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High quality draft genome sequence of Mycoplasma testudineum strain BH29T, isolated from the respiratory tract of a desert tortoise

Standards in Genomic Sciences volume 13, Article number: 9 (2018) Cite this article

Abstract

Mycoplasma testudineum is one of the pathogens that can cause upper respiratory tract disease in desert tortoises, Gopherus agassizii. We sequenced the genome of M. testudineum BH29T (ATCC 700618T = MCCM 03231T), isolated from the upper respiratory tract of a Mojave desert tortoise with upper respiratory tract disease. The sequenced draft genome, organized in 25 scaffolds, has a length of 960,895 bp and a G + C content of 27.54%. A total of 788 protein-coding sequences, six pseudogenes and 35 RNA genes were identified. The potential presence of cytadhesin-encoding genes is investigated. This genome will enable comparative genomic studies to help understand the molecular bases of the pathogenicity of this and other Mycoplasma species.

Introduction

Species of the genus Mycoplasma have extremely small genomes, likely contributing to the need of the species to gain resources from host cells, and while Mycoplasma form a variety of relationships with hosts, many are pathogenic in vertebrates [1]. In North American tortoises, an upper respiratory tract disease is associated with both Mycoplasma testudineum and its close relative, Mycoplasma agassizii [2,3,4,5]. North American tortoise populations are in decline, with infectious disease as a possible agent in these declines [6,7,8], though importantly, our knowledge of the mechanisms of disease progression and its impacts on populations is lacking [9, 10]. To understand URTD, we must improve our understanding of the pathogens associated with the disease. By sequencing the genome of M. testudineum , we may gain insight into proteins associated with its pathogenicity and virulence.

Until now, DNA sequence data available for this species in GenBank was limited to ribosomal RNA genes and the associated intergenic spacer region, as well as the RNA polymerase beta subunit gene. To obtain genomic data on the species, we extracted DNA from a culture of the type-strain, BH29T, which was collected from the upper respiratory tract of a wild Mojave desert tortoise, Gopherus agassizii [3]. This sequencing work is part of a larger project addressing mycoplasmal variation among host species.

Organism information

Classification and features

M. testudineum infects the upper respiratory tracts of tortoises causing upper respiratory tract disease [3, 4]; however, recent investigations in wild tortoises suggest it may be present in the host without pathogenicity [11]. This microbe has been found in five tortoise species inhabiting North America— G. agassizii , G. morafkai, G. evgoodei, G. berlandieri, and G. polyphemus [3, 11,12,13]—and its presence has yet to be investigated in the sixth tortoise congener, G. flavomarginatus (located in north-central Mexico). From wild samples, there is some indication that M. testudineum may have a facilitative relationship with M. agassizii in tortoise hosts, but interactions with other community members are unknown [11].

M. testudineum is a sugar-fermenting, coccoid Mycoplasma , which is very similar in phenotype to the closely-related M. agassizii [3] (Table 1, Fig. 1). M. testudineum grows in culture at 22–30°C, with an optimal growth at 30°C [3] (Table 1). These temperatures are frequently experienced in their hosts during the seasons when tortoises are found to be most active [14, 15], though tortoise body temperatures can fluctuate well above or below these temperatures within a day and over the seasons [14,15,16].

Table 1 Classification and general features of Mycoplasma testudineum strain BH29T
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Fig. 1
figure 1

Transmission electron micrograph of thin section of Mycoplasma testudineum strain BH29T. Image from ref. [3], reproduced with permission from the publisher

