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. 2016 Dec 8;10:264–268. doi: 10.1016/j.dib.2016.12.006

Data on genome analysis of Mycoplasmagallisepticum during intracellular infection

Daria Matyushkina a,, Olga Pobeguts a, Irina Garanina a,b, Vladislav Babenko c, Maria Vakhitova d, Gleb Fisunov a, Vadim Govorun a,b,d
PMCID: PMC5217774  PMID: 28070539

Abstract

The genus Mycoplasma relates to Gram-positive bacteria that lack a cell wall and are capable to cause chronic disease in humans and animals. Among the agents of infection and disease in domestic poultry and wild birds, Mycoplasma gallisepticum is the most important mycoplasma species, causing considerable losses in the poultry industry. In the present paper, we provide data on adaptation of M. gallisepticum to the eukaryotic host cells on the genomic level. The major changes were predominantly localized in the VlhA-hemagglutinin genes which are important components of pathogenesis. The ability of mycoplasmas to change dramatically the repertoire of surface antigens and to vary the immunogenicity of these components allows them to remain undetected by the immune system of the host. The data presented in this article are related to the article entitled “Phase Transition of the Bacterium upon Invasion of a Host Cell as a Mechanism of Adaptation: a Mycoplasma gallisepticum Model.” (Matyushkina et al., 2016) [1]. Data posted in repository https://www.ncbi.nlm.nih.gov/bioproject/315515. Bioproject ID: PRJNA315515.

Keywords: Host-pathogen interaction, Mycoplasma, Genome, Vlh antiges, Nucleotide polymorphism


Specifications Table

Subject area Biology
More specific subject area Genomics
Type of data Table
How data was acquired Data was acquired on Ion Torrent PGM (Life Technologies) and 454 GS FLX+ (Roche)
Data format Raw, processed
Experimental factors Mycoplasma gallisepticum S6 cells were cultured as described previously[2]. Chicken erythroblast cell line HD3 (clone A6 of line LSCC[3], [4]) was cultivated as described in[5]. The gentamicin invasion assay and isolation of intracellular mycoplasma were carried out as described in[1]. Genomic DNA from individual clones was isolated as previously described[2].
Experimental features Sequencing was performed according to Life Technologies and Roche protocols for DNA-seq.
Data source location N/A
Data accessibility Data is within this article and raw data was deposited at NCBI repositoryhttps://www.ncbi.nlm.nih.gov/bioproject/315515. Bioproject ID: PRJNA315515.

Value of the data

  • This data set will be of value for the scientific community working in the area of host-pathogen interaction since it represents the genome changes of bacterium Mycoplasma gallisepticum upon invasion of a host cell.

  • The data will also be of value for studies in the area of infection and immunity because basic genome changes were predominantly localized in the VlhA-hemagglutinin genes which are the primary strategy for survival among bacterial pathogens.

  • These data may have implications for the development of preventive strategies.

1. Data

The data represents the genomic polymorphisms of Mycoplasma gallisepticum clones after infection and isolation from HD3 cells. Table 1 represent data obtained during acute (24 h) infection. Table 2 represent data obtained during chronic (7 weeks) infection. In analysis were taken 10 different colonies of mycoplasma isolated from HD3 cells after acute infection, 10 different colonies of mycoplasma isolated from HD3 cells after chronic infection and 12 different colonies of control laboratory strain.

Table 1.

Comparative genomic analysis of M. gallisepticum isolated from HD3 cells after acute (24 h) infection with laboratory strain of M. gallisepticum S6.

ORF name Gene name Position Ref MIEC Quality Combined depth across samples Mean allele frequency across samples
GCW_00395 23S ribosomal RNA 83344 T C 68.3 422 1
GCW_01160 VlhA.1.01 variable lipoprotein family protein 264070 C T,A 999 239 1
GCW_01340 23S ribosomal RNA 317111 T C 37.2 431 1
GCW_01345 5S ribosomal RNA 318386 G A 999 479 1
GCW_01455 Upstream of mobile element protein 348358 A T 999 229 0.8325
GCW_01960 VlhA, cluster 2 465075 A G 999 92 1
465216 T A 55.7 128 1
GCW_92037 Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain 483621 A T,G 51.4 85 0.8354
GCW_92457 VlhA, cluster 3 588982 G A,C 63.6 162 1


 

 

 

 

 

 

 


GCW_03335 VlhA, cluster 4 800656 T C,A 999 482 1
801100 T C 999 666 1


 

 

 

 

 

 


GCW_93371 816612 G T 999 121 1
816905 A T 999 595 1
817621 G T,A 999 762 1
817733 A G 999 935 1
818171 C A,G 20.9 99 1
GCW_93372 Upstream of VlhA, cluster 4 818493 T G 999 449 1
GCW_00585 Serine protease 137223 G A 999 836 0.6297
GCW_91948 Upstream of VlhA, cluster 2 462290 G A 156 168 0.7728
GCW_92433 Upstream of VlhA, cluster 3 577485 G T 999 384 0.6192
GCW_92454 VlhA, cluster 3 586155 G T 999 238 0.5183
GCW_03035 30S ribosomal protein S12 722693 C A 999 438 0.654
GCW_03140 Major facilitator superfamily permease 750922 G C 999 489 0.6667
GCW_03470 Asparagine synthase 839170 A G 999 907 0.6487

MIEC – mycoplasma isolated from eukaryotic cells; Ref – references strain of M. gallisepticum S6.

