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. 2016 May 26;4(3):e00437-16. doi: 10.1128/genomeA.00437-16

Draft Genome Sequence of Frankia Strain G2, a Nitrogen-Fixing Actinobacterium Isolated from Casuarina equisetifolia and Able To Nodulate Actinorhizal Plants of the Order Rhamnales

Imen Nouioui a, Maher Gtari b, Markus Göker c, Faten Ghodhbane-Gtari b, Louis S Tisa d, Maria P Fernandez e, Philippe Normand e, Marcel Huntemann f, Alicia Clum f, Manoj Pillay f, Neha Varghese f, T B K Reddy f, Natalia Ivanova f, Tanja Woyke f, Nikos C Kyrpides f, Hans-Peter Klenk a,✉
PMCID: PMC4882949  PMID: 27231368

Abstract

Frankia sp. strain G2 was originally isolated from Casuarina equisetifolia and is characterized by its ability to nodulate actinorhizal plants of the Rhamnales order, but not its original host. It represents one of the largest Frankia genomes so far sequenced (9.5 Mbp).

GENOME ANNOUNCEMENT

The genus Frankia contains actinobacteria known for their ability to fix nitrogen and to infect the roots of eight actinorhizal plant families (1–3). Phylogenetic studies of Frankia strains based on 16S rRNA (4), gyr B (5), gln II (5, 6) genes and 16S-23S rRNA Intergenic Spacer Region (7) indicate four groups. Group 1 forms nodules on Betulaceae, Myricaceae, and Casuarinaceae. Group 2 contains microsymbionts of Coriariaceae, Datiscaceae, Dryadoideae (Rosaceae), and Ceanothus (Rhamnaceae). Group 3 includes strains associated with Morella (Myricaceae), Colletieae (Rhamnaceae), Elaeagnaceae, and Gymnostoma (Casuarinaceae). Group 4 includes atypical, non-infective (Nod-) and/or ineffective (Fix-) Frankia strains. Our knowledge about the biology of this genus has been well improved due to the information provided by sequenced Frankia genomes (8–21). Group 3 has a broad host range, considerable genetic diversity between the strains (5, 7), high potential for a saprophytic lifestyle (7–22), and a variable genome size ranging from 7.5 to 10.45 Mbp. Strain G2 (=DSM45899=CECT9038) was selected for genome sequencing within the Genomic Encyclopaedia of Type Strains, Phase II: From Individual Species to Whole Genera (23), the second production phase of the Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains Initiative (24). The candidate type strain G2 for a novel Frankia species, selected to enrich the diversity of group 3, was isolated from Casuarina equisetifolia nodules collected in the INRA Research Station, Saint-François, Grande Terre, Guadeloupe (25). It has the potential to produce natural products such as the red-pigmented antibiotics (benzo[a]naphthacenequinones) (26). It is infective on members of the actinorhizal Rhamnales, but not on its original host plant C. equisetifolia (25). The draft genome of strain G2 was sequenced using Illumina technology (27) with a 300 bp insert standard shotgun library on an Illumina HiSeq-2500 1-TB platform, which generated 6,201,478 reads totaling 936.4 Mbp, at the Joint Genome Institute (JGI) (28). The assembly was realized using Velvet (version 1.2.07) (29) and Allpaths-LG (version r46652) (30). Annotation was performed using the JGI annotation pipeline (31) and the data are available from the IMG data management system (32). The final draft assembly contained 90 contigs in 83 scaffolds, totaling 9.537,992 bp in size based on 856.6 Mbp of data with 171.3 × input read coverage. The genome draft encodes 7,790 protein genes, 47 tRNAs, and 2 rRNA regions, with an overall G+C content of 70.9%. Genome annotation was performed as described by Tisa et al. (21). As expected, since Frankia is a nitrogen fixing actinobacterium, six nitrogenase genes, nifH, nifE, nifD, nifK, nifW, and nifN, have been detected.

Project information is available in the Genomes Online Database (33) and DNA from the DNA Bank Network (34).

Nucleotide sequence accession number.

This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession no. FAOZ00000000. The version described in this paper is the first version.

ACKNOWLEDGMENTS

This work was conducted under the auspices of U.S. Department of Energy Office of Science, Biological and Environmental Research Program and the University of California, Lawrence Berkeley National Laboratory (under contract DE-AC02-05CH11231).

We are grateful to Marlen Jando and Meike Döppner (both at DSMZ) for their contribution to culturing Frankia strains and for DNA extractions and quality control.

Footnotes

Citation Nouioui I, Gtari M, Göker M, Ghodhbane-Gtari F, Tisa LS, Fernandez MP, Normand P, Huntemann M, Clum A, Pillay M, Varghese N, Reddy TBK, Ivanova N, Woyke T, Kyrpides NC, Klenk H-P. 2016. Draft genome sequence of Frankia strain G2, a nitrogen-fixing actinobacterium isolated from Casuarina equisetifolia and able to nodulate actinorhizal plants of the order Rhamnales. Genome Announc 4(3):e00437-16. doi:10.1128/genomeA.00437-16.

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