Frankia strain AvcI1, isolated from root nodules of Alnus viridis subsp. crispa, is a member of Frankia lineage Ia, which is able to reinfect plants of the Betulaceae and Myricaceae families. Here, we report a 7.7-Mbp draft genome sequence with a G+C content of 72.41% and 6,470 candidate protein-encoding genes

Abebe-Akele, Feseha

Morris, Krystalynne

Oshone, Rediet

Simpson, Stephen D.

Swanson, Erik

Thomas, William Kelley

Tisa, Louis S.

English

UNH Scholars' Repository

University of New HampshireUniversity of New Hampshire Scholars' RepositoryNew Hampshire Agricultural Experiment Station Research Institutes, Centers and Programs12-31-2015Permanent draft genome sequence of Frankia sp.strain AvcI1, a nitrogen-fixing actinobacteriumisolated from the root nodules of Alnus viridissubsp. crispa grown in CanadaErik SwansonUniversity of New Hampshire, DurhamRediet OshoneUniversity of New Hampshire, DurhamStephen D. SimpsonUniversity of New Hampshire, Durham, Stephen.Simpson@unh.eduKrystalynne MorrisUniversity of New Hampshire, Durham, Krystalynne.Morris@unh.eduFeseha Abebe-AkeleUniversity of New Hampshire, DurhamSee next page for additional authorsFollow this and additional works at: https://scholars.unh.edu/nhaesThis Article is brought to you for free and open access by the Research Institutes, Centers and Programs at University of New Hampshire Scholars'Repository. It has been accepted for inclusion in New Hampshire Agricultural Experiment Station by an authorized administrator of University of NewHampshire Scholars' Repository. For more information, please contact nicole.hentz@unh.edu.Recommended CitationSwanson E, Oshone R, Simpson S, Morris K, Abebe-Akele F, Thomas WK, Tisa LS. 2015. Permanent draft genome sequence ofFrankia sp. strain AvcI1, a nitrogen-fixing actinobacterium isolated from the root nodules of Alnus viridis subsp. crispa grown inCanada. Genome Announc 3(6):e01511-15. https://dx.doi.org/10.1128/genomeA.01511-15AuthorsErik Swanson, Rediet Oshone, Stephen D. Simpson, Krystalynne Morris, Feseha Abebe-Akele, William KelleyThomas, and Louis S. TisaThis article is available at University of New Hampshire Scholars' Repository: https://scholars.unh.edu/nhaes/374Permanent Draft Genome Sequence of Frankia sp. Strain AvcI1, aNitrogen-Fixing Actinobacterium Isolated from the Root Nodules ofAlnus viridis subsp. crispa Grown in CanadaErik Swanson, Rediet Oshone, Stephen Simpson, Krystalynne Morris, Feseha Abebe-Akele, W. Kelley Thomas, Louis S. TisaUniversity of New Hampshire, Durham, New Hampshire, USAFrankia strain AvcI1, isolated from root nodules of Alnus viridis subsp. crispa, is a member of Frankia lineage Ia, which is able toreinfect plants of the Betulaceae andMyricaceae families. Here, we report a 7.7-Mbp draft genome sequence with a GC contentof 72.41% and 6,470 candidate protein-encoding genes.Received 1 November 2015 Accepted 4 November 2015 Published 31 December 2015Citation Swanson E, Oshone R, Simpson S, Morris K, Abebe-Akele F, Thomas WK, Tisa LS. 2015. Permanent draft genome sequence of Frankia sp. strain AvcI1, a nitrogen-fixingactinobacterium isolated from the root nodules of Alnus viridis subsp. crispa grown in Canada. Genome Announc 3(6):e01511-15. doi:10.1128/genomeA.01511-15.Copyright © 2015 Swanson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Louis S. Tisa, louis.tisa@unh.edu.Frankia spp. are filamentous nitrogen-fixing actinobacteria thatare found as free-living microbes in the soil and in symbioticassociation with dicotyledonous plants, termed actinorhizalplants (1–3). Actinorhizal plants are found worldwide in a broadrange of ecological and environmental conditions (4), and thissymbiosis allows them to colonize harsh environmental terrains.Although the genus Frankia has not yet been described to thespecies level, it has become an area of greater