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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

Venn diagram illustrating the identified number of ISs in ISfinder, OASIS and IScan. OASIS found a total of 37 427 ISs (in copy numbers) in the 1319 benchmarked genomes while IScan only found 2902 ISs, demonstrating a better performance of OASIS over IScan. In addition to identifying 18 112 ISfinder elements, OASIS found 19 365 new ISs, indicating the advantage of OASIS in finding novel ISs.
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gks778-F2: Venn diagram illustrating the identified number of ISs in ISfinder, OASIS and IScan. OASIS found a total of 37 427 ISs (in copy numbers) in the 1319 benchmarked genomes while IScan only found 2902 ISs, demonstrating a better performance of OASIS over IScan. In addition to identifying 18 112 ISfinder elements, OASIS found 19 365 new ISs, indicating the advantage of OASIS in finding novel ISs.

Mentions: A total number of 41 821 copies representing 6829 unique IS sets were identified by OASIS in 1240 genomes out of the 1737 analyzed (Table 1 and Figure 2). Among those, 16.4% of the unique IS sets are single-copy ISs. The remaining sets belong to multicopy ISs and comprise 97.3% of the total copies, with the largest multicopy set in a single genome containing 232 elements. OASIS took a total of 9 h and 40 min to annotate all 1737 genomes on a 4-core 2.8-Ghz processor, with a maximum per-genome running time of 6 min.Figure 2.


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

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

Venn diagram illustrating the identified number of ISs in ISfinder, OASIS and IScan. OASIS found a total of 37 427 ISs (in copy numbers) in the 1319 benchmarked genomes while IScan only found 2902 ISs, demonstrating a better performance of OASIS over IScan. In addition to identifying 18 112 ISfinder elements, OASIS found 19 365 new ISs, indicating the advantage of OASIS in finding novel ISs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gks778-F2: Venn diagram illustrating the identified number of ISs in ISfinder, OASIS and IScan. OASIS found a total of 37 427 ISs (in copy numbers) in the 1319 benchmarked genomes while IScan only found 2902 ISs, demonstrating a better performance of OASIS over