Abstract
Members of the actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different families of actinorhizal plants. We report a draft genome sequence for Frankia sp. strain BMG5.12, a nitrogen-fixing actinobacterium isolated from Tunisian soils with the ability to infect Elaeagnus angustifolia and Myrica gale.
GENOME ANNOUNCEMENT
Among the Actinobacteria, the genus Frankia is well known for its facultative lifestyle as a plant symbiont of dicotyledonous plants and as a free-living soil dweller (1–3). The symbiosis allows actinorhizal plants to colonize harsh environmental terrains under diverse ecological conditions. Based on several criteria, including the 16S rRNA gene (4), glnII (5, 6), gyrB (6), and a 16S-23S rRNA intertranscribed spacer region (7), phylogenetic analysis has identified four distinct clusters among the Frankia strains. Genomes for representatives from each of these clusters have been sequenced (8–12) and have provided vital baseline information for genomic approaches toward understanding these novel bacteria.
Members of cluster III Frankia strains are considered broad-host-range symbionts and are known to associate with five plant families (Betulaceae, Myricaceae, Elaeagnaceae, Rhamnaceae, and Casuarinaceae). Frankia sp. strain BMG5.12 was chosen for sequencing as another cluster III representative with broad-host-range properties. Strain BMG 5.12 was isolated from Tunisian soils that were devoid of Elaeagnus plants and it was found to infect these host plants (13). Strain BMG5.12 was sequenced to find information about the potential ecological roles of the Frankia strains and their interactions with actinorhizal plants. As a representative from a harsh dry climate, the Frankia sp. BMG5.12 genome may provide insight on its ability to adapt to these arid hot soils that have high salinity.
The draft genome sequence of Frankia sp. BMG5.12 was generated at the Department of Energy (DOE) Joint Genome Institute (JGI) using Illumina technology (14). An Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform, which generated 9,945,424 reads totaling 1,491.8 Mbp. All techniques for DNA isolation, library construction, and sequencing were performed according to JGI standards and protocols (http://www.jgi.doe.gov). The Illumina sequence data were assembled using Velvet (version 1.1.04) (14) and Allpaths-LG (version r41043) (15). The final draft assembly contained 139 contigs in 139 scaffolds. The total size of the genome is 7.6 Mbp, and the final assembly is based on 932.3 Mbp of Illumina data, which provide an average 122.9× coverage of the genome.
The draft genome sequence of Frankia sp. BMG5.12 was resolved to 139 scaffolds consisting of 7,589,313 bp, with a G+C content of 71.67%, 6,253 candidate protein-coding genes, 51 tRNA genes, and 2 rRNA regions.
Nucleotide sequence accession numbers.
The Frankia sp. BMG5.12 genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession no. ARFH00000000. The version described in this paper is the first version, accession no. ARFH01000000.
ACKNOWLEDGMENTS
The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. This project (L.S.T.) was supported in part by Agriculture and Food Research Initiative grant no. 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 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, Pagani I, Pati A, 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(4):e00468-13. doi:10.1128/genomeA.00468-13.
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