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OASIS: an automated program for global investigation of bacterial and archaeal insertion sequences.

Robinson DG, Lee MC, Marx CJ - Nucleic Acids Res. (2012)

Bottom Line: At a broad scale, we found that most IS families are quite widespread; however, they are not present randomly across taxa.The number of ISs increases with genome length, but there is both tremendous variation and no increase in IS density for genomes >2 Mb.Surprisingly, even after controlling for 16S rRNA sequence divergence, the same ISs were more likely to be shared between genomes labeled as the same species rather than as different species.

View Article: PubMed Central - PubMed

Affiliation: Department of Organismic and Evolutionary Biology and Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.

ABSTRACT
Insertion sequences (ISs) are simple transposable elements present in most bacterial and archaeal genomes and play an important role in genomic evolution. The recent expansion of sequenced genomes offers the opportunity to study ISs comprehensively, but this requires efficient and accurate tools for IS annotation. We have developed an open-source program called OASIS, or Optimized Annotation System for Insertion Sequences, which automatically annotates ISs within sequenced genomes. OASIS annotations of 1737 bacterial and archaeal genomes offered an unprecedented opportunity to examine IS evolution. At a broad scale, we found that most IS families are quite widespread; however, they are not present randomly across taxa. This may indicate differential loss, barriers to exchange and/or insufficient time to equilibrate across clades. The number of ISs increases with genome length, but there is both tremendous variation and no increase in IS density for genomes >2 Mb. At the finer scale of recently diverged genomes, the proportion of shared IS content falls sharply, suggesting loss and/or emergence of barriers to successful cross-infection occurs rapidly. Surprisingly, even after controlling for 16S rRNA sequence divergence, the same ISs were more likely to be shared between genomes labeled as the same species rather than as different species.

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Related in: MedlinePlus

Flowchart portraying the full workflow of OASIS.
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gks778-F1: Flowchart portraying the full workflow of OASIS.

Mentions: ISs may occur once in a genome or may consist of a set of almost identical copies (2). ISs in a particular genome can therefore be classified into two major groups in terms of copy number: multicopy and single-copy ISs. As there are distinct levels of information available in each of these cases, different algorithms perform better with each class. As such, we have designed OASIS to find these two groups of ISs in two separate steps: first finding multicopy ISs and then single-copy ISs. The overall schematic pipeline is shown in Figure 1.Figure 1.


OASIS: an automated program for global investigation of bacterial and archaeal insertion sequences.

Robinson DG, Lee MC, Marx CJ - Nucleic Acids Res. (2012)

Flowchart portraying the full workflow of OASIS.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3526298&req=5

gks778-F1: Flowchart portraying the full workflow of OASIS.
Mentions: ISs may occur once in a genome or may consist of a set of almost identical copies (2). ISs in a particular genome can therefore be classified into two major groups in terms of copy number: multicopy and single-copy ISs. As there are distinct levels of information available in each of these cases, different algorithms perform better with each class. As such, we have designed OASIS to find these two groups of ISs in two separate steps: first finding multicopy ISs and then single-copy ISs. The overall schematic pipeline is shown in Figure 1.Figure 1.

Bottom Line: At a broad scale, we found that most IS families are quite widespread; however, they are not present randomly across taxa.The number of ISs increases with genome length, but there is both tremendous variation and no increase in IS density for genomes >2 Mb.Surprisingly, even after controlling for 16S rRNA sequence divergence, the same ISs were more likely to be shared between genomes labeled as the same species rather than as different species.

View Article: PubMed Central - PubMed

Affiliation: Department of Organismic and Evolutionary Biology and Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.

ABSTRACT
Insertion sequences (ISs) are simple transposable elements present in most bacterial and archaeal genomes and play an important role in genomic evolution. The recent expansion of sequenced genomes offers the opportunity to study ISs comprehensively, but this requires efficient and accurate tools for IS annotation. We have developed an open-source program called OASIS, or Optimized Annotation System for Insertion Sequences, which automatically annotates ISs within sequenced genomes. OASIS annotations of 1737 bacterial and archaeal genomes offered an unprecedented opportunity to examine IS evolution. At a broad scale, we found that most IS families are quite widespread; however, they are not present randomly across taxa. This may indicate differential loss, barriers to exchange and/or insufficient time to equilibrate across clades. The number of ISs increases with genome length, but there is both tremendous variation and no increase in IS density for genomes >2 Mb. At the finer scale of recently diverged genomes, the proportion of shared IS content falls sharply, suggesting loss and/or emergence of barriers to successful cross-infection occurs rapidly. Surprisingly, even after controlling for 16S rRNA sequence divergence, the same ISs were more likely to be shared between genomes labeled as the same species rather than as different species.

Show MeSH
Related in: MedlinePlus