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Comparative genome analysis of Mycoplasma pneumoniae.

Xiao L, Ptacek T, Osborne JD, Crabb DM, Simmons WL, Lefkowitz EJ, Waites KB, Atkinson TP, Dybvig K - BMC Genomics (2015)

Bottom Line: Within the two subtypes, conservation of most genes, including the CARDS toxin gene and arginine deiminase genes, was observed.The major variation occurs in the P1 and ORF6 genes associated with the adhesin complex.Multiple hsdS genes (encodes S subunit of type I restriction enzyme) with variable tandem repeat copy numbers were found in all 15 genomes.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. lixiao@uab.edu.

ABSTRACT

Background: Mycoplasma pneumoniae is a common pathogen that causes upper and lower respiratory tract infections in people of all ages, responsible for up to 40% of community-acquired pneumonias. It also causes a wide array of extrapulmonary infections and autoimmune phenomena. Phylogenetic studies of the organism have been generally restricted to specific genes or regions of the genome, because whole genome sequencing has been completed for only 4 strains. To better understand the physiology and pathogenicity of this important human pathogen, we performed comparative genomic analysis of 15 strains of M. pneumoniae that were isolated between the 1940s to 2009 from respiratory specimens and cerebrospinal fluid originating from the USA, China and England.

Results: Illumina MiSeq whole genome sequencing was performed on the 15 strains and all genome sequences were completed. Results from the comparative genomic analysis indicate that although about 1500 SNP and indel variants exist between type1 and type 2 strains, there is an overall high degree of sequence similarity among the strains (>99% identical to each other). Within the two subtypes, conservation of most genes, including the CARDS toxin gene and arginine deiminase genes, was observed. The major variation occurs in the P1 and ORF6 genes associated with the adhesin complex. Multiple hsdS genes (encodes S subunit of type I restriction enzyme) with variable tandem repeat copy numbers were found in all 15 genomes.

Conclusions: These data indicate that despite conclusions drawn from 16S rRNA sequences suggesting rapid evolution, the M. pneumoniae genome is extraordinarily stable over time and geographic distance across the globe with a striking lack of evidence of horizontal gene transfer.

No MeSH data available.


Related in: MedlinePlus

Whole genome alignment of the 15 sequenced strains using MAUVE. Regions colored in mauve are conserved across all strains. Differently colored blocks are conserved in some strains. Blocks that are lower are inverted relative to the other strains. Open boxes indicate the location of genes. tRNA genes are shaded in green and rRNA genes are shaded in red. Genes affected by the indicated variants are labeled. Numbers above intervals indicate locations relative to the M129 strain. a Alignment showing all 15 strains. b Close up of the type 2-specific insertion. M129 and FH are shown and are typical of the other type 1 and 2 strains, respectively. Lines indicate relative point of insertion. c Close up of the type 1-specific insertion. M129 and FH are shown and are typical of the other type 1 and 2 strains, respectively. Lines indicate relative point of insertion
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Fig2: Whole genome alignment of the 15 sequenced strains using MAUVE. Regions colored in mauve are conserved across all strains. Differently colored blocks are conserved in some strains. Blocks that are lower are inverted relative to the other strains. Open boxes indicate the location of genes. tRNA genes are shaded in green and rRNA genes are shaded in red. Genes affected by the indicated variants are labeled. Numbers above intervals indicate locations relative to the M129 strain. a Alignment showing all 15 strains. b Close up of the type 2-specific insertion. M129 and FH are shown and are typical of the other type 1 and 2 strains, respectively. Lines indicate relative point of insertion. c Close up of the type 1-specific insertion. M129 and FH are shown and are typical of the other type 1 and 2 strains, respectively. Lines indicate relative point of insertion

Mentions: The 15 sequenced genomes were aligned using a variety of methods. To determine their overall similarity, the genomes were aligned to the reference M129 genome using BRIG, a BLAST-based alignment method. Overall, the genomes were 99 % to > 99 % identical; the similarity within each subtype group was less than 0.1 % difference among the strains. There was one distinct region where identity dropped to about 95 % in the type 2 strains (Fig. 1). This region corresponds to the P1 gene (Fig. 1). We also aligned the genomes using MAUVE to detect large chromosomal rearrangements, deletions, and duplications (Fig. 2a). MAUVE detected two subtype-specific insertions (Fig. 2b and c): the type 1-specific 557178–560601 (M129 numbering) insertion and type 2-specific 713023–713984 (M129 numbering) insertion. All of the genes affected by these insertions were hypothetical proteins, with the exception of a tRNA gene (MPNt26) in the type 1 specific insertion. MPNt26 codes for a serine TCG tRNA. Both type 1 and type 2 strains have another serine TCG tRNA gene (MPNt25) immediately upstream of the insertion point. The genomes (including M. hominis as an outgroup) were aligned with MAFFT and a phylogenetic tree was generated using MrBayes (Fig. 3). Not surprisingly, the 15 strains fall into 2 groups representing type 1 and type 2.Fig. 1


Comparative genome analysis of Mycoplasma pneumoniae.