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To determine the placement of M. testudineum in the mycoplasmal phylogeny, all 16S rRNA gene sequences from the type strains of Mycoplasma species were obtained from the SILVA database [17] and aligned using MUSCLE 3.8.31 [18], and a phylogenetic tree was constructed using the maximum likelihood method implemented in MEGA7 [19] (Fig. 2). M. agassizii is a sister group of M. testudineum in the resultant tree, and the M. testudineum / M. agassizii clade is a sister group of Mycoplasma pulmonis —the agent of murine respiratory mycoplasmosis, which also seems to be present in humans who are in contact with rodents [20]. All three species fall within the hominis group of Mycoplasma (see ref. [21] for group definitions). The M. testudineum 16S rRNA gene sequence is 93.1 and 89.2% identical to those of M. agassizii and M. pulmonis , respectively. Remarkably, these species are not closely related to Mycoplasma testudinis , isolated from the cloaca of a spur-thighed tortoise ( Testudo graeca ) in the UK [22], which are placed in the pneumoniae group. A previous taxonomic analysis placed M. testudinis within the pneumoniae group (in agreement with our results), but placed M. testudineum and M. agassizii in different hominis subgroups: the hyorhinis and the fermentans groups, respectively [23]. Our result is, however, in agreement with that by Volokhov et al. [24], which was also based on 16S rRNA data.

Fig. 2
figure 2

Phylogenetic tree of the Mycoplasma genus based on 16S rRNA gene sequences showing the phylogenetic position of M. testudineum BH29T (●). All 16S sequences from the Mycoplasma genus were obtained from the SILVA database [17]. Only sequences in the ‘The All-Species Living Tree’ Project (LTP), release 128, were retained. This dataset only contains sequences from type strains, designated with a superscripted “T”. Clostridium botulinum strain ATCC 25763 was also included in the dataset as outgroup. Sequences were aligned using MUSCLE 3.8.31 [18]. A phylogenetic tree was obtained using the maximum likelihood method implemented in MEGA7 [19], with 1000 bootstrap replicates. Species with available genomes at the NCBI Genomes database or the Genomes Online Database are represented in bold face. GenBank accession numbers are shown in parentheses. Bootstrap support values above 50% are represented. The scale bar represents a divergence of 0.05 nucleotide substitutions per nucleotide position

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Genome sequencing information

Genome project history

The type strain of M. testudineum , strain BH29T, was selected for sequencing. This strain was isolated from a nasal flush of the choana of a Mojave desert tortoise, which was filtered through a 0.45 μm filter and then grown in SP4 broth [2, 3]. Sequencing was conducted in October 2016. The Whole Genome Shotgun project was deposited at DDBJ/ENA/GenBank under the accession number NNCE00000000. The version described in this paper is the first version, NNCE01000000. A summary of the project information in compliance with MIGS version 2.0 [25] is shown in Table 2.

Table 2 Project information
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Growth conditions and genomic DNA preparation

Freeze-dried M. testudineum , strain BH29T, was obtained from the ATCC in November 2014 (ATCC 700618T) and had been cultured by the ATCC on Spiroplasma SP4 medium at 30°C in aerobic conditions. Genomic DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit protocol for Gram-negative bacteria and eluted with ultra-pure water. Extracted DNA was quantified on a Qiagen QIAxpert system and with Picogreen analysis.

Genome sequencing and assembly

Genome sequencing was conducted using the Illumina Nextera XT DNA Library Preparation Kit (Illumina, Inc., San Diego, USA) with the Illumina NextSeq500 platform (150 bp, paired-end) and 2 ng of starting genomic DNA at the Nevada Genomics Center (University of Nevada, Reno). Sequencing was performed in multiplex with multiple samples, using dual index sequences from the Illumina Nextera XT Index Kit, v2 (index 1, N701; index 2, S502). A total of 455,422 read pairs were obtained. Using Trimmomatic, version 0.36 [26], reads were trimmed to remove Nextera adapter sequences and low quality nucleotides from either end (average Phred score Q ≤ 5, four bp sliding window), and sequences trimmed to < 35 bp were removed. After trimming, 412,763 read pairs and 36,907 single-reads (the pairs of which were removed) remained. De novo genome assembly was performed using SPAdes 3.10.1 [27], using as inputs the trimmed paired reads, and the trimmed single reads (assembly k-mer sizes 21, 33, 55, and 77; with read error-correction enabled and ‘--careful’ mode mismatch correction). After removing scaffolds of less than 500 bp, the final assembly consisted of 25 scaffolds with a total length of 960,895 bp, an average length of 38,435 bp, and an N50 of 130,815 bp. The coverage was 64×.

