Data on genome analysis of Mycoplasmagallisepticum during intracellular infection

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.


a b s t r a c t
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  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.

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.

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.

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].

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). 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. Russian Science Foundation, Russia Grant 14-24-00159 (Systems research of minimal cell on a Mycoplasma gallisepticum model).

Transparency document. Supplementary material
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.