14 research outputs found

    Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region

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    Mycobacterium tuberculosis, the causative agent of most human tuberculosis, infects one third of the world's population and kills an estimated 1.7 million people a year. With the world-wide emergence of drug resistance, and the finding of more functional genetic diversity than previously expected, there is a renewed interest in understanding the forces driving genome evolution of this important pathogen. Genetic diversity in M. tuberculosis is dominated by single nucleotide polymorphisms and small scale gene deletion, with little or no evidence for large scale genome rearrangements seen in other bacteria. Recently, a single report described a large scale genome duplication that was suggested to be specific to the Beijing lineage. We report here multiple independent large-scale duplications of the same genomic region of M. tuberculosis detected through whole-genome sequencing. The duplications occur in strains belonging to both M. tuberculosis lineage 2 and 4, and are thus not limited to Beijing strains. The duplications occur in both drug-resistant and drug susceptible strains. The duplicated regions also have substantially different boundaries in different strains, indicating different originating duplication events. We further identify a smaller segmental duplication of a different genomic region of a lab strain of H37Rv. The presence of multiple independent duplications of the same genomic region suggests either instability in this region, a selective advantage conferred by the duplication, or both. The identified duplications suggest that large-scale gene duplication may be more common in M. tuberculosis than previously considere

    Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication

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    Rhizopus oryzae is the primary cause of mucormycosis, an emerging, life-threatening infection characterized by rapid angioinvasive growth with an overall mortality rate that exceeds 50%. As a representative of the paraphyletic basal group of the fungal kingdom called β€œzygomycetes,” R. oryzae is also used as a model to study fungal evolution. Here we report the genome sequence of R. oryzae strain 99–880, isolated from a fatal case of mucormycosis. The highly repetitive 45.3 Mb genome assembly contains abundant transposable elements (TEs), comprising approximately 20% of the genome. We predicted 13,895 protein-coding genes not overlapping TEs, many of which are paralogous gene pairs. The order and genomic arrangement of the duplicated gene pairs and their common phylogenetic origin provide evidence for an ancestral whole-genome duplication (WGD) event. The WGD resulted in the duplication of nearly all subunits of the protein complexes associated with respiratory electron transport chains, the V-ATPase, and the ubiquitin–proteasome systems. The WGD, together with recent gene duplications, resulted in the expansion of multiple gene families related to cell growth and signal transduction, as well as secreted aspartic protease and subtilase protein families, which are known fungal virulence factors. The duplication of the ergosterol biosynthetic pathway, especially the major azole target, lanosterol 14Ξ±-demethylase (ERG11), could contribute to the variable responses of R. oryzae to different azole drugs, including voriconazole and posaconazole. Expanded families of cell-wall synthesis enzymes, essential for fungal cell integrity but absent in mammalian hosts, reveal potential targets for novel and R. oryzae-specific diagnostic and therapeutic treatments

    Comparative Genomic Characterization of Francisella tularensis Strains Belonging to Low and High Virulence Subspecies

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    Tularemia is a geographically widespread, severely debilitating, and occasionally lethal disease in humans. It is caused by infection by a gram-negative bacterium, Francisella tularensis. In order to better understand its potency as an etiological agent as well as its potential as a biological weapon, we have completed draft assemblies and report the first complete genomic characterization of five strains belonging to the following different Francisella subspecies (subsp.): the F. tularensis subsp. tularensis FSC033, F. tularensis subsp. holarctica FSC257 and FSC022, and F. tularensis subsp. novicida GA99-3548 and GA99-3549 strains. Here, we report the sequencing of these strains and comparative genomic analysis with recently available public Francisella sequences, including the rare F. tularensis subsp. mediasiatica FSC147 strain isolate from the Central Asian Region. We report evidence for the occurrence of large-scale rearrangement events in strains of the holarctica subspecies, supporting previous proposals that further phylogenetic subdivisions of the Type B clade are likely. We also find a significant enrichment of disrupted or absent ORFs proximal to predicted breakpoints in the FSC022 strain, including a genetic component of the Type I restriction-modification defense system. Many of the pseudogenes identified are also disrupted in the closely related rarely human pathogenic F. tularensis subsp. mediasiatica FSC147 strain, including modulator of drug activity B (mdaB) (FTT0961), which encodes a known NADPH quinone reductase involved in oxidative stress resistance. We have also identified genes exhibiting sequence similarity to effectors of the Type III (T3SS) and components of the Type IV secretion systems (T4SS). One of the genes, msrA2 (FTT1797c), is disrupted in F. tularensis subsp. mediasiatica and has recently been shown to mediate bacterial pathogen survival in host organisms. Our findings suggest that in addition to the duplication of the Francisella Pathogenicity Island, and acquisition of individual loci, adaptation by gene loss in the more recently emerged tularensis, holarctica, and mediasiatica subspecies occurred and was distinct from evolutionary events that differentiated these subspecies, and the novicida subspecies, from a common ancestor. Our findings are applicable to future studies focused on variations in Francisella subspecies pathogenesis, and of broader interest to studies of genomic pathoadaptation in bacteria

    Summary of Large Scale Duplication Boundaries.

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    <p>*Numbers in parenthesis are nucleotide positions for the duplication boundaries derived from PCR amplification.</p>Β§<p>Genes in square brackets correspond to the partial duplication boundaries for T67 (L2 and R2 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0026038#pone-0026038-g003" target="_blank">Figure 3</a>) - see text for details.</p

    Coverage plots around duplication boundaries.

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    <p>Each plot shows the fold coverage for the alignment of the corresponding strain to H37Rv around the upstream (left column) or downstream (right column) duplication boundaries. Color coding for coverage plots is as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0026038#pone-0026038-g002" target="_blank">Figure 2</a>. Genes in red are predicted repeats or transposable elements in H37Rv. Vertical green bars indicate the positions of PCR primers used (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0026038#pone-0026038-t003" target="_blank">Table 3</a>).</p

    PCR verification of tandem duplications.

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    <p>(A) Schematic representation of primer design strategy. The duplicated region is shown as a grey box, present as a single copy in the reference genome (top) and as a tandem duplication below. Primers A and B amplify the left flank and C and D amplify the right flank. Only when C and B and brought into close proximity by a tandem duplication can a product be generated using primers C and B. (B) 0.9% agarose gel loaded with 5 ul of PCR reactions using primers C and B specific for isolate M141 (top), M41 (middle) and cdc606 (bottom). Lane 1 contains the 2 log ladder (New England Biolabs, N3200). (C) 0.9% agarose gel loaded with 5 ul of PCR reactions using primers A and B (lanes 2–5) or C and D (lanes 7–10) specific for each isolate as indicated on the left. Lanes 1 and 6 contain the 2 log ladder (New England Biolabs, N3200).</p
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