Genome annotation

Gene prediction was carried out using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) 4.2 [28]. For each predicted protein, (i) families were identified using the Pfam 31.0 [29] batch search tool (“gathering threshold” option), (ii) COG categories were assigned using eggNOG-mapper [30] based on eggNOG 4.5.1 data [31], (iii) signal peptides were identified using the SignalP server 4.1 [32], and (iv) transmembrane helices were inferred using the TMHMM server v. 2.0 [33]. CRISPR repeats were identified using PGAP and CRISPRFinder [34].

Genome properties

The properties of the draft genome are summarized in Table 3. The final assembly consisted of 25 scaffolds, with a total length of 960,895 bp and a G + C content of 27.54%. The small genome size and low G + C content is consistent with those of other Mycoplasma genomes sequenced [35, 36]. PGAP [28] identified a total of 788 protein-coding genes, 6 pseudogenes, and 35 RNA genes. The identified RNA genes include 3 rRNAs (one 5S, one 16S and one 23S), 3 ncRNAs and 29 tRNAs. PGAP identified 4 CRISPR repeats, and CRISPRFinder [34] identified 4 “confirmed” repeats, and another 3 that were flagged as “questionable” by the server. The numbers of protein-coding genes in each COG category [37] are summarized in Table 4.

Table 3 Genome statistics
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Table 4 Number of genes associated with general COG functional categories
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Insights from the genome sequence

Brown et al. [3] sequenced most of the 16S rRNA gene of M. testudineum strain BH29T (GenBank ID: AY366210). They had previously sequenced the homologous region for M. testudineum strain H3110, which differed only in one nucleotide position (GenBank ID: U19768, ref. [23]). Comparison of their BH29T sequence and that obtained by us revealed 5 point differences and an indel of 14 nucleotides (present in Brown et al.’s sequence but not in ours) (Fig. 3). Remarkably, 4 of the 5 point differences were located toward the ends of Brown et al.’s sequence, and thus may represent sequencing errors. The other differences probably represent mutations accumulated since the isolation of the strain in 1995. Our 16S rRNA gene sequence is identical to that generated by Volokhov et al. [24], with the exception of the first nucleotide of Volokhov et al.’s sequence. Nevertheless, the placement of M. testudineum in the tree (Fig. 2) is not affected by the particular sequence used.

Fig. 3
figure 3

Comparison of the 16S rRNA gene sequences generated by Brown et al. [3], by Volokhov et al. [24], and in our study. All three sequences correspond to M. testudineum BH29T. Asterisks represent identical sites

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In general, Mycoplasma cells need to adhere to mucosal epithelial cells of the hosts as a pre-requisite for pathogenesis. The mechanisms of adhesion are relatively well understood in Mycoplasma pneumoniae and its close relatives, but much less so in other Mycoplasma groups [38]. We used BLASTP and TBLASTN (E < 10− 5; low-complexity regions filtered out) to search for homologs of M. pneumoniae cytadhesins P1, P30, P65, P40 and P90 —proteins involved in adhesion— and cytadhesin accessory proteins Hmw1, Hmw2 and Hmw3 in all available Mycoplasma genomic data (nr database). We only found homologs in species closely related to M. pneumoniae ( Mycoplasma genitalium , Mycoplasma gallisepticum , Mycoplasma pirum , Mycoplasma alvi , Mycoplasma imitans , and M. testudinis ), as previously noted [38, 39]. Searches against the M. testudineum BH29T proteome detected no hits, and none of the 788 predicted M. testudineum proteins contained any of the Pfam domains present in the M. pneumoniae cytadhesins and accessory proteins (domains “CytadhesinP1”, “Adhesin_P1”, “Cytadhesin_P30”, “MgpC” and “EAGR_box”). These observations may have at least three alternative explanations: (i) the adhesion proteins used by M. pneumoniae may be specific to its group, (ii) adhesion proteins evolve very fast, perhaps due to co-evolutionary races, thus hindering the detection of distant homologs, or (iii) M. testudineum may exhibit limited adhesion capabilities. In support of the first possibility, M. pulmonis , the most closely related species to the M. testudineum / M. agassizii clade (Fig. 2), is known to have adhesion mechanisms different from M. pneumoniae : M. pneumoniae exhibits a specialized attachment organelle, whereas M. pulmonis adhesion takes place by generalized interaction of the pathogen and the host cell membranes [40]. The adhesins of M. pulmonis are unknown. In support of the second scenario, putative cytadhesins identified in M. pirum and M. gallisepticum are only 26–29% identical at the amino acid level to those of M. pneumoniae [41, 42].

