genus (5–8). Cluster I consists of Frankia strains that associate with host plants in the Casuarinaceae, Betulaceae, and Myricaceae families, while members of cluster II are infective on Rosaceae, Coriariaceae, Datiscaceae, and the genus Ceonothus (Rhamnaceae). Cluster III members are the most promiscuous and are infective on Eleagnaceae, Rhamnaceae, Myricaceae, Gymnostoma, and occasionally the genus Alnus. Cluster IV consists of “atypical” Frankia strains that are unable to reinfect actinorhizal host plants or form ineffective root nodule structures that are unable to fix nitrogen. Genomes for representatives from each cluster have been sequenced (9–25) and have provided a rich database. Analysis of that resource has revealed several physiological properties, including metabolic diversity, natural product biosynthesis, and stress tolerance.

Besides being broad-host-range symbionts, members of cluster III have the greatest metabolic diversity and possess larger genomes than the other clusters. Many of these strains have adapted to harsh environmental conditions. Frankia sp. strain EI5c was obtained from a single-spore colony isolation from cultures of Frankia sp. strain EI5 (UFI 132715) (26), which was isolated from root nodules of Elaeagnus angustifolia (27). This strain uses both intracellular (root hair infection) and intercellular pathways of infection. Frankia sp. strain EI5c was sequenced to provide information on this lineage and its interactions with actinorhizal plants. Furthermore, this database will also be used to help clarify the diversity of cluster III members with the goal of speciation.

The draft genomes of Frankia sp. strain EI5c were 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 24,085,096 reads (260-bp insert size) totaling 3,612.7 Mbp. The Illumina sequence data were assembled using CLC Genomics workbench version 8.0.1 and AllPaths-LG version r41043 (29). The final draft assembly for Frankia EI5c consisted of 159 contigs with an N50 contig size of 128.2 kb. The final assembled genome contained a total sequence of 6,617,243 bp with a G+C content of 72.14 % and is based on 1,290.3 Mb of Illumina draft data, providing an average 195× coverage of the genome.

The assembled Frankia sp. strain EI5c 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 5,458 candidate protein-encoding genes and 46 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 LRTK00000000. The version described in this paper is the first version, LRTK01000000.

ACKNOWLEDGMENT

Partial funding was provided by the New Hampshire Agricultural Experiment Station. This is Scientific Contribution Number 2672. This work was also supported by the USDA National Institute of Food and Agriculture Hatch 022821 (L.S.T.), by Agriculture and Food Research Initiative Grant 2015-67014-22849 from the USDA National Institute of Food and Agriculture (L.S.T.), and by the College of Life Sciences and Agriculture at the University of New Hampshire–Durham. Sequencing was performed on an Illumina HiSeq2500 purchased with NSF MRI Grant DBI-1229361to W.K.T.

Footnotes

Citation D’Angelo T, Oshone R, Abebe-Akele F, Simpson S, Morris K, Thomas WK, Tisa LS. 2016. Permanent draft genome sequence for Frankia sp. strain EI5c, a single-spore isolate of a nitrogen-fixing actinobacterium, isolated from the root nodules of Elaeagnus angustifolia. Genome Announc 4(4):e00660-16. doi:10.1128/genomeA.00660-16.

