Here, we report the first genome sequence of aNocardiaplant endophyte, N. casuarinaestrain BMG51109, isolated fromCasu-arina glaucaroot nodules. The improved high-quality draft genome sequence contains 8,787,999 bp with a 68.90% GC contentand 7,307 predicted protein-coding genes

Beauchemin, Nicholas

Chen, Amy

Ghodhbane-Gtari, Faten

Gtari, Maher

Gueddou, Abdellatif

Hezbri, Karima

Huntemann, Marcel

Ivanova, Natalia

Ktari, Amir

Kyrpides, Nikos

Louati, Moussa

Markowitz, Victor

Mavrommatis, Kostas

Nouioui, Imen

Pagani, Ioanna

Sen, Arnab

Tisa, Louis S.

Wall, Luis

Woyke, Tanja

English

PubMed

Here, we report the first genome sequence of a Nocardia plant endophyte, N.&nbsp;casuarinae strain BMG51109, isolated from Casuarina glauca root nodules. The improved high-quality draft genome sequence contains 8,787,999&nbsp;bp with a 68.90% GC content and 7,307 predicted protein-coding genes

Tisa, Louis S

eScholarship - University of California

Permanent Improved High-Quality Draft Genome Sequence of Nocardia casuarinae Strain BMG51109, an Endophyte of Actinorhizal Root Nodules of Casuarina glauca

