Open access
28 February 2013

Genome Sequence of Mycoplasma feriruminatoris sp. nov., a Fast-Growing Mycoplasma Species

ABSTRACT

Members of the “Mycoplasma mycoides cluster” represent important livestock pathogens worldwide. We report the genome sequence of Mycoplasma feriruminatoris sp. nov., the closest relative to the “Mycoplasma mycoides cluster” and the fastest-growing Mycoplasma species described to date.

GENOME ANNOUNCEMENT

Species belonging to the “Mycoplasma mycoides cluster” represent important livestock pathogens causing substantial economic losses in cattle, goats, and sheep. Recently, a group of Mycoplasma strains closely related to the “M. mycoides cluster” has been identified by multilocus sequence typing (1). These five strains were isolated from a Rocky Mountain goat and four Alpine ibexes. We assessed the taxonomic position of these strains and suggest that they represent a novel species named M. feriruminatoris sp. nov. (J. Jores, M. Heller, C. Schnee, A. Fischer, and J. Frey, unpublished results). This species is the fastest-growing Mycoplasma species described so far, with a generation time of less than 30 min. Here we report the genome sequence of Mycoplasma feriruminatoris sp. nov. G5847T (=DSM 26019T = NCTC 13622T). This genome was sequenced with Illumina GAIIx paired-end sequencing, with reads of about 75 bases. The reads were assembled using Velvet 1.1 (2). The best assembly resulted from a subsample of 140× genome coverage of Illumina reads. The draft genome comprises 92 contigs totaling a length of 1,019,436 bp; 25 contigs that were longer than 10,000 bp covered 89% of the assembly. The N50 contig size is 46,000 bp.
The average G+C content of the genome is 24.1%. Open reading frames (ORFs) were predicted using Prodigal 2.50 (3). A total of 879 ORFs, 29 tRNAs, and the 23S, 16S, and 5S rRNA operons were predicted. Functional annotation was produced by the Institute for Genome Sciences Annotation Engine (4) (http://ae.igs.umaryland.edu/cgi/index.cgi). The average gene length is 1,058 bp, and the coding density of the genome is 91%. Of the 879 ORFs, 692 have been assigned functions, have received annotations based on membership in a protein family, or have been identified as containing a particular domain. The remaining ORFs are hypothetical. Four genes encode proteins involved in fatty acid and phospholipid metabolism; 29 encode proteins involved in amino acid, purine, pyrimidine, nucleoside and nucleotide, cofactor, prosthetic group, and carrier metabolism; 57 encode proteins involved in central, intermediary, and energy metabolism; and 221 encode proteins involved in DNA metabolism, transcription, protein synthesis, and protein fate. In addition, 123 gene products are involved in transport and binding, 13 have regulatory functions, 10 are involved in signal transduction, 45 are cell envelope lipoproteins, and 63 are involved in cellular processes. Seven genes have mobile element functions. One of them encodes a phage integrase family protein, which has homologs only in Mycoplasma bovis, Mycoplasma agalactiae, and Mycoplasma hyorhinis.
Due to their minimal genome size, mycoplasmas have become model organisms to study fundamental questions of biological life. More recently, they have become the target species in synthetic biology and constructions of synthetic genomes (5, 6). One of the rate-limiting factors in such studies is the slow generation time of most Mycoplasma species relative to other microbial organisms. Understanding the basis of the short generation time of M. feriruminatoris sp. nov. should accelerate the use of Mycoplasma as a template for designer organisms with fully synthetic genomes.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number ANFU00000000. The version described in this paper is the first version, ANFU01000000.

ACKNOWLEDGMENTS

This work was supported by the German Federal Ministry for Economic Cooperation and Development (contract no. 81121408, project no. 09.7860.1-001.00). The Centre for International Migration and Development (CIM) supported A.F. The functional annotation was conducted using the IGS Annotation Engine, University of Maryland School of Medicine.
We thank Vish Nene, Marc Ciosi, and Jandouwe Villinger for their comments on the manuscript.

REFERENCES

1.
Fischer A, Shapiro B, Muriuki C, Heller M, Schnee C, Bongcam-Rudloff E, Vilei EM, Frey J, and Jores J. 2012. The origin of the “Mycoplasma mycoides Cluster” coincides with domestication of ruminants. PLoS One 7:e36150.
2.
Zerbino DR and Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821–829.
3.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, and Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119.
4.
Galens K, Orvis J, Daugherty S, Creasy HH, Angiuoli S, White O, Wortman J, Mahurkar A, and Giglio MG. 2011. The IGS standard operating procedure for automated prokaryotic annotation. Stand. Genomics Sci. 4:244–251.
5.
Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA III, Smith HO, and Venter JC. 2007. Genome transplantation in bacteria: changing one species to another. Science 317:632–638.
6.
Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA III, Smith HO, and Venter JC. 2010. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329:52–56.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 1Number 128 February 2013
eLocator: 10.1128/genomea.00216-12

History

Received: 17 December 2012
Accepted: 31 December 2012
Published online: 28 February 2013

Contributors

Authors

Anne Fischer
International Livestock Research Institute, Nairobi, Kenya
International Centre for Insect Physiology and Ecology, Nairobi, Kenya
Ivette Santana-Cruz
Institute for Genome Sciences, Baltimore, Maryland, USA
Michelle Giglio
Institute for Genome Sciences, Baltimore, Maryland, USA
Suvarna Nadendla
Institute for Genome Sciences, Baltimore, Maryland, USA
Elliott Drabek
Institute for Genome Sciences, Baltimore, Maryland, USA
Edy M. Vilei
Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
Present address: Edy M. Vilei, Suisselab AG, Zollikofen, Switzerland.
Joachim Frey
Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
Joerg Jores
International Livestock Research Institute, Nairobi, Kenya

Notes

Address correspondence to Anne Fischer, [email protected].

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