REFERENCES

  • 1.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, Berlin. [Google Scholar]
  • 2.Chaia EE, Wall LG, Huss-Danell K. 2010. Life in soil by actinorhizal root nodule endophyte Frankia: a review. Symbiosis 51:201–226. doi: 10.1007/s13199-010-0086-y. [DOI] [Google Scholar]
  • 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. doi: 10.1080/153249801753127615. [DOI] [Google Scholar]
  • 4.Benson DR, Dawson JO. 2007. Recent advances in the biogeography and genecology of symbiotic Frankia and its host plants. Physiol Plant 130:318–330. doi: 10.1111/j.1399-3054.2007.00934.x. [DOI] [Google Scholar]
  • 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. doi: 10.1099/00207713-46-1-1. [DOI] [PubMed] [Google Scholar]
  • 6.Cournoyer B, Lavire C. 1999. Analysis of Frankia evolution radiation using glnII sequences. FEMS Microbiol Lett 177:29–34. [DOI] [PubMed] [Google Scholar]
  • 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 glnII sequences. Antonie Van Leeuwenhoek 100:579–587. doi: 10.1007/s10482-011-9613-y. [DOI] [PubMed] [Google Scholar]
  • 8.Ghodhbane-Gtari F, Nouioui I, Chair M, Boudabous A, Gtari M. 2010. 16S–23S rRNA intergenic spacer region variability in the genus Frankia. Microbiol Ecol 60:487–495. doi: 10.1007/s00248-010-9641-6. [DOI] [PubMed] [Google Scholar]
  • 9.Ghodhbane-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, Nouioui 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. doi: 10.1128/genomeA.00085-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.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 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. doi: 10.1128/genomeA.00520-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Gtari M, Ghodhbane-Gtari F, Nouioui I, Ktari A, Hezbri K, 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 W, Sbissi I, Ayari A, Yamanaka T, Normand P, Tisa LS, Boudabous A. 2015. Cultivating the uncultured: growing the recalcitrant cluster-2 Frankia strains. Sci Rep 5:13112. doi: 10.1038/srep13112. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.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 actinobacterium isolated from the root nodules of Casuarina cunninghamiana Grown in Egypt. Genome Announc 2(3):e00493-14 doi: 10.1128/genomeA.00493-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Mansour 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-fixing actinobacterium isolated from the root nodule of Casuarina cunninghamiana. Genome Announc 2(1):e01205-13 doi: 10.1128/genomeA.01205-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.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. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.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. doi: 10.1101/gr.5798407. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Nouioui I, Beauchemin N, Cantor MN, 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, Ovchinnikova G. 2013. Draft genome sequence of Frankia sp. strain BMG5.12, a nitrogen-fixing actinobacterium isolated from Tunisian soils. Genome Announc 1(4):e00468-13. doi: 10.1128/genomeA.00468-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.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 the root nodule of Comptonia peregrina. Genome Announc 4(1):e01588-15. doi: 10.1128/genomeA.01588-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 18.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, Pitluck 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. doi: 10.1128/JB.06208-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19.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. doi: 10.1128/genomeA.01387-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Sen A, Beauchemin N, Bruce D, Chain P, Chen A, Walston Davenport K, Deshpande S, Detter C, Furnholm T, Ghodbhane-Gtari F, 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 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. doi: 10.1128/genomeA.00103-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.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. doi: 10.1128/genomeA.01483-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.Swanson E, Oshone R, Simpson S, Morris K, Abebe-Akele F, Thomas WK, Tisa TLS. 2015. Permanent draft genome sequence of Frankia sp. strain AvcI1, a nitrogen-fixing actinobacterium isolated from the root nodule of Alnus viridis subsp. crispa grown in Canada. Genome Announc 3(6):e01511-15. doi: 10.1128/genomeA.01511-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 23.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. doi: 10.1007/s12038-013-9364-1. [DOI] [PubMed] [Google Scholar]
  • 24.Tisa LS, Beauchemin N, Cantor MN, Furnholm T, Ghodhbane-Gtari F, Goodwin L, Copeland A, Gtari M, Huntemann M, Ivanova N, Kyrpides N, Markowitz V, Mavrommatis K, Mikhailova N, Nouioui I, Oshone R, Ovchinnikova G, Pagani I, Palaniappan K, Pati A. 2015. Permanent draft genome sequence of Frankia sp. strain DC12, an atypical, noninfective ineffective isolate from Datisca cannabina. Genome Announc 3(4):e00889-15. doi: 10.1128/genomeA.00889-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 25.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, 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. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 26.Lumini E, Bosco M. 1996. PCR-restriction fragment length polymorphism identification and host range of single-spore isolates of the flexible Frankia sp. strain UFI 132715. Appl Environ Microbiol 62:3026–3029. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Margheri M, Vagnoli CL, Favilli F, Sili C. 1985. Proprietà morfolisiologiche di Frankia ceppo EanII57 da Elaeagnus angustifolia, infectivity su Alnus glutinosa. Ann Microbiol (Milan) 35:143–153. [Google Scholar]
  • 28.Bennett S. 2004. Solexa Ltd. Pharmacogenomics 5:433–438. doi: 10.1517/14622416.5.4.433. [DOI] [PubMed] [Google Scholar]
  • 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. doi: 10.1073/pnas.1017351108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 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. doi: 10.1093/nar/gkj024. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 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. doi: 10.1093/bioinformatics/btp393. [DOI] [PubMed] [Google Scholar]

Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES