Open access
31 December 2015

Complete Genome Sequence of Curtobacterium sp. Strain MR_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts


Here, we present the 3,443,800-bp complete genome sequence of Curtobacterium sp. strain MR_MD2014 (phylum Actinobacteria). This strain was isolated from soil in Woods Hole, MA, as part of the 2014 Microbial Diversity Summer Program at the Marine Biological Laboratory in Woods Hole, MA.


Members of the genus Curtobacterium, first defined in 1972 by Yamada and Komagata (1), belong to the family Microbacteriaceae, within the phylum Actinobacteria. Several Curtobacterium isolates associate with plants as either pathogens or nonpathogens. Their cells are generally Gram-positive irregularly shaped motile rods. Here, Curtobacterium sp. strain MR_MD2014 was cocultured with Streptomyces sp. strain CCM_MD2014 from the topsoil collected near a rusted fire hydrant in Woods Hole, MA (41°31′44.65″N 70°40′21.5″W) on 7 July 2014, on starch-arginine-tryptophan (SAT) medium using protocols modified from El-Nakeeb and Lechevalier (2). This strain was then isolated from the coculture by selective culture, using antibiotic discs on a modified LB agar. The identity of each of the isolates was verified using the 16S rRNA gene sequence. This strain was cultivated as part of a student-led microbial isolation and sequencing initiative at the 2014 Microbial Diversity Summer Program at the Marine Biological Laboratory in Woods Hole, MA.
From the original coculture, total DNA extraction was carried out by 1 h of lysozyme digestion, followed by use of the Promega Wizard genomic DNA purification kit. The isolated DNA was quantified using the Promega QuantiFluor double-stranded DNA (dsDNA) system and then size selected for a minimum length of 4 kb. The size-selected DNA was sequenced on the Pacific Biosciences RSII sequencing platform with P5C3 chemistry. The sequenced fragments were assembled using HGAP3 on the SMRT Portal (3). The final assembled circular genome had a size of 3,443,800 bp, with 89× sequencing coverage and a G+C composition of 71.95%.
The genome was annotated using NCBI Prokaryotic Genome Annotation Pipeline version 2.8 (rev. 449627) (4, 5). The identified genes were composed of 2,675 coding sequences (CDSs), 4 rRNA operons, 48 tRNAs, and 1 noncoding RNA (ncRNA) gene. CRISPRFinder (6) identified one definite clustered regularly interspaced short palindromic repeat (CRISPR) and 13 potential CRISPRs in the genome. The PHAST server (7) predicted three prophages, two of which were incomplete, and one of which was of questionable quality. REBASE (8) identified 3 candidate methylase genes and one methylated motif, GGm6AGGC, which was found using Pacific Biosciences SMRT Portal analysis. This was unambiguously assigned to the type IIG restriction enzyme Csp2014I (see organism number 14032 on the REBASE website for details).
Phylogenetic analysis of the 16S rRNA gene sequence using SSU-align (version 0.1) (9) and RAxML (version 8.2.3) (10) revealed that strain MR_MD2014 belongs to the genus Curtobacterium, in the family Microbacteriaceae. The 16S rRNA gene-based analysis did not provide sufficient data for a refined classification of this strain at the species level. A phylogenetic reconstruction based upon 42 conserved single-copy-marker genes using CheckM (11) identified Curtobacterium sp. YR515 as being the most similar to the strain MR_MD2014 (see An average nucleotide identity (ANI) calculation using IMG (12) confirmed that the closest available genome to this strain is Curtobacterium sp. YR515, with only 85.3% average nucleotide identity across shared genes.

Nucleotide sequence accession numbers.

The complete nucleotide sequence of this genome is available through GenBank under the accession no. CP009755. The version described here is CP009755.1.