Xiao L, Ptacek T, Osborne JD, Crabb DM, Simmons WL, Lefkowitz EJ, Waites KB, Atkinson TP, Dybvig K - BMC Genomics (2015)

Whole genome alignment of the 15 sequenced strains using MAUVE. Regions colored in mauve are conserved across all strains. Differently colored blocks are conserved in some strains. Blocks that are lower are inverted relative to the other strains. Open boxes indicate the location of genes. tRNA genes are shaded in green and rRNA genes are shaded in red. Genes affected by the indicated variants are labeled. Numbers above intervals indicate locations relative to the M129 strain. a Alignment showing all 15 strains. b Close up of the type 2-specific insertion. M129 and FH are shown and are typical of the other type 1 and 2 strains, respectively. Lines indicate relative point of insertion. c Close up of the type 1-specific insertion. M129 and FH are shown and are typical of the other type 1 and 2 strains, respectively. Lines indicate relative point of insertion
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4537597&req=5

Fig2: Whole genome alignment of the 15 sequenced strains using MAUVE. Regions colored in mauve are conserved across all strains. Differently colored blocks are conserved in some strains. Blocks that are lower are inverted relative to the other strains. Open boxes indicate the location of genes. tRNA genes are shaded in green and rRNA genes are shaded in red. Genes affected by the indicated variants are labeled. Numbers above intervals indicate locations relative to the M129 strain. a Alignment showing all 15 strains. b Close up of the type 2-specific insertion. M129 and FH are shown and are typical of the other type 1 and 2 strains, respectively. Lines indicate relative point of insertion. c Close up of the type 1-specific insertion. M129 and FH are shown and are typical of the other type 1 and 2 strains, respectively. Lines indicate relative point of insertion
Mentions: The 15 sequenced genomes were aligned using a variety of methods. To determine their overall similarity, the genomes were aligned to the reference M129 genome using BRIG, a BLAST-based alignment method. Overall, the genomes were 99 % to > 99 % identical; the similarity within each subtype group was less than 0.1 % difference among the strains. There was one distinct region where identity dropped to about 95 % in the type 2 strains (Fig. 1). This region corresponds to the P1 gene (Fig. 1). We also aligned the genomes using MAUVE to detect large chromosomal rearrangements, deletions, and duplications (Fig. 2a). MAUVE detected two subtype-specific insertions (Fig. 2b and c): the type 1-specific 557178–560601 (M129 numbering) insertion and type 2-specific 713023–713984 (M129 numbering) insertion. All of the genes affected by these insertions were hypothetical proteins, with the exception of a tRNA gene (MPNt26) in the type 1 specific insertion. MPNt26 codes for a serine TCG tRNA. Both type 1 and type 2 strains have another serine TCG tRNA gene (MPNt25) immediately upstream of the insertion point. The genomes (including M. hominis as an outgroup) were aligned with MAFFT and a phylogenetic tree was generated using MrBayes (Fig. 3). Not surprisingly, the 15 strains fall into 2 groups representing type 1 and type 2.Fig. 1

Bottom Line: Within the two subtypes, conservation of most genes, including the CARDS toxin gene and arginine deiminase genes, was observed.The major variation occurs in the P1 and ORF6 genes associated with the adhesin complex.Multiple hsdS genes (encodes S subunit of type I restriction enzyme) with variable tandem repeat copy numbers were found in all 15 genomes.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. lixiao@uab.edu.

ABSTRACT

Background: Mycoplasma pneumoniae is a common pathogen that causes upper and lower respiratory tract infections in people of all ages, responsible for up to 40% of community-acquired pneumonias. It also causes a wide array of extrapulmonary infections and autoimmune phenomena. Phylogenetic studies of the organism have been generally restricted to specific genes or regions of the genome, because whole genome sequencing has been completed for only 4 strains. To better understand the physiology and pathogenicity of this important human pathogen, we performed comparative genomic analysis of 15 strains of M. pneumoniae that were isolated between the 1940s to 2009 from respiratory specimens and cerebrospinal fluid originating from the USA, China and England.

Results: Illumina MiSeq whole genome sequencing was performed on the 15 strains and all genome sequences were completed. Results from the comparative genomic analysis indicate that although about 1500 SNP and indel variants exist between type1 and type 2 strains, there is an overall high degree of sequence similarity among the strains (>99% identical to each other). Within the two subtypes, conservation of most genes, including the CARDS toxin gene and arginine deiminase genes, was observed. The major variation occurs in the P1 and ORF6 genes associated with the adhesin complex. Multiple hsdS genes (encodes S subunit of type I restriction enzyme) with variable tandem repeat copy numbers were found in all 15 genomes.

Conclusions: These data indicate that despite conclusions drawn from 16S rRNA sequences suggesting rapid evolution, the M. pneumoniae genome is extraordinarily stable over time and geographic distance across the globe with a striking lack of evidence of horizontal gene transfer.

No MeSH data available.


Related in: MedlinePlus