University of New Hampshire

University of New Hampshire
University of New Hampshire Scholars' Repository
New Hampshire Agricultural Experiment Station Research Institutes, Centers and Programs
8-4-2016
Permanent improved high-quality draft genome
sequence of Nocardia casuarinae strain
BMG51109, an endophyte ofactinorhizal root
nodules of Casuarina glauca
Faten Ghodhbane-Gtari
Université Tunis El Manar
Nicholas Beauchemin
University of New Hampshire, Durham
Moussa Louati
Université Tunis El Manar
Imen Nouioui
Université Tunis El Manar
Amir Ktari
Université Tunis El Manar
See next page for additional authors
Follow this and additional works at: https://scholars.unh.edu/nhaes
This 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 New
Hampshire Scholars' Repository. For more information, please contact nicole.hentz@unh.edu.
Recommended Citation
Ghodhbane-Gtari F, Beauchemin N, Louati M, Nouioui I, Ktari A, Hezbri K, Gueddou A, Chen A, Huntemann M, Ivanova N,
Kyrpides N, Markowitz V, MavrommatisK,Pagani I, Sen A, Wall L, Woyke T, Gtari M, Tisa LS. 2016. Permanent improved high-
quality draft genome sequence of Nocardia casuarinaestrain BMG51109, an endophyte ofactinorhizal root nodules ofCasuarina
glauca. Genome Announc 4(4):e00799-16. https://dx.doi.org/10.1128/genomeA.00799-16
Authors
Faten Ghodhbane-Gtari, Nicholas Beauchemin, Moussa Louati, Imen Nouioui, Amir Ktari, Karima Hezbri,
Abdellatif Gueddou, Amy Chen, Marcel Huntemann, Natalia Ivanova, Nikos Kyrpides, Victor Markowitz,
Kostas Mavrommatis, Ioanna Pagani, Arnab Sen, Luis Wall, Tanja Woyke, Maher Gtari, and Louis S. Tisa
This article is available at University of New Hampshire Scholars' Repository: https://scholars.unh.edu/nhaes/332
Permanent Improved High-Quality Draft Genome Sequence of
Nocardia casuarinae Strain BMG51109, an Endophyte of Actinorhizal
Root Nodules of Casuarina glauca
Faten Ghodhbane-Gtari,a Nicholas Beauchemin,b Moussa Louati,a Imen Nouioui,a Amir Ktari,a Karima Hezbri,a Abdellatif Gueddou,a
Amy Chen,c Marcel Huntemann,c Natalia Ivanova,c Nikos Kyrpides,c Victor Markowitz,c Kostas Mavrommatis,c Ioanna Pagani,c
Arnab Sen,d Luis Wall,e Tanja Woyke,c Maher Gtari,a Louis S. Tisab
University of Tunis-El Manar, Tunis, Tunisiaa; University of New Hampshire, Durham, New Hampshire, USAb; DOE Joint Genome Institute, Walnut Creek, California, USAc;
University of North Bengal, Siliguri, Indiad; University of Quilmes, Quilmes, Argentinae
Here, we report the first genome sequence of a Nocardia plant endophyte, N. casuarinae strain BMG51109, isolated from Casu-
arina glauca root nodules. The improved high-quality draft genome sequence contains 8,787,999 bp with a 68.90% GC content
and 7,307 predicted protein-coding genes.
Received 13 June 2016 Accepted 15 June 2016 Published 4 August 2016
Citation Ghodhbane-Gtari F, Beauchemin N, Louati M, Nouioui I, Ktari A, Hezbri K, Gueddou A, Chen A, Huntemann M, Ivanova N, Kyrpides N, Markowitz V, Mavrommatis K,
Pagani I, Sen A, Wall L, Woyke T, Gtari M, Tisa LS. 2016. Permanent improved high-quality draft genome sequence of Nocardia casuarinae strain BMG51109, an endophyte of
actinorhizal root nodules of Casuarina glauca. Genome Announc 4(4):e00799-16. doi:10.1128/genomeA.00799-16.
Copyright © 2016 Ghodhbane-Gtari 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 Nocardia are ubiquitous soil-borne aer-obic microorganisms belonging to a large group of actino-
bacteria that are best known for their pathogenicity and their
harmful infections for humans or animals (1). However, several
Nocardia spp. have been consistently reported as plant endophytes
and isolated from disinfected roots (N. callitridis [2]), stems (N.
artemisiae [3] and N. endophytica [4]), and actinorhizal root nod-
ules (N. autotrophica [5], N. casuarinae [6], and Nocardia sp. [7–
9]). The potential role of the Nocardia endophyte has been postu-
lated, especially in the case of actinorhizal symbiosis (5, 10). To the
best of our knowledge, these plant-associated Nocardia spp. have
not had their genomes sequenced.
We report here the genome sequence of Nocardia casuarinae
strain BMG51109, which was isolated from root nodules of Casu-
arina glauca growing in Tunisia (6). N. casuarinae strain
BMG51109 was sequenced to provide new insights into the role
that this microbe plays in actinorhizal plants.
The draft genome of N. casuarinae strain BMG51109 was gen-
erated at the DOE Joint Genome Institute (JGI; Walnut Creek,
CA, USA) using Pacific Biosciences (PacBio) technology. A
PacBio SMRTbell library was constructed and sequenced on the
PacBio RS platform, which generated 583,909 filtered subreads
totaling 1.4 Gbp. All general aspects of library construction and
sequencing performed at the JGI can be found at http://www.jgi
.doe.gov. The raw reads were assembled using HGAP version 2.0.0
(11). The final draft assembly contained 4 contigs in 4 scaffolds,
totaling 8.8 Mbp in size. The input read coverage was 155.7.
Project information is accessible in the Genomes Online Data-
base (12). Genes were identified using Prodigal (13), followed by a
round of manual curation using GenePRIMP (14) as part of the
microbial annotation pipeline of the JGI (15). Additional gene
prediction analysis and manual functional annotation were per-
formed within the Integrated Microbial Genomes–Expert Review
(IMG-ER) platform (http://img.jgi.doe.gov) developed by JGI
(16).
The high-quality draft genome of N. casuarinae strain
BMG51109 was resolved to 4 scaffolds consisting of 7,730,817 bp,
with a GC content of 68.90%, 7,822 candidate protein-coding
genes, 55 tRNA genes, and 3 rRNA regions.
Nucleotide sequence accession numbers. The Nocardia
casuarinae strain BMG51109 genome sequence has been de-
posited at DDBJ/EMBL/GenBank under the accession number
JAFQ00000000. The version described in this paper is the first
version, JAFQ01000000.
ACKNOWLEDGMENTS
Partial funding by the New Hampshire Agricultural Experiment Station.
This is Scientific Contribution Number 2678. 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 no.
DE-AC02-05CH11231. This project (L.S.T.) was supported in part by the
USDA National Institute of Food and Agriculture, Hatch 022821, and the
College of Life Sciences and Agriculture at the University of New Hamp-
shire, Durham, NH, USA. M.G. and F.G.-G. were supported in part by the
Visiting Scientist and Postdoctoral Scientist Program administered by the
NH AES at the University of New Hampshire.
FUNDING INFORMATION
This work, including the efforts of Louis S. Tisa, was funded by
USDA | National Institute of Food and Agriculture (NIFA) (Hatch
022821). This work, including the efforts of Tanja Woyke, was
funded by U.S. Department of Energy (DOE) (DE-AC02-05CH11231).
REFERENCES
1. Goodfellow M. 2014. Family Nocardiaceae, p 595– 650. In Rosenberg E,
DeLong EF, Lory S, Stackebrandt E, Thompson F (ed), The prokaryotes—
Actinobacteria. Springer, Berlin.
2. Kaewkla O, Franco CM. 2010. Nocardia callitridis sp. nov., an endophytic
crossmark
Genome AnnouncementsJuly/August 2016 Volume 4 Issue 4 e00799-16 genomea.asm.org 1
actinobacterium isolated from a surface-sterilized root of an Australian
native pine tree. Int J Syst Evol Microbiol 60:1532–1536. http://dx.doi.org/
10.1099/ijs.0.016337-0.
