Abstract
Members of the actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different families of actinorhizal plants. We report a high-quality draft genome sequence for Frankia sp. strain QA3, a nitrogen-fixing actinobacterium isolated from root nodules of Alnus nitida.
GENOME ANNOUNCEMENT
The genus Frankia consists of filamentous actinobacteria that form nitrogen-fixing symbiotic associations with a wide variety of woody angiosperms termed actinorhizal plants (1–3). The symbiosis allows actinorhizal plants to colonize harsh environmental terrains under diverse ecological conditions. Phylogenetic analysis based on several criteria, including the 16S rRNA gene (4), glnII (5, 6), and the 16S-23S rRNA intertranscribed spacer region (7), has identified four distinct clusters among the Frankia strains. Genomes for representatives from each of these clusters have been sequenced (8–10) and have provided vital baseline information for genomic approaches toward understanding these novel bacteria.
Members of cluster I Frankia strains are known to associate with Betulaceae, Myricaceae, and Casuarinaceae plants (except Gymnostoma) and include both narrow-host-range and mid-host-range symbionts. Since only two members of cluster I have been sequenced, strains ACN14a and CcI3 (8), another cluster I strain was sequenced to increase our understanding of this Frankia group and its host plant range. Frankia sp. strain QA3 was chosen for sequencing as another cluster I representative with mid-host-range properties. The strain was isolated from root nodules of Alnus nitida collected at an elevation of 1,240 m in the mountainous region of Bahrin, District Swat, Pakistan (11). Frankia sp. strain QA3 is also resistant to elevated levels of toxic heavy metals (12) and has potential applications in bioremediation. Strain QA3 was sequenced to provide information about the potential ecological roles of the Frankia strains and their interaction with actinorhizal plants.
The draft genome of Frankia sp. strain QA3 was generated at the Department of Energy (DOE) Joint Genome Institute (JGI) using a combination of 454-GS-FLX-Titanium (13) and Illumina GAii (14) techniques. A standard 454 titanium standard library, which generated 261,792 reads, a paired-end 454 library with an average insert size of 8 kb, which generated 728,635 reads totaling 258.7 Mb of 454 data, and an Illumina GAii shotgun library, which generated 116,789,226 reads totaling 8,876 Mb were created. All techniques for DNA isolation, library construction, and sequencing were performed according to JGI standards and protocols (http://www.jgi.doe.gov). The 454 Titanium standard data and the 454 paired-end data were assembled together with Newbler, version 2.3 (13), and resulted in 177.9 Mb of 454 draft data, which provided an average 23.4× coverage of the genome. The Illumina sequencing data were assembled with Velvet, version 1.0.13 (15), and the resulting 8,345.8 Mb of Illumina draft data provided an average 1,098.1× coverage of the genome. For finishing, the gaps and misassemblies were resolved by editing in Consed, by PCR, and by bubble PCR primer walks.
The high-quality draft genome of Frankia QA3 was resolved to 1 scaffold containing 121 contigs consisting of 7,590,853 bp with a G+C content of 72.6%, 6,493 candidate protein-encoding genes, 46 tRNA genes, and 3 rRNA regions.
Nucleotide sequence accession number.
The whole draft genome sequences of Frankia strain QA3 have been deposited in GenBank with accession number AJWA00000000.
ACKNOWLEDGMENTS
The work conducted by the U.S. Department of Energy Joint Genome Institue is supported by the Office of Science of the U.S. Department of Energy under contact number DE-AC02-05CH11231. This project (L.S.T.) was supported in part by Agriculture and Food Research Initiative grant 2010-65108-20581 from the USDA National Institute of Food and Agriculture, Hatch grant NH530, and the college of Life Sciences and Agriculture at the University of New Hampshire, Durham, NH. M.G. and F.G.-G. were supported in part by a Visiting Scientist and Postdoctoral Scientist Program administered by the NH AES at the University of New Hampshire.
Footnotes
Citation 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, Woyke T, Wishart J, 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.
REFERENCES
- 1. Benson DR, Silvester WB. 1993. Biology of Frankia strains, actinomycete symbionts of actinorhizal plants. Microbiol. Rev. 57:293–319 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Schwencke J, Caru 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 [Google Scholar]
- 3. Chaia EE, Wall LG, Huss-Danell K. 2010. Life in soil by actinorhizal root nodule endophyte Frankia. A review. Symbiosis 51:201–226 [Google Scholar]
- 4. Normand P, Orso S, Cournoyer B, Jeannin P, Chapelon C, Dawson JO, Evtushenko L, Mirsra 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] [PubMed] [Google Scholar]
- 5. Cournoyer B, Lavire C. 1999. Analysis of Frankia evolution radiation using glnII sequences. FEMS Microbiol. Lett. 117:29–34 [DOI] [PubMed] [Google Scholar]
- 6. 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] [PubMed] [Google Scholar]
- 7. 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 [DOI] [PubMed] [Google Scholar]
- 8. 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] [PMC free article] [PubMed] [Google Scholar]
- 9. 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 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Ghodbhane-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):e00085-13. doi:10.1128/genomeA.00085-13 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Hafeez F, Akkermans ADL, Chaudhary AH. 1984. Morphology, physiology, and infectivity of two Frankia isolates, An1 and An2 from root nodules of Alnus nitida. Plant Soil 78:45–59 [Google Scholar]
- 12. Richards JW, Krumholz GD, Chval MS, Tisa LS. 2002. Heavy metal resistance patterns of Frankia strains. Appl. Environ. Microbiol. 68:923–927 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J-B, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, Dade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14. Bennett S. 2004. Solexa Ltd. Pharmacogenomics 5:433–438 [DOI] [PubMed] [Google Scholar]
- 15. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821–829 [DOI] [PMC free article] [PubMed] [Google Scholar]