Concatenated nuclear gene alignment (Gblock)

Nuclear genes used in this study, Gblock data set. See Supplemental Table S2. CAD, 1, 3291; PGD, 3292, 3999; SNF, 4000, 4206; AATS, 4207, 5232; PER, 5233, 5778; SINA, 5781, 6125; TPI, 6126, 6527

Concatenated mitochondial gene alignment (Gblock)

Mitochondrial genes used in this study, Gblock data set. See Supplemental Table S2. ATP6, 1, 666; ATP8, 667, 747; Cox1, 748, 2274; Cox2, 2275, 2955; Cox3, 2956, 3738; CytB, 3739, 4869; ND1, 4870, 5793; ND2, 5794, 6651; ND3, 6652, 6999; ND4, 7000, 8307; ND4L, 8308, 8601; ND5, 8602, 10305; ND6, 10306, 10812

Comprehensive bioinformatics analysis of <i>Mycoplasma pneumoniae</i> genomes to investigate underlying population structure and type-specific determinants

<div><p><i>Mycoplasma pneumoniae</i> 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 <i>M</i>. <i>pneumoniae</i> 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 <i>M</i>. <i>pneumoniae</i> to date, underscoring the power of combining complementary sequencing technologies to overcome difficult-to-sequence regions and highlighting potential differential genomic signatures in <i>M</i>. <i>pneumoniae</i>.</p></div

Correction: Comprehensive bioinformatics analysis of <i>Mycoplasma pneumoniae</i> genomes to investigate underlying population structure and type-specific determinants

Correction: Comprehensive bioinformatics analysis of <i>Mycoplasma pneumoniae</i> genomes to investigate underlying population structure and type-specific determinant

28S.aln5.22.09

This is the uncut 28S rDNA file for T2+T1, with annotations about included regions. Ribosomal genes are complex to align across deep divergences (240 million years for flies). That means that divergent domains (expansion regions are excluded in most phylogenetic analyses of this gene.), so the annotations in this file (at the bottom) correspond to positions that are cut-out (excluded) in our phylogenetic analysis. If you sequenced 28S this will allow you to fit your sequence into our alignment without confusion about missing pieces. Brachyceran or only Schizophoran sequences were separated from lower Diptera for some regions in this alignment, in order to include alignable regions within these sections for just higher flies. The cut version of this file is FLY2.28s.nex (not annotated)