3. Zhao GZ, Li J, Zhu WY, Klenk HP, Xu LH, Li WJ. 2011. Nocardia
artemisiae sp. nov., an endophytic actinobacterium isolated from a
surface-sterilized stem of Artemisia annua L. Int J Syst Evol Microbiol
61:2933–2937. http://dx.doi.org/10.1099/ijs.0.029306-0.
4. Xing K, Qin S, Fei SM, Lin Q, Bian GK, Miao Q, Wang Y, Cao CL, Tang
SK, Jiang JH, Li WJ. 2011. Nocardia endophytica sp. nov., an endophytic
actinomycete isolated from the oil-seed plant Jatropha curcas L. Int J Syst
Evol Microbiol 61:1854 –1858. http://dx.doi.org/10.1099/ijs.0.027391-0.
5. Dobritsa SV, Sharaya LS. 1986. Genome identity of different Nocardia
autotrophica isolates from Alnus spp. root nodules and rhizosphere. In
Szabo G, Biro S, Goodfellow M (ed), Biological, biochemical and biomed-
ical aspects of Actinomycetes Part B, vol 32. Akadémiai Kiadó, Budapest.
6. Ghodhbane-Gtari F, Nouioui I, Salem K, Ktari A, Montero-Calasanz
Mdel C, Tisa LS, Klenk HP, Gtari M. 2014. Nocardia casuarinae sp. nov.,
an actinobacterial endophyte isolated from root nodules of Casuarina
glauca. Antonie Van Leeuwenhoek 105:1099 –1106. http://dx.doi.org/
10.1007/s10482-014-0168-6.
7. Malishkaite YB, Nechaeva GA, Kuimova TF, Evtushenko LI, Agre NS.
1987. Nocardia strains from actinorhizal plant nodules. Microbiology 56:
100 –106.
8. Pariiskaya AN, Novik SN, Agre NS, Kalakutskii LV. 1982. Nocardia
Isolated from nitrogen-fixing nodules on the roots of the gray and black
alder. Microbiology 51:117–121.
9. Ghodhbane-Gtari F, Essoussi I, Chattaoui M, Chouaia B, Jaouani A,
Daffonchio D, Boudabous A, Gtari M. 2010. Isolation and characteriza-
tion of non-Frankia actinobacteria from root nodules of Alnus glutinosa,
Casuarina glauca and Elaeagnus angustifolia. Symbiosis 50:51–57. http://
dx.doi.org/10.1007/s13199-009-0029-7.
10. Ghodhbane-Gtari F, Tisa LS. 2014. Ecology and physiology of non-
Frankia actinobacteria from actinorhizal plants, p 27– 42. In Katsey EI
(ed), Plasticity in plant-growth-promoting and phytopathogenic bacteria.
Springer, New York.
11. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C,
Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J.
2013. Nonhybrid, finished microbial genome assemblies from long-read
SMRT sequencing data. Nat Methods 10:563–569. http://dx.doi.org/
10.1038/nmeth.2474.
12. Reddy TB, Thomas AD, Stamatis D, Bertsch J, Isbandi M, Jansson J,
Mallajosyula J, Pagani I, Lobos EA, Kyrpides NC. 2015. The Ge-
nomes OnLine Database (GOLD) v.5: a metadata management system
based on a four level (meta)genome project classification. Nucleic Ac-
ids Res 43:D1099 –D1106. http://dx.doi.org/10.1093/nar/gku950.
13. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ.
2010. Prodigal: prokaryotic gene recognition and translation initiation site
identification. BMC Bioinformatics 11:119. http://dx.doi.org/10.1186/
1471-2105-11-119.
14. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD,
Lykidis A, Kyrpides NC. 2010. GenePRIMP: a gene prediction improve-
ment pipeline for prokaryotic genomes. Nat Methods 7:455–U462. http://
dx.doi.org/10.1038/nmeth.1457.
15. Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM, Kyrpi-
des NC. 2009. The DOE-JGI standard operating procedure for the anno-
tations of microbial genomes. Stand Genomic Sci 1:63– 67. http://
dx.doi.org/10.4056/sigs.632.
16. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpi-
des NC. 2009. IMG ER: a system for microbial genome annotation expert
review and curation. Bioinformatics 25:2271–2278. http://dx.doi.org/
10.1093/bioinformatics/btp393.
Ghodhbane-Gtari et al.
Genome Announcements2 genomea.asm.org July/August 2016 Volume 4 Issue 4 e00799-16


