Frankia sp. strain BR is a member of Frankia lineage Ic and is able to reinfect plants of the Casuarinaceae family. Here, we report a 5.2-Mbp draft genome sequence with a G+C content of 70.0% and 4,777 candidate protein-encoding genes

Abebe-Akele, Feseha

D\u27Angelo, Timothy

Morris, Krystalynne

Oshone, Rediet

Simpson, Stephen

Thomas, W. Kelley

Tisa, Louis S.

English

PubMed

ABSTRACT
          
            Frankia
            sp. strain BR is a member of
            Frankia
            lineage Ic and is able to reinfect plants of the
            Casuarinaceae
            family. Here, we report a 5.2-Mbp draft genome sequence with a G+C content of 70.0% and 4,777 candidate protein-encoding genes.
          </jats:p

Timothy D'Angelo

Rediet Oshone

Feseha Abebe-Akele

Stephen Simpson

Krystalynne Morris

W. Kelley Thomas

Louis S. Tisa

Crossref

Genome Announcements

Permanent Draft Genome Sequence of
            <i>Frankia</i>
            sp. Strain BR, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of
            <i>Casuarina equisetifolia</i>

UNH Scholars' Repository

University of New HampshireUniversity of New Hampshire Scholars' RepositoryMolecular, Cellular and Biomedical SciencesScholarship Molecular, Cellular and Biomedical Sciences9-15-2016Permanent Draft Genome Sequence of Frankia sp.Strain BR, a Nitrogen-Fixing ActinobacteriumIsolated from the Root Nodules of CasuarinaequisetifoliaTimothy D'AngeloUniversity of New Hampshire, DurhamRediet OshoneUniversity of New Hampshire, DurhamFeseha Abebe-AkeleUniversity of New Hampshire, DurhamStephen SimpsonUniversity of New Hampshire, DurhamKrystalynne MorrisUniversity of New Hampshire, DurhamSee next page for additional authorsFollow this and additional works at: https://scholars.unh.edu/mcbs_facpubThis Article is brought to you for free and open access by the Molecular, Cellular and Biomedical Sciences at University of New Hampshire Scholars'Repository. It has been accepted for inclusion in Molecular, Cellular and Biomedical Sciences Scholarship by an authorized administrator of Universityof New Hampshire Scholars' Repository. For more information, please contact nicole.hentz@unh.edu.Recommended CitationD’Angelo, T, R. Oshone, F. Abebe-Akele, S. Simpson, K. Morris, W. K. Thomas, and L. S. Tisa. 2016. Permanent Draft GenomeSequence for Frankia sp. Strain BR, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equisetifolia.Genome Announc 4(5):e01000-16 doi:10.1128/genomeA.01000-16.AuthorsTimothy D'Angelo, Rediet Oshone, Feseha Abebe-Akele, Stephen Simpson, Krystalynne Morris, W. KelleyThomas, and Louis S. TisaThis article is available at University of New Hampshire Scholars' Repository: https://scholars.unh.edu/mcbs_facpub/171Permanent Draft Genome Sequence of Frankia sp. Strain BR, aNitrogen-Fixing Actinobacterium Isolated from the Root Nodules ofCasuarina equisetifoliaTimothy D’Angelo, Rediet Oshone, Feseha Abebe-Akele, Stephen Simpson, Krystalynne Morris, W. Kelley Thomas, Louis S. TisaUniversity of New Hampshire, Durham, New Hampshire, USAFrankia sp. strain BR is a member of Frankia lineage Ic and is able to reinfect plants of the Casuarinaceae family. Here, we reporta 5.2-Mbp draft genome sequence with a GC content of 70.0% and 4,777 candidate protein-encoding genes.Received 25 July 2016 Accepted 26 July 2016 Published 15 September 2016Citation D’Angelo T, Oshone R, Abebe-Akele F, Simpson S, Morris K, Thomas WK, Tisa LS. 2016. Permanent draft genome sequence of Frankia sp. strain BR, a nitrogen-fixingactinobacterium isolated from the root nodules of Casuarina equisetifolia. Genome Announc 4(5):e01000-16. doi:10.1128/genomeA.01000-16.Copyright © 2016 D’Angelo et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Louis S. Tisa, louis.tisa@unh.edu.Members of the genus Frankia are nitrogen-fixing actinobac-teria that form an endophytic symbiosis with actinorhizalplants (1). This group of woody dicotyledonous plants is distrib-uted worldwide and comprises over 200 species from eight angio-sperm families (2). Because of its symbiosis with Frankia spp.,actinorhizal plants play important ecological roles as pioneer spe-cies and are used in agroforestry, land reclamation, crop protec-tion, and soil stabilization projects (3–5). Molecular phylogeneticapproaches have identified four major clusters of Frankia (6–9),and genomes for representatives from each cluster have been se-quenced (10–28). The availability of these Frankia genome data-bases has opened up the use of “omics” approaches. Furthermore,analysis of Frankia genomes has revealed new potential in respectto metabolic diversity, natural product biosynthesis, and stresstolerance, which may aid the cosmopolitan nature of the acti-norhizal symbiosis.Actinorhizal plants belonging to the Casuarinaceae family areable to grow under saline conditions and have been used exten-sively as a green barrier (28–33). Casuarina trees are native totropical areas of Australia and the South Pacific and have subse-quently been transplanted to other tropical areas of the world,particularly Africa (34). In countries such as Egypt, Tunisia, andSenegal, Casuarina trees are actively used in agroforestry and aswindbreaks and shelterbelts for agriculture in arid areas (32, 35,36). Members of Frankia cluster 1c have the most restricted hostrange and are able to infect onlyCasuarina andAllocasuarina hostplants (1, 18). Frankia sp. strain BR was isolated from axenic Ca-suarina equisetifolia root nodules that had been inoculated withcrushedC. equisetifolia root nodules fromBrazil (37). The Frankiasp. strain BR genome was sequenced to provide information oncluster 1c lineage and symbiosis with Casuarina trees.Sequencing of the draft genome of Frankia sp. strain BR wasperformed at the Hubbard Center for Genome Studies (Univer-sity of New Hampshire, Durham, NH, USA) using Illumina tech-nology techniques (38). A standard Illumina shotgun library wasconstructed and sequenced using the Illumina HiSeq2500 plat-form, which generated 24,720,192 reads (260-bp insert size) total-ing 3,708Mbp. The Illumina sequence data were assembled usingCLC Genomics workbench version 8.5 and ALLPaths-LG versionr41043 (39). The final draft assembly for Frankia sp. strain BRconsisted of 180 contigs with an N50 contig size of 60.2 kb and450.4 coverage of the genome. The final assembled genome con-tained a total sequence length of 5,227,240 bpwith aGC contentof 70.0%.The assembled Frankia sp. strain BR was annotated via theIntegrated Microbial Genomes (IMG) platform developed by theJoint Genome Institute, Walnut Creek, CA, USA (40, 41), result-ing in 4,777 candidate protein-encoding genes and 46 tRNA andtwo rRNA regions.Accession number(s). This whole-genome shotgun sequencehas been deposited at DDBJ/EMBL/GenBank under the accessionnumber LRTJ00000000. The version described in this paper is thefirst version, LRTJ01000000.ACKNOWLEDGMENTSPartial funding was provided by the New Hampshire Agricultural Exper-iment Station. This is Scientific Contribution Number 2681. This workwas supported by USDA National Institute of Food and AgricultureHatch Project 022821 (L.S.T.), Agriculture and Food Research InitiativeGrant 2015-67014-22849 from the USDA National Institute of Food andAgriculture (L.S.T.), and the College of Life Science and Agriculture at theUniversity of New Hampshire–Durham. Sequencing was performed onan IlluminaHiSeq2500 purchasedwith anNSFMRI grant (DBI-1229361)to W.K.T.FUNDING INFORMATIONThis work, including the efforts of W. Kelley Thomas, was funded byNational Science Foundation (NSF) (DBI-1229361). This work,including the efforts of Louis S. Tisa, was funded by USDA |National Institute of Food and Agriculture (NIFA) (Hatch 022821and 2015-67014-22849).REFERENCES1. Normand P, Benson DR, Berry AM, Tisa LS. 2014. Family Frankiaceae,p. 339–356. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thomp-son F (ed), The prokaryote—actinobacteria, 4th ed. Springer, Berlin.2. Benson DR, Vandenheuvel B, Potter D. 2004. 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Permanent Draft Genome Sequence of Frankia sp. Strain BR, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equisetifolia

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Permanent Draft Genome Sequence of Frankia sp. Strain BR, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equisetifolia

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