Table 2.

Comparative genomic analysis of M. gallisepticum isolated from HD3 cells after chronic (7 weeks) infection with laboratory strain of M. gallisepticum S6.

ORF name Gene name Position Ref MIEC Quality Combined depth across samples Mean allele frequency across samples
GCW_90633 Upstream of mobile element protein 152250 A T,G 999 7417 1
GCW_01160 vlhA, cluster 1 264070 C T,A 999 1465 1
GCW_01345 5S ribosomal RNA 318386 G A 999 6909 1
GCW_01395 Asparaginyl-tRNA synthetase 332883 G T 999 2712 0.9444
GCW_01520 M42 glutamyl-aminopeptidase family protein 359323 T C 999 1107 0.9444
GCW_01960 vlhA, cluster 2 465075 A G 999 2067 1
465121 C A,G 97.5 403 1
465125 T A 999 429 1
465131 A T,G 159 301 1
465137 G A 171 326 1
465154 C G 999 531 1
465159 G C 175 702 1
465166 T C 999 867 1
465216 T A 999 2494 1
GCW_92037 Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain 483621 A G,T 999 703 1
GCW_02455 Upstream of VlhA, cluster 3 588982 G A 999 1135 1
GCW_03040 30S ribosomal protein S4 723019 T C 999 6594 1
GCW_03045 Hypothetical protein DUF3682, eukaryotic protein 724257 G C 999 7035 0.9444
GCW_03335 Upstream of VlhA family protein 801100 T C 999 5441 1
GCW_93371 vlhA, cluster 4 816612 G T 999 5428 1
816905 A T 999 6345 1
817733 A G 999 7904 1
818171 C A,G 999 1297 1
818177 A T,G 30.6 1407 1
818179 C T,G 50.5 1371 1
818184 T G 87.6 1185 1
818186 T A 77.6 1097 1
818187 G T 51.6 1038 1
818188 G T 88.5 1024 1
818193 G C 41.6 908 1
818194 G C 50.6 874 1
818202 T A 47.7 576 1
818225 T G 94.2 251 1
818226 G T,A 95.8 261 1
818228 A G 106 331 1
818255 T C,A 999 991 1

MIEC – mycoplasma isolated from eukaryotic cells; Ref – references strain of M. gallisepticum S6.

2. Experimental design, materials and methods

2.1. Cell culturing

M. gallisepticum S6 cells were cultured as described previously [2]. Chicken erythroblast cell line HD3 (clone A6 of line LSCC [3], [4]) was cultivated as described in [5]. The gentamicin invasion assay and isolation of intracellular mycoplasma were carried out as described in [1]. Genomic DNA from individual cultures was isolated as previously described [2].

2.2. Genome sequencing and analysis

Genomic DNA from individual cultures was isolated as previously described [2]. The DNA (100 ng for each sample) was disrupted into 200–300 bp fragments using the Covaris S220 System (Covaris, Woburn, Massachusetts, USA). Barcode shotgun libraries for mycoplasma isolated from eukaryotic cells (MIEC) were prepared by the Ion Xpress™Plus Fragment Library Kit (Life Technologies). PCR emulsion was performed by the Ion PGM™Template OT2 200 Kit (Life Technologies). DNA sequencing was performed by the Ion Torrent PGM (Life Technologies) with the Ion 318 chip v2 and the Ion PGM™Sequencing 200 Kit v2 (Life Technologies). Control M. gallisepticum S6 strain was sequenced by using the Roche 454 Life Sciences Genome Sequencer FLX following the manufacturer׳s instructions (Roche 454 Life Science, USA). Assembly of raw sequencing reads with an average length of 540 bases was performed by the GS de novo assembly software version 2.8 (Roche 454 Life Science, USA).

For the detection of nucleotide variants relatively to the reference, a reference-based mapping approaches via bowtie2 [6] and samtools mpileup [7] tools were used. On average 93% of reads mapped to the reference genome. We skipped alignments with mapping quality (mapQ) less than 10. Variants were called using the samtools mpileup command with options -C50 -D -S. Variants were filtered using the following criteria: (1) the depth of high-quality coverage larger than 20, (2) in average across all samples at least 50% of reads at the site supporting the call, (3) at least 5 samples have the variant, (4) a homozygous call under a diploid model. We identified nucleotide polymorphisms by comparing calls between the control genomes and the MIEC genomes.

Acknowledgements

We are grateful to professor S. V. Razin (Institute of Gene Biology, Russian Academy of Sciences) for donating HD3 cells, professor M. A. Lagarkova for culturing the HD3 cell. The work was funded by Russian Science Foundation, Russia Grant 14-24-00159 (Systems research of minimal cell on a Mycoplasma gallisepticum model).

Footnotes

Transparency document

Transparency data associated with this article can be found in the online version at: http://dx.doi.org/10.1016/j.dib.2016.12.006.

Transparency document. Supplementary material

Supplementary material

mmc1.docx (10KB, docx)

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