Permanent improved high-quality draft genome sequence of Nocardia casuarinae strain BMG51109, an endophyte ofactinorhizal root nodules of Casuarina glauca

UNH Scholars' Repository

University of New HampshireUniversity of New Hampshire Scholars' RepositoryNew Hampshire Agricultural Experiment Station Research Institutes, Centers and Programs8-4-2016Permanent improved high-quality draft genomesequence of Nocardia casuarinae strainBMG51109, an endophyte ofactinorhizal rootnodules of Casuarina glaucaFaten Ghodhbane-GtariUniversité Tunis El ManarNicholas BeaucheminUniversity of New Hampshire, DurhamMoussa LouatiUniversité Tunis El ManarImen NouiouiUniversité Tunis El ManarAmir KtariUniversité Tunis El ManarSee 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 CitationGhodhbane-Gtari F, Beauchemin N, Louati M, Nouioui I, Ktari A, Hezbri K, Gueddou A, Chen A, Huntemann M, Ivanova N,Kyrpides N, Markowitz V, MavrommatisK,Pagani I, Sen A, Wall L, Woyke T, Gtari M, Tisa LS. 2016. Permanent improved high-quality draft genome sequence of Nocardia casuarinaestrain BMG51109, an endophyte ofactinorhizal root nodules ofCasuarinaglauca. Genome Announc 4(4):e00799-16. https://dx.doi.org/10.1128/genomeA.00799-16AuthorsFaten Ghodhbane-Gtari, Nicholas Beauchemin, Moussa Louati, Imen Nouioui, Amir Ktari, Karima Hezbri,Abdellatif Gueddou, Amy Chen, Marcel Huntemann, Natalia Ivanova, Nikos Kyrpides, Victor Markowitz,Kostas Mavrommatis, Ioanna Pagani, Arnab Sen, Luis Wall, Tanja Woyke, Maher Gtari, and Louis S. TisaThis article is available at University of New Hampshire Scholars' Repository: https://scholars.unh.edu/nhaes/332Permanent Improved High-Quality Draft Genome Sequence ofNocardia casuarinae Strain BMG51109, an Endophyte of ActinorhizalRoot Nodules of Casuarina glaucaFaten Ghodhbane-Gtari,a Nicholas Beauchemin,b Moussa Louati,a Imen Nouioui,a Amir Ktari,a Karima Hezbri,a Abdellatif Gueddou,aAmy Chen,c Marcel Huntemann,c Natalia Ivanova,c Nikos Kyrpides,c Victor Markowitz,c Kostas Mavrommatis,c Ioanna Pagani,cArnab Sen,d Luis Wall,e Tanja Woyke,c Maher Gtari,a Louis S. TisabUniversity of Tunis-El Manar, Tunis, Tunisiaa; University of New Hampshire, Durham, New Hampshire, USAb; DOE Joint Genome Institute, Walnut Creek, California, USAc;University of North Bengal, Siliguri, Indiad; University of Quilmes, Quilmes, ArgentinaeHere, we report the first genome sequence of aNocardia plant endophyte, N. casuarinae strain BMG51109, isolated from Casu-arina glauca root nodules. The improved high-quality draft genome sequence contains 8,787,999 bp with a 68.90% GC contentand 7,307 predicted protein-coding genes.Received 13 June 2016 Accepted 15 June 2016 Published 4 August 2016Citation Ghodhbane-Gtari F, Beauchemin N, Louati M, Nouioui I, Ktari A, Hezbri K, Gueddou A, Chen A, Huntemann M, Ivanova N, Kyrpides N, Markowitz V, Mavrommatis K,Pagani I, Sen A, Wall L, Woyke T, Gtari M, Tisa LS. 2016. Permanent improved high-quality draft genome sequence of Nocardia casuarinae strain BMG51109, an endophyte ofactinorhizal root nodules of Casuarina glauca. Genome Announc 4(4):e00799-16. doi:10.1128/genomeA.00799-16.Copyright © 2016 Ghodhbane-Gtari 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 Nocardia are ubiquitous soil-borne aer-obic microorganisms belonging to a large group of actino-bacteria that are best known for their pathogenicity and theirharmful infections for humans or animals (1). However, severalNocardia spp. have been consistently reported as plant endophytesand isolated from disinfected roots (N. callitridis [2]), stems (N.artemisiae [3] and N. endophytica [4]), and actinorhizal root nod-ules (N. autotrophica [5], N. casuarinae [6], and Nocardia sp. [7–9]). The potential role of the Nocardia endophyte has been postu-lated, especially in the case of actinorhizal symbiosis (5, 10). To thebest of our knowledge, these plant-associated Nocardia spp. havenot had their genomes sequenced.We report here the genome sequence of Nocardia casuarinaestrain BMG51109, which was isolated from root nodules of Casu-arina glauca growing in Tunisia (6). N. casuarinae strainBMG51109 was sequenced to provide new insights into the rolethat this microbe plays in actinorhizal plants.The draft genome of N. casuarinae strain BMG51109 was gen-erated at the DOE Joint Genome Institute (JGI; Walnut Creek,CA, USA) using Pacific Biosciences (PacBio) technology. APacBio SMRTbell library was constructed and sequenced on thePacBio RS platform, which generated 583,909 filtered subreadstotaling 1.4 Gbp. All general aspects of library construction andsequencing performed at the JGI can be found at http://www.jgi.doe.gov. The raw reads were assembled using HGAP version 2.0.0(11). The final draft assembly contained 4 contigs in 4 scaffolds,totaling 8.8 Mbp in size. The input read coverage was 155.7.Project information is accessible in the Genomes Online Data-base (12). Genes were identified using Prodigal (13), followed by around of manual curation using GenePRIMP (14) as part of themicrobial annotation pipeline of the JGI (15). Additional geneprediction analysis and manual functional annotation were per-formed within the Integrated Microbial Genomes–Expert Review(IMG-ER) platform (http://img.jgi.doe.gov) developed by JGI(16).The high-quality draft genome of N. casuarinae strainBMG51109 was resolved to 4 scaffolds consisting of 7,730,817 bp,with a GC content of 68.90%, 7,822 candidate protein-codinggenes, 55 tRNA genes, and 3 rRNA regions.Nucleotide sequence accession numbers. The Nocardiacasuarinae strain BMG51109 genome sequence has been de-posited at DDBJ/EMBL/GenBank under the accession numberJAFQ00000000. The version described in this paper is the firstversion, JAFQ01000000.ACKNOWLEDGMENTSPartial funding by the New Hampshire Agricultural Experiment Station.This is Scientific Contribution Number 2678. The work conducted by theU.S. Department of Energy Joint Genome Institute is supported by theOffice of Science of the U.S. Department of Energy under contract no.DE-AC02-05CH11231. This project (L.S.T.) was supported in part by theUSDA National Institute of Food and Agriculture, Hatch 022821, and theCollege of Life Sciences and Agriculture at the University of New Hamp-shire, Durham, NH, USA. M.G. and F.G.