To extend our search, we obtained a list of known Mycoplasma adhesins from the UniProt database [43] (search: “ Mycoplasma adhesin”). Again, BLASTP and TBLASTN searches (E < 10− 5; low-complexity regions filtered out) against the M. testudineum BH29T proteome/genome did not identify any significant hits. M. pneumoniae proteins GAPDH and EF-Tu and M. hominis protein OppA have been reported to be adhesins in addition to their traditional functions [44,45,46]. We found homologs of all three proteins in M. testudineum . It should be noted, however, that this does not guarantee that these proteins act as adhesins in M. testudineum . For instance, whereas M. pneumoniae EF-Tu binds fibronectin [45], M. genitalium EF-Tu, which is 96% identical, does not [47]. The M. testudineum protein is only 70% identical to that of M. pneumoniae , and serine 343, proline 345, and threonine 357 (replacement of which significantly reduces the fibronectin binding of EF-Tu in M. pneumoniae ; ref. [47]) are not conserved in M. testudineum . Additional work will be required to understand the mechanisms of adhesion in M. testudineum and its close relatives.

Conclusions

We have obtained a draft genome sequence of M. testudineum BH29T isolated from the upper respiratory tract of a desert tortoise with URTD in the Mojave Desert. Our analysis revealed some features typical of Mycoplasma genomes: a very small size and low G + C content. The new genome will enable comparative genomic studies to help understand the molecular bases of the pathogenicity of this and other Mycoplasma species.

Abbreviations

ATCC:

American Type Culture Collection

BLAST:

Basic local alignment search tool

COG:

Clusters of Orthologous Groups

EF-Tu:

Elongation factor Tu

GAPDH:

Glyceraldehyde-3-phosphate dehydrogenase

MIGS:

Minimum information on the genome sequence

NCBI:

National Center for Biotechnology Information

OppA:

Substrate-binding domain of the oligopeptide permease

References

  1. Brown DR. Mycoplasmosis and immunity of fish and reptiles. Front Biosci. 2002;7:d1338–46.

    Article  CAS  PubMed  Google Scholar 

  2. Brown MB, Schumacher IM, Klein PA, Harris K, Correll T, Jacobson ER. Mycoplasma agassizii causes upper respiratory tract disease in the desert tortoise. Infect Immun. 1994;62(10):4580–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Brown D, Merritt J, Jacobson E, Klein P, Tully J, Brown M. Mycoplasma testudineum sp. nov., from a desert tortoise (Gopherus agassizii) with upper respiratory tract disease. Int J Syst Evol Microbiol. 2004;54(5):1527–9.

    Article  CAS  PubMed  Google Scholar 

  4. Jacobson ER, Berry KH. Mycoplasma testudineum in free-ranging desert tortoises, Gopherus agassizii. J Wildl Dis. 2012;48(4):1063–8.