The isolation and culturing of this organism were carried out as part of the 2014 Microbial Diversity Summer Program at the Marine Biological Laboratory in Woods Hole, MA. The course was supported by generous grants from the Simons Foundation (grant 309981 to the Marine Biological Laboratory), the Beckman Foundation, and the Howard Hughes Medical Institute. This material is based upon work supported by the National Aeronautics and Space Administration (grant NNA13AA92A), the National Science Foundation (grant MCB-1417876), and the U.S. Department of Energy (grant DE-FG02-85ER13361). R.M.M. was supported by a fellowship from Alabama EPSCoR GRSP, Auburn University's Cell and Molecular Biosciences (CMB) Summer Fellowship, Selman A. Waksman Endowed Scholarship in Microbial Diversity, the Bernard Davis Endowed Scholarship (grant 47802012050), the Auburn Graduate School Travel Award, and the Joseph Kirby Farrington Endowed Fund for Excellence. These funders had no role in the study design, data collection and interpretation, or the decision to submit the work for publication.
Promega Corporation donated the molecular reagents used in this project. The sequencing for this organism was supported and carried out by Pacific Biosciences. We thank George O’Toole, Alison Butler, Emil Ruff, Arpita Bose, Suzanne Kern, Louis Kerr, Kurt Dahlstrom, Alice Michel, and Cristian Salgado for their assistance and advice.
R.J.R. works for New England BioLabs, a company that sells research reagents, including restriction enzymes and DNA methylases, to the scientific community. J.K. and M.B. are full-time employees at Pacific Biosciences, a company that develops single-molecule real-time sequencing technologies, including the sequencing platform used in this project.
This report was prepared as an account of work sponsored by an agency of the U.S. Government. Neither the U.S. Government nor any agency thereof, nor any of their employees, makes any warranty, expressed or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Any reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the U.S. Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the U.S. Government or any agency thereof.


Yamada K, Komagata K. 1972. Taxonomic studies on coryneform bacteria. V. Classification of coryneform bacteria. Appl Microbiol 18:417–431.
El-Nakeeb MA, Lechevalier HA. 1963. Selective isolation of aerobic actinomycetes. Appl Microbiol 11:75–77.
Chin C, 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.
Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity GM, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O. 2008. Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta) genomic annotation. Omics J Integr Biol 12:137–141.
Tatusova T, DiCuccio MD, Badretdin A, Chetvernin V, Ciufo S, Li W. 2013. Prokaryotic genome annotation pipeline, the NCBI handbook, 2nd ed. National Center for Biotechnology Information, Bethesda, MD.
Grissa I, Vergnaud G, Pourcel C. 2007. CRISPRFinder: a Web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:W52–W57.
Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. 2011. PHAST: a fast phage search tool. Nucleic Acids Res 39:W347–W352.
Roberts RJ, Vincze T, Posfai J, Macelis D. 2014. REBASE—a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 43:D298–D299.
Nawrocki EP. 2009. Structural RNA homology search and alignment using covariance models. Ph.D. thesis. Washington University in St. Louis, St. Louis, MO.
Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055.
Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, Pati A. 2015. Microbial species delineation using whole genome sequences. Nucleic Acids Res 43:6761–6771.

Information & Contributors


Published In

cover image Genome Announcements
Genome Announcements
Volume 3Number 631 December 2015
eLocator: 10.1128/genomea.01504-15


Received: 30 October 2015
Accepted: 4 November 2015
Published online: 31 December 2015



Richard M. Mariita
Department of Biological Sciences, Auburn University, Alabama, USA
Srijak Bhatnagar
Microbiology Graduate Group, University of California Davis, Davis, California, USA
Kurt Hanselmann
Department of Earth Sciences, ETH Zurich, Zürich, Switzerland
Mohammad J. Hossain
Department of Biological Sciences, Auburn University, Alabama, USA
Jonas Korlach
Pacific Biosciences, Menlo Park, California, USA
Matthew Boitano
Pacific Biosciences, Menlo Park, California, USA
Richard J. Roberts
New England BioLabs, Ipswich, Massachusetts, USA
Mark R. Liles
Department of Biological Sciences, Auburn University, Alabama, USA
Anthony G. Moss
Department of Biological Sciences, Auburn University, Alabama, USA
Jared R. Leadbetter
Linde Center for Global Environmental Science, California Institute of Technology, Pasadena, California, USA
Dianne K. Newman
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
Howard Hughes Medical Institute, Pasadena, California, USA
Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
Scott C. Dawson
Department of Microbiology and Molecular Genetics, University of California Davis, Davis, California, USA


Address correspondence to Scott C. Dawson, [email protected].
R.M.M. and S.B. are co-first authors.

Metrics & Citations


Note: There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.

Citation counts come from the Crossref Cited by service.


If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download.

View Options

Figures and Media






Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy