Frankia stains CpI1-S and CpI1-P are members of Frankia lineage Ia that are able to reinfect plants of the Betulaceae and Myricaceae families. Here, we report two 7.6-Mbp draft genome sequences with 6,396 and 6,373 candidate protein-coding genes for CpI1-S and CpI1-P, respectively

Abebe-Akele, Feseha

Hurst, Sheldon G., IV

Morris, Krystalynne

Oshone, Rediet

Simpson, Stephen D.

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 Programs1-14-2016Permanent draft genome sequences for twovariants of Frankia sp. strain CpI1, the first Frankiastrain isolated from root nodules of ComptoniaperegrinaRediet OshoneUniversity of New Hampshire, DurhamSheldon G. Hurst IVUniversity of New Hampshire, DurhamFeseha Abebe-AkeleUniversity of New Hampshire, DurhamStephen D. SimpsonUniversity of New Hampshire, Durham, Stephen.Simpson@unh.eduKrystalynne MorrisUniversity of New Hampshire, Durham, Krystalynne.Morris@unh.eduSee 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 CitationOshone R, Hurst SG, IV, Abebe-Akele F, Simpson S, Morris K, Thomas WK, Tisa LS. 2016. Permanent draft genome sequences fortwo variants of Frankia sp. strain CpI1, the first Frankia strain isolated from root nodules of Comptonia peregrina. Genome Announc4(1):e01588-15. https://dx.doi.org/10.1128/genomeA.01588-15AuthorsRediet Oshone, Sheldon G. Hurst IV, Feseha Abebe-Akele, Stephen D. Simpson, Krystalynne Morris, WilliamKelley Thomas, and Louis S. TisaThis article is available at University of New Hampshire Scholars' Repository: https://scholars.unh.edu/nhaes/372Permanent Draft Genome Sequences for Two Variants of Frankia sp.Strain CpI1, the First Frankia Strain Isolated from Root Nodules ofComptonia peregrinaRediet Oshone, Sheldon G. Hurst IV, Feseha Abebe-Akele, Stephen Simpson, Krystalynne Morris, W. Kelley Thomas, Louis S. TisaUniversity of New Hampshire, Durham, New Hampshire, USAFrankia stains CpI1-S and CpI1-P are members of Frankia lineage Ia that are able to reinfect plants of the Betulaceae andMyri-caceae families. Here, we report two 7.6-Mbp draft genome sequences with 6,396 and 6,373 candidate protein-coding genes forCpI1-S and CpI1-P, respectively.Received 17 November 2015 Accepted 18 November 2015 Published 14 January 2016Citation Oshone R, Hurst SG, IV, Abebe-Akele F, Simpson S, Morris K, Thomas WK, Tisa LS. 2016. Permanent draft genome sequences for two variants of Frankia sp. strain CpI1,the first Frankia strain isolated from root nodules of Comptonia peregrina. Genome Announc 4(1):e01588-15. doi:10.1128/genomeA.01588-15.Copyright © 2016 Oshone 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.Actinorhizal symbiosis is the association between an actinobac-terium from the genus Frankia and a wide variety of dicoty-ledonous plants representing 8 different families of angiosperms,resulting in the formation of root nodule structure (1–3). Thesymbiosis allows these ecologically important pioneer plants tocolonize harsh environments that are found worldwide (4). Mo-lecular phylogenetic approaches have identified four majorFrankia lineages (5–8). Cluster I contains two subclusters: onesubcluster (cluster Ia) represents Frankia strains with the ability toinfect a wider range of host plants, including members of theBetu-laceae and Myricaceae families, and the other subcluster (clusterIb) contains strains limited to Casuarina and Allocasuarina hostplants. Members of cluster II infect host plants of the subfamilyDryadoideae (Rosaceae), Coriariaceae, and Datiscaceae, and of thegenus Ceanothus (Rhamnaceae). The members of cluster III arethe most promiscuous and infect Elaeagnaceae, Rhamnaceae,Myricaceae,Gymnostoma (Casuarinaceae), and occasionallyAlnusspecies. The fourth Frankia lineage consists of the atypical strains,which are unable to reinfect actinorhizal host plants or form inef-fective root nodule structures that are unable to fix nitrogen. Thegenomes for representatives from each cluster have been se-quenced (9–24).In 1978, the first Frankia isolate, CpI1, was obtained from rootnodules of Comptonia peregrina and fulfilled Koch’s postulates(25). Following this initial success, many other strains from dif-ferent host plants have been isolated, including the recent isola-tion of a member of cluster II (20). Two variants of Frankia sp.strain CpI1 were identified that had different carbon source re-quirements for growth. The Frankia sp. strain CpI1 succinate vari-ant (CpI1-S) will use succinate and other dicarboxylic acids forgrowth, while the Frankia sp. strain CpI1 propionate variant(CpI1-P) will not (26). These two variants also show differences intheir heavy metal tolerances and antibiotic resistance patterns (27,28). Frankia sp. strains CpI1-S and CpI1-P were chosen for se-quencing to provide more information on the differences betweenthese two variants.The draft genome sequences of Frankia sp. strains CpI1-S andCpI1-P were generated at the Hubbard Genome Center (Univer-sity of New Hampshire, Durham, NH) using Illumina technologytechniques (29). A standard Illumina shotgun library was con-structed and sequenced using the Illumina HiSeq 2000 platform,which generated 10,867,000 reads (260-bp insert size) totaling1,628.6 Mbp for CpI1-S and 20,978,588 reads (260-bp insert size)totaling 3,146.7 Mbp for CpI1-P. The Illumina sequence data wereassembled using CLC Genomics Workbench (version 8.0.1) andAllPaths-LG (version r41043) (30). The final draft assembly forFrankia sp. CpI1-S consisted of 153 contigs containing a totalsequence of 7,614,630 bp, with an N50 contig size of 99.4 kb and206.3 coverage of the genome. For Frankia sp. CpI1-P, the finaldraft assembly consisted of 181 contigs containing 7,593,325 bp,with an N50 contig size of 98.1 kb and 287 coverage of the ge-nome.The assembled Frankia sp. CpI1-S and CpI1-P genomes wereannotated via the Integrated Microbial Genomes (IMG) platformdeveloped by the Joint Genome Institute, Walnut Creek, CA, USA(31, 32), and resulted in 6,396 and 6,373 candidate protein-codinggenes for strains CpI1-S and CpI1-P, respectively.Nucleotide sequence accessionnumbers.This whole-genomeshotgun project has been deposited at DDBJ/EMBL/GenBank un-der the accession numbers JYFN00000000 (CpI1-S) andLJJX00000000 (CpI1-P). The versions described in this paper areversions JYFN01000000 and LJJX01000000, respectively.ACKNOWLEDGMENTSPartial funding was provided by the New Hampshire Agricultural Exper-iment Station. This is Scientific Contribution no. 2641. This work wassupported by the USDA National Institute of Food and Agriculture Hatch022821 (to L.S.T.), Agriculture and Food Research Initiative grant 2015-67014-22849 from the USDA National Institute of Food and Agriculture(to L.S.T.), and the College of Life Science and Agriculture at the Univer-sity of New Hampshire-Durham. Sequencing was performed on an Illu-mina HiSeq 2500 purchased with an NSF MRI grant DBI-1229361toW.K.T.crossmarkGenome AnnouncementsJanuary/February 2016 Volume 4 Issue 1 e01588-15 genomea.asm.org 1 on January 26, 2016 by UNIV OF NEW HAMPSHIRE LIBRARYhttp://genomea.asm.org/Downloaded from FUNDING INFORMATIONThe National Science Foundation (NSF) provided funding to W. KelleyThomas under grant number DBI-122936. 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Permanent draft genome sequences for two variants of Frankia sp. strain CpI1, the first Frankia strain isolated from root nodules of Comptonia peregrina

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Permanent draft genome sequences for two variants of Frankia sp. strain CpI1, the first Frankia strain isolated from root nodules of Comptonia peregrina

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