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. 2015 Aug 6;3(4):e00889-15. doi: 10.1128/genomeA.00889-15

Draft Genome Sequence of Frankia sp. Strain DC12, an Atypical, Noninfective, Ineffective Isolate from Datisca cannabina

Louis S Tisa a,✉, Nicholas Beauchemin a, Michael N Cantor b, Teal Furnholm a, Faten Ghodhbane-Gtari a,c, Lynne Goodwin b, Alex Copeland d, Maher Gtari a,c, Marcel Huntemann d, Natalia Ivanova d, Nikos Kyrpides d, Victor Markowitz d, Kostas Mavrommatis d, Natalia Mikhailova d, Imen Nouioui c, Rediet Oshone a, Galina Ovchinnikova d, Ioanna Pagani d, Krishnaveni Palaniappan d, Amrita Pati d, Arnab Sen e, Nicole Shapiro d, Ernest Szeto d, Luis Wall f, Jessie Wishart a, Tanja Woyke d
PMCID: PMC4541282  PMID: 26251504

Abstract

Frankia sp. strain DC12, isolated from root nodules of Datisca cannabina, is a member of the fourth lineage of Frankia, which is unable to reinfect actinorhizal plants. Here, we report its 6.88-Mbp high-quality draft genome sequence, with a G+C content of 71.92% and 5,858 candidate protein-coding genes.

GENOME ANNOUNCEMENT

Frankia spp. are well known as plant symbionts of dicotyledonous plants and also are found as free-living soil dwellers (1–3). This genus has not yet been described to the species level, but it has become an area of recent interest. Four major Frankia lineages have been identified (4–7). Three of them are known to reinfect their host plant, while the fourth lineage (termed atypical Frankia isolates) are unable to reinfect actinorhizal plants or will reinfect the host plant but form ineffective nodules. Our understanding of this genus has been greatly enhanced by the sequencing of several Frankia genomes from the different Frankia lineages (8–18).

As a member of the fourth Frankia lineage, Frankia sp. strain DC12 was chosen for sequencing. This atypical noninfective (Nod−) and non-nitrogen-fixing (Fix−) Frankia strain was isolated from root nodules of Datisca cannabina L. collected from Swat, Pakistan (19, 20). Strain DC12 is also resistant to elevated levels of toxic heavy metals (21), and the spores germinate well under controlled conditions, enabling single genomic units to be isolated (22). Strain DC12 was sequenced to provide information about the potential ecological roles of the atypical Frankia strains and interaction with actinorhizal plants.

The draft genome of Frankia sp. strain DC12 was generated at the Department of Energy (DOE) Joint Genome Institute (JGI) using Illumina data (23). An Illumina short-insert paired-end library with an average (± standard deviation) insert size of 242 ± 59 bp, which generated 16,229,834 reads, and an Illumina long-insert paired-end library with an average insert size of 6,525 ± 1,400 bp, which generated 20,981,340 reads totaling 4,533 Mbp of Illumina data, were generated and sequenced. All techniques for DNA isolation, library construction, and sequencing were performed according to JGI standards and protocols (http://www.jgi.doe.gov). The Illumina sequencing data were assembled with Velvet version 1.0.13 (24) and AllPaths version r41043 (25). The final draft assembly contained 12 contigs in 1 scaffold. The total size of the genome is 6.88 Mbp, and the final assembly is based on 4,533 Mbp of Illumina draft data, which provides an average 657× coverage of the genome. For finishing, the gaps and misassemblies were resolved by editing in Consed, PCR, and sequencing of bridging PCR fragments with Sanger and/or PacBio technologies.

Project information is available in the Genomes Online Database (26). Genes were identified using Prodigal (27), followed by a round of manual curation using GenePRIMP (28) as part of the microbial annotation pipeline of the JGI (29). Additional gene prediction analysis and manual functional annotation were performed within the Integrated Microbial Genomes-Expert Review (IMG-ER) platform (http://img.jgi.doe.gov) developed by the Joint Genome Institute (Walnut Creek, CA, USA) (30).

The high-quality draft genome of Frankia sp. DC12 was resolved to 1 scaffold consisting of 6,884,336 bp, with a G+C content of 71.92%, 5,858 candidate protein-coding genes, 46 tRNA genes, and 3 rRNA regions.

Nucleotide sequence accession numbers.

The Frankia sp. strain DC12 genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession no. LANG00000000. The version described in this paper is the first version, LANG01000000.

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 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 NH585, 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 Agricultural Experiment Station at the University of New Hampshire. A.S. acknowledges DBT, WB government grant (206/Bt-Estd./RD-22/2014).

We thank the late Antoon D. L. Akkermans for providing this strain to L.S.T. many years ago.

Footnotes

Citation 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, Sen A, Shapiro N, Szeto E, Wall L, Wishart J, Woyke T. 2015. 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.

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