    Article  PubMed  Google Scholar 

  5. Brown MB, McLaughlin GS, Klein PA, Crenshaw BC, Schumacher IM, Brown DR, Jacobson ER. Upper respiratory tract disease in the gopher tortoise is caused by Mycoplasma agassizii. J Clin Microbiol. 1999;37:2262–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Desert Tortoise Recovery Team. Desert tortoise (Mojave population): recovery plan. Portland: US Fish and Wildlife Service; 1994.

    Google Scholar 

  7. Seigel RA, Smith RB, Seigel NA. Swine flu or 1918 pandemic? Upper respiratory tract disease and the sudden mortality of gopher tortoises (Gopherus polyphemus) on a protected habitat in Florida. J Herpetol. 2003;37(1):137–44.

    Article  Google Scholar 

  8. Enge KM, Berish JE, Bolt R, Dziergowski A, Mushinsky HR. Biological status report: gopher tortoise. Tallahassee: Florida Fish and Wildlife Conservation Commission; 2006.

    Google Scholar 

  9. Sandmeier FC, Tracy CR, Hunter K. Upper respiratory tract disease (URTD) as a threat to desert tortoise populations: a reevaluation. Biol Conserv. 2009;142(7):1255–68.

    Article  Google Scholar 

  10. Diemer Berish JE, Wendland LD, Kiltie RA, Garrison EP, Gates CA. Effects of mycoplasmal upper respiratory tract disease on morbidity and mortality of gopher tortoises in northern and Central Florida. J Wildl Dis. 2010;46(3):695–705.

    Article  Google Scholar 

  11. Weitzman CL, Gov R, Sandmeier FC, Snyder SJ, Tracy CR. Co-infection does not predict disease in Gopherus tortoises. Royal Soc Open Sci. 2017;4(10):171003.

  12. Berry KH, Brown MB, Vaughn M, Gowan TA, Hasskamp MA, Torres MCM. Mycoplasma agassizii in Morafka's desert tortoise (Gopherus morafkai) in Mexico. J Wildl Dis. 2015;51(1):89–100.

    Article  PubMed  Google Scholar 

  13. McGuire JL, Smith LL, Guyer C, Lockhart JM, Lee GW, Yabsley MJ. Surveillance for upper respiratory tract disease and Mycoplasma in free-ranging gopher tortoises (Gopherus polyphemus) in Georgia, USA. J Wildl Dis. 2014;50(4):733–44.

    Article  PubMed  Google Scholar 

  14. Anderson NJ. The thermal biology of the gopher tortoise (Gopherus polyphemus) and the importance of microhabitat selection. MS dissertation. Hammond: Southeastern Louisiana University; 2001.

    Google Scholar 

  15. McGinnis SM, Voigt WG. Thermoregulation in the desert tortoise, Gopherus agassizii. Comp Biochem Physiol A Physiol. 1971;40(1):119–26.

    Article  Google Scholar 

  16. Snyder SJ. Effects of fire on desert tortoise (Gopherus agassizii) thermal ecology. PhD dissertation. Reno: University of Nevada; 2014.

  17. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(Database issue):D590–6.

    CAS  PubMed  Google Scholar 

  18. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870–4.

    Article  CAS  PubMed  Google Scholar 

  20. Piasecki T, Chrzastek K, Kasprzykowska U. Mycoplasma pulmonis of rodents as a possible human pathogen. Vector Borne Zoonotic Dis. 2017;17(7):475–7.

    Article  PubMed  Google Scholar 

  21. Weisburg W, Tully J, Rose D, Petzel J, Oyaizu H, Yang D, Mandelco L, Sechrest J, Lawrence T, Van Etten J. A phylogenetic analysis of the mycoplasmas: basis for their classification. J Bacteriol. 1989;171(12):6455–67.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Hill AC. Mycoplasma testudinis, a new species isolated from a tortoise. Int J Syst Evol Microbiol. 1985;35(4):489–92.