interest. Based onphylogenetic analysis, Frankia strains have been classified intofourmain lineages (5–8).Members of lineage 1 are found infectiveon host plants of the Betulaceae, Myricaceae, and Casuarinaceaefamilies, while lineage 2 represents strains that are infective onRosaceae, Coriariaceae, Datiscaceae, and the genus Ceanothus(Rhamnaceae). Members of lineage 3 are the most promiscuousand are infective on Eleagnaceae,Rhamnaceae,Myricaceae,Gynm-nostoma, and occasionally Alnus. The fourth Frankia lineage con-sists of the “atypical” strains that are unable to reinfect actinorhi-zal host plants or form ineffective root nodule structures that areunable to fix nitrogen. Genomes for representatives from eachcluster have been sequenced (9–21). Analysis of Frankia genomeshas revealed new potential in respect to metabolic diversity, nat-ural product biosynthesis, and stress tolerance, which may helpaid the cosmopolitan nature of the actinorhizal symbiosis.Cluster I contains two subclusters: one subcluster (cluster Ia)represents Frankia strainswith the ability to infect awider range ofhost plants, including members of the Betulaceae andMyricaceaefamilies, and the other subcluster (cluster Ib) contains strains lim-ited toCasuarina andAllocasuarina host plants. As another mem-ber of cluster Ia, Frankia sp. strain AvcI1 was chosen for sequenc-ing to providemore information on this lineage and its interactionwith actinorhizal plants. Frankia sp. strain AvcI1 was isolatedfrom root nodules of Alnus viridis subsp. crispa collected fromAtikokan, Ontario, Canada (22, 23).The draft genome of Frankia sp. strain AvcI1 was generated atthe Hubbard Genome Center (University of New Hampshire,Durham,NH,USA) using Illumina technology (24) techniques. Astandard Illumina shotgun library was constructed and sequencedusing the Illumina HiSeq2000 platform, which generated27,505,182 reads (260-bp insert size) totaling 4,125.8 Mbp. TheIllumina sequence data were assembled using CLC GenomicsWorkbench version 8.0.1 and AllPaths-LG version r41043 (25).The final draft assembly contained 77 contigs with an N50 of107.5 kb. The total size of the genome is 7.7 Mbp, and the finalassembly is based on 4,125.1 Mb of Illumina draft data and pro-vided an average 399 coverage of the genome.The high-quality draft genome of Frankia sp. strain AvcI1 wasresolved to 7,741,902 bp with a GC content of 72.41%. Theassembled Frankia sp. strain AvcI1 genome was annotated viathe Integrated Microbial Genomes (IMG) platform developed bythe Joint Genome Institute, Walnut Creek, CA, USA (26, 27) andresulted in 6,470 candidate protein-encoding genes, 46 tRNAgenes, and 2 rRNA regions.Nucleotide sequence accessionnumbers.Thiswhole-genomeshotgun project has been deposited at DDBJ/EMBL/GenBank un-der the accessionnumber LJFZ00000000. The versiondescribed inthis paper is the first version, LJFZ01000000.ACKNOWLEDGMENTSPartial funding was provided by the New Hampshire Agricultural Exper-iment Station. This is Scientific Contribution Number 2630. This workwas supported by the USDA National Institute of Food and AgricultureHatch 022821 (L.S.T.), Agriculture and Food Research Initiative Grant2015-67014-22849 from the USDA National Institute of Food and Agri-culture (L.S.T.), and the College of Life Science and Agriculture at theUniversity of New Hampshire–Durham. 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Permanent draft genome sequence of Frankia sp. strain AvcI1, a nitrogen-fixing actinobacterium isolated from the root nodules of Alnus viridis subsp. crispa grown in Canada

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Permanent draft genome sequence of Frankia sp. strain AvcI1, a nitrogen-fixing actinobacterium isolated from the root nodules of Alnus viridis subsp. crispa grown in Canada

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