Draft Genome Sequences of Mycoplasma auris and Mycoplasma yeatsii, Two Species of the Ear Canal of Caprinae

Abstract

We report here the draft genome sequences of Mycoplasma auris and Mycoplasma yeatsii, two species commonly isolated from the external ear canal of Caprinae.

GENOME ANNOUNCEMENT

Mycoplasma auris and Mycoplasma yeatsii, of the hominis and spiroplasma phylogenetic groups, respectively, are two recently described species of the Mycoplasma genus (1, 2). Both species appear to have little clinical relevance, yet they are commonly isolated from the external ear canal of Caprinae (3–8), often in association with Mycoplasma agalactiae (hominis group) and/or Mycoplasma mycoides subsp. capri (spiroplasma group), two pathogens of small ruminants that are responsible for contagious agalactia (9). Ruminant Mycoplasma species of these two remote groups were shown to have exchanged a significant amount of genetic information by horizontal gene transfer (HGT) (10). Thus, the ear canal may offer an ecological niche in which HGT can occur between pathogenic and nonpathogenic Mycoplasma species.

Genome sequences are available for M. agalactiae and for M. mycoides subsp. capri, but not for M. auris and for M. yeatsii. To fill this gap, we report here the complete genome sequence of M. yeatsii strain 13926 and M. auris strain 15026, isolated in France from ear swabs of a domestic goat (within a flock with a clinical history of mycoplasmosis [7]) and an Alpine ibex (during an abnormal mortality episode with recurrent isolations of M. agalactiae [11]), in 2003 and 2008, respectively. Whole-genome sequences were obtained using a combination of Illumina (single reads) and 454 (mate paired with 8-kb insert size), resulting in a 50× (M. auris) and 69× (M. yeatsii) median coverages. Assembly was performed using Newbler 2.3, and the annotation was conducted using a customized version of the CAAT-Box platform (12) with an automatic preannotation for coding sequences (CDSs) followed by expert validation, as detailed previously (11). Genome analysis and comparisons were mainly conducted using the MolliGen 3.0 platform (13).

Sequence data showed that the estimated genome sizes (767,867 bp and 896,612 bp for M. auris and M. yeatsii, respectively), the G+C% (27.20 and 25.76% for M. auris and M. yeatsii, respectively), the gene density (89.13 and 85.24% for M. auris and M. yeatsii, respectively), and the highest similarity scores of CDSs were consistent with the phylogenetic grouping of these species (2). M. auris displayed 26 CDSs (out of 616) with no homolog in ruminant Mycoplasma species sequenced so far, one of which has similarities with an Mycoplasma hominis CDS annotated as the virulence-associated protein D. Of the 32 M. yeatsii-specific CDSs (out of 687), 16 correspond to lipoproteins containing a DUF285 domain, also found in a large family of surface proteins shared by other ruminant Mycoplasma species (14). Finally, both genomes displayed sequences related to an integrative conjugative element, with only M. auris having a complete element. Altogether, these data indicate that M. auris and M. yeatsii may be equipped with or able to acquire virulence genes from other Mycoplasma species sharing their habitat.

Nucleotide sequence accession numbers.

These Whole-Genome Shotgun projects have been deposited at DDBJ/EMBL/GenBank under the accession no. AORI00000000 for M. auris 15026 and AORK00000000 for M. yeatsii 13926. The versions described in this paper are the first versions, accession no. AORI01000000 and AORK01000000, respectively.