    Google Scholar 

  23. Brown D, Crenshaw B, McLaughlin G, Schumacher I, McKenna C, Klein P, Jacobson E, Brown M. Taxonomic analysis of the tortoise mycoplasmas Mycoplasma agassizii and Mycoplasma testudinis by 16S rRNA gene sequence comparison. Int J Syst Evol Microbiol. 1995;45(2):348–50.

    CAS  Google Scholar 

  24. Volokhov DV, Simonyan V, Davidson MK, Chizhikov VE. RNA polymerase beta subunit (rpoB) gene and the 16S–23S rRNA intergenic transcribed spacer region (ITS) as complementary molecular markers in addition to the 16S rRNA gene for phylogenetic analysis and identification of the species of the family Mycoplasmataceae. Mol Phylogenet Evol. 2012;62(1):515–28.

    Article  CAS  PubMed  Google Scholar 

  25. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV. The minimum information about a genome sequence (MIGS) specification. Nat Biotecnol. 2008;26(5):541.

    Article  CAS  Google Scholar 

  26. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–77.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44(14):6614–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016;44(D1):D279–85.

    Article  CAS  PubMed  Google Scholar 

  30. Huerta-Cepas J, Forslund K, Pedro Coelho L, Szklarczyk D, Juhl Jensen L, von Mering C, Bork P. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol. 2017;34(8):2115–22.

    Article  PubMed  PubMed Central  Google Scholar 

  31. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 2015;44(D1):D286–93.

    Article  PubMed  PubMed Central  Google Scholar 

  32. Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8(10):785–6.

    Article  CAS  PubMed  Google Scholar 

  33. TMHMM Server v. 2.0. [http://www.cbs.dtu.dk/services/TMHMM/]. Accessed Aug 2017.

  34. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35(suppl_2):W52–7.

    Article  PubMed  PubMed Central  Google Scholar 

  35. Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, et al. The minimal gene complement of mycoplasma genitalium. Science. 1995;270(5235):397–403.

    Article  CAS  PubMed  Google Scholar 

  36. Citti C, Blanchard A. Mycoplasmas and their host: emerging and re-emerging minimal pathogens. Trends Microbiol. 2013;21(4):196–203.

    Article  CAS  PubMed  Google Scholar 

  37. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003;4:41.

    Article  PubMed  PubMed Central  Google Scholar 

  38. Browning GF, Noormohammadi AH, Markham PF. Identification and characterization of virulence genes in mycoplasmas. Mollicutes. 2014;10(1):77–90.

  39. Fischer A, Santana-Cruz I, Hegerman J, Gourlé H, Schieck E, Lambert M, Nadendla S, Wesonga H, Miller RA, Vashee S. High quality draft genomes of the Mycoplasma mycoides subsp. mycoides challenge strains Afadé and B237. Stand Genomic Sci. 2015;10(1):89.

    Article  PubMed  PubMed Central  Google Scholar 

  40. Cassell GH. The pathogenic potential of mycoplasmas: Mycoplasma pulmonis as a model. Rev Infect Dis. 1982;4(Supplement 1):S18–34.

    Article  PubMed  Google Scholar 

  41. Tham T, Ferris S, Bahraoui E, Canarelli S, Montagnier L, Blanchard A. Molecular characterization of the P1-like adhesin gene from Mycoplasma pirum. J Bacteriol. 1994;176(3):781–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Keeler C, Hnatow LL, Whetzel PL, Dohms JE. Cloning and characterization of a putative cytadhesin gene (mgc1) from Mycoplasma gallisepticum. Infect Immun. 1996;64(5):1541–7.

    PubMed  PubMed Central  Google Scholar 

  43. Uniprot Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 2015;43(Database issue):D204–12.

    Article  Google Scholar 

  44. Dumke R, Hausner M, Jacobs E. Role of Mycoplasma pneumoniae glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in mediating interactions with the human extracellular matrix. Microbiology. 2011;157(Pt 8):2328–38.

