Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants.
Mycoplasma pneumoniae is a significant cause of respiratory illness worldwide. Despite a minimal and highly conserved genome, genetic diversity within the species may impact disease. We performed whole genome sequencing (WGS) analysis of 107 M. pneumoniae isolates, including 67 newly sequenced using...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2017-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5391922?pdf=render |
| _version_ | 1811325994457366528 |
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| author | Maureen H Diaz Heta P Desai Shatavia S Morrison Alvaro J Benitez Bernard J Wolff Jason Caravas Timothy D Read Deborah Dean Jonas M Winchell |
| author_facet | Maureen H Diaz Heta P Desai Shatavia S Morrison Alvaro J Benitez Bernard J Wolff Jason Caravas Timothy D Read Deborah Dean Jonas M Winchell |
| author_sort | Maureen H Diaz |
| collection | DOAJ |
| description | Mycoplasma pneumoniae is a significant cause of respiratory illness worldwide. Despite a minimal and highly conserved genome, genetic diversity within the species may impact disease. We performed whole genome sequencing (WGS) analysis of 107 M. pneumoniae isolates, including 67 newly sequenced using the Pacific BioSciences RS II and/or Illumina MiSeq sequencing platforms. Comparative genomic analysis of 107 genomes revealed >3,000 single nucleotide polymorphisms (SNPs) in total, including 520 type-specific SNPs. Population structure analysis supported the existence of six distinct subgroups, three within each type. We developed a predictive model to classify an isolate based on whole genome SNPs called against the reference genome into the identified subtypes, obviating the need for genome assembly. This study is the most comprehensive WGS analysis for M. pneumoniae to date, underscoring the power of combining complementary sequencing technologies to overcome difficult-to-sequence regions and highlighting potential differential genomic signatures in M. pneumoniae. |
| first_indexed | 2024-04-13T14:42:59Z |
| format | Article |
| id | doaj.art-f645f87dba1f4474830c0fbefbadfa66 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-13T14:42:59Z |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-f645f87dba1f4474830c0fbefbadfa662022-12-22T02:42:51ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01124e017470110.1371/journal.pone.0174701Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants.Maureen H DiazHeta P DesaiShatavia S MorrisonAlvaro J BenitezBernard J WolffJason CaravasTimothy D ReadDeborah DeanJonas M WinchellMycoplasma pneumoniae is a significant cause of respiratory illness worldwide. Despite a minimal and highly conserved genome, genetic diversity within the species may impact disease. We performed whole genome sequencing (WGS) analysis of 107 M. pneumoniae isolates, including 67 newly sequenced using the Pacific BioSciences RS II and/or Illumina MiSeq sequencing platforms. Comparative genomic analysis of 107 genomes revealed >3,000 single nucleotide polymorphisms (SNPs) in total, including 520 type-specific SNPs. Population structure analysis supported the existence of six distinct subgroups, three within each type. We developed a predictive model to classify an isolate based on whole genome SNPs called against the reference genome into the identified subtypes, obviating the need for genome assembly. This study is the most comprehensive WGS analysis for M. pneumoniae to date, underscoring the power of combining complementary sequencing technologies to overcome difficult-to-sequence regions and highlighting potential differential genomic signatures in M. pneumoniae.http://europepmc.org/articles/PMC5391922?pdf=render |
| spellingShingle | Maureen H Diaz Heta P Desai Shatavia S Morrison Alvaro J Benitez Bernard J Wolff Jason Caravas Timothy D Read Deborah Dean Jonas M Winchell Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants. PLoS ONE |
| title | Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants. |
| title_full | Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants. |
| title_fullStr | Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants. |
| title_full_unstemmed | Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants. |
| title_short | Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants. |
| title_sort | comprehensive bioinformatics analysis of mycoplasma pneumoniae genomes to investigate underlying population structure and type specific determinants |
| url | http://europepmc.org/articles/PMC5391922?pdf=render |
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