-G. were supported in part by theVisiting Scientist and Postdoctoral Scientist Program administered by theNH AES at the University of New Hampshire.FUNDING INFORMATIONThis work, including the efforts of Louis S. Tisa, was funded byUSDA | National Institute of Food and Agriculture (NIFA) (Hatch022821). This work, including the efforts of Tanja Woyke, wasfunded by U.S. Department of Energy (DOE) (DE-AC02-05CH11231).REFERENCES1. Goodfellow M. 2014. Family Nocardiaceae, p 595– 650. In Rosenberg E,DeLong EF, Lory S, Stackebrandt E, Thompson F (ed), The prokaryotes—Actinobacteria. Springer, Berlin.2. Kaewkla O, Franco CM. 2010. Nocardia callitridis sp. nov., an endophyticcrossmarkGenome AnnouncementsJuly/August 2016 Volume 4 Issue 4 e00799-16 genomea.asm.org 1actinobacterium isolated from a surface-sterilized root of an Australiannative pine tree. Int J Syst Evol Microbiol 60:1532–1536. http://dx.doi.org/10.1099/ijs.0.016337-0.3. Zhao GZ, Li J, Zhu WY, Klenk HP, Xu LH, Li WJ. 2011. Nocardiaartemisiae sp. nov., an endophytic actinobacterium isolated from asurface-sterilized stem of Artemisia annua L. Int J Syst Evol Microbiol61:2933–2937. http://dx.doi.org/10.1099/ijs.0.029306-0.4. Xing K, Qin S, Fei SM, Lin Q, Bian GK, Miao Q, Wang Y, Cao CL, TangSK, Jiang JH, Li WJ. 2011. Nocardia endophytica sp. nov., an endophyticactinomycete isolated from the oil-seed plant Jatropha curcas L. Int J SystEvol Microbiol 61:1854 –1858. http://dx.doi.org/10.1099/ijs.0.027391-0.5. Dobritsa SV, Sharaya LS. 1986. Genome identity of different Nocardiaautotrophica isolates from Alnus spp. root nodules and rhizosphere. InSzabo G, Biro S, Goodfellow M (ed), Biological, biochemical and biomed-ical aspects of Actinomycetes Part B, vol 32. Akadémiai Kiadó, Budapest.6. Ghodhbane-Gtari F, Nouioui I, Salem K, Ktari A, Montero-CalasanzMdel C, Tisa LS, Klenk HP, Gtari M. 2014. Nocardia casuarinae sp. nov.,an actinobacterial endophyte isolated from root nodules of Casuarinaglauca. Antonie Van Leeuwenhoek 105:1099 –1106. http://dx.doi.org/10.1007/s10482-014-0168-6.7. Malishkaite YB, Nechaeva GA, Kuimova TF, Evtushenko LI, Agre NS.1987. Nocardia strains from actinorhizal plant nodules. Microbiology 56:100 –106.8. Pariiskaya AN, Novik SN, Agre NS, Kalakutskii LV. 1982. NocardiaIsolated from nitrogen-fixing nodules on the roots of the gray and blackalder. Microbiology 51:117–121.9. Ghodhbane-Gtari F, Essoussi I, Chattaoui M, Chouaia B, Jaouani A,Daffonchio D, Boudabous A, Gtari M. 2010. Isolation and characteriza-tion of non-Frankia actinobacteria from root nodules of Alnus glutinosa,Casuarina glauca and Elaeagnus angustifolia. Symbiosis 50:51–57. http://dx.doi.org/10.1007/s13199-009-0029-7.10. Ghodhbane-Gtari F, Tisa LS. 2014. Ecology and physiology of non-Frankia actinobacteria from actinorhizal plants, p 27– 42. In Katsey EI(ed), Plasticity in plant-growth-promoting and phytopathogenic bacteria.Springer, New York.11. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C,Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J.2013. Nonhybrid, finished microbial genome assemblies from long-readSMRT sequencing data. Nat Methods 10:563–569. http://dx.doi.org/10.1038/nmeth.2474.12. Reddy TB, Thomas AD, Stamatis D, Bertsch J, Isbandi M, Jansson J,Mallajosyula J, Pagani I, Lobos EA, Kyrpides NC. 2015. The Ge-nomes OnLine Database (GOLD) v.5: a metadata management systembased on a four level (meta)genome project classification. Nucleic Ac-ids Res 43:D1099 –D1106. http://dx.doi.org/10.1093/nar/gku950.13. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ.2010. Prodigal: prokaryotic gene recognition and translation initiation siteidentification. BMC Bioinformatics 11:119. http://dx.doi.org/10.1186/1471-2105-11-119.14. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD,Lykidis A, Kyrpides NC. 2010. GenePRIMP: a gene prediction improve-ment pipeline for prokaryotic genomes. Nat Methods 7:455–U462. http://dx.doi.org/10.1038/nmeth.1457.15. Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM, Kyrpi-des NC. 2009. The DOE-JGI standard operating procedure for the anno-tations of microbial genomes. Stand Genomic Sci 1:63– 67. http://dx.doi.org/10.4056/sigs.632.16. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpi-des NC. 2009. IMG ER: a system for microbial genome annotation expertreview and curation. Bioinformatics 25:2271–2278. http://dx.doi.org/10.1093/bioinformatics/btp393.Ghodhbane-Gtari et al.Genome Announcements2 genomea.asm.org July/August 2016 Volume 4 Issue 4 e00799-16

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Permanent improved high-quality draft genome sequence of Nocardia casuarinae strain BMG51109, an endophyte ofactinorhizal root nodules of Casuarina glauca

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