    Article  CAS  PubMed  Google Scholar 

  45. Dallo SF, Kannan TR, Blaylock MW, Baseman JB. Elongation factor Tu and E1 beta subunit of pyruvate dehydrogenase complex act as fibronectin binding proteins in Mycoplasma pneumoniae. Mol Microbiol. 2002;46:1041–51.

    Article  CAS  PubMed  Google Scholar 

  46. Henrich B, Hopfe M, Kitzerow A, Hadding U. The adherence-associated lipoprotein P100, encoded by an Opp operon structure, functions as the oligopeptide-binding domain OppA of a putative oligopeptide transport system in Mycoplasma hominis. J Bacteriol. 1999;181:4873–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Balasubramanian S, Kannan TR, Hart PJ, Baseman JB. Amino acid changes in elongation factor Tu of Mycoplasma pneumoniae and Mycoplasma genitalium influence fibronectin binding. Infect Immun. 2009;77(9):3533–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87(12):4576–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Murray RGE. The higher taxa, or, a place for everything...? In: Krieg NR, Holt JG, editors. Bergey’s manual of systematic bacteriology, vol. 1. Baltimore: Williams & Wilkins; 1984. p. 31–4.

    Google Scholar 

  50. Edward DG, Freundt EA. Proposal for Mollicutes as name of the class established for the order Mycoplasmatales. Int J Syst Evol Microbiol. 1967;17(3):267–8.

    Google Scholar 

  51. Edward DGF, Freundt E. Type strains of species of the order Mycoplasmatales, including designation of neotypes for Mycoplasma mycoides subsp. mycoides, Mycoplasma agalactiae subsp. agalactiae, and Mycoplasma arthritidis. Int J Syst Evol Microbiol. 1973;23(1):55–61.

    Google Scholar 

  52. Freundt E. The classification of the pleuropneumonia group of organisms (Borrelomycetales). Int J Syst Evol Microbiol. 1955;5(2):67–78.

    Google Scholar 

  53. Nowak J. Morphologie, nature et cycle évolutif du microbe de la péripneumonie des bovidés. Ann Inst Pasteur (Paris). 1929;43:1330–52.

    Google Scholar 

  54. Freundt EA. The mycoplasmas. In: Buchanan RE, Gibbons NE, editors. Bergey’s manual of determinative bacteriology. 8th ed. Baltimore: Williams and Wilkins; 1974. p. 929–54.

    Google Scholar 

  55. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet. 2000;25(1):25–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors are very grateful to Kris Kruse from the Nevada Genomics Center for technical assistance, and to Marco Fondi for helpful discussions. They are also grateful to the Nevada Genomics Center for providing sequencing services for free.

Funding

This work was made possible by a grant from the National Institute of General Medical Sciences (P20GM103440) from the National Institutes of Health. The funder did not play any role in the study.

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Authors and Affiliations

  1. Biology Department, University of Nevada, Reno, USA

    Chava L. Weitzman, C. Richard Tracy & David Alvarez-Ponce

  2. Nevada Center for Bioinformatics, University of Nevada, Reno, USA

    Richard L. Tillett

  3. Biology Department, Colorado State University, Pueblo, USA

    Franziska C. Sandmeier

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Contributions

CLW, FCS, CRT and DAP conceived the work. CLW conducted laboratory work. RLT and DAP conducted bioinformatic analyses. CLW and DAP drafted the manuscript. All authors contributed to interpreting data and improving the manuscript. All authors read and approved the final manuscript.

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Correspondence to David Alvarez-Ponce.

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Weitzman, C.L., Tillett, R.L., Sandmeier, F.C. et al. High quality draft genome sequence of Mycoplasma testudineum strain BH29T, isolated from the respiratory tract of a desert tortoise. Stand in Genomic Sci 13, 9 (2018). https://doi.org/10.1186/s40793-018-0309-z

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Keywords

Environmental Microbiome

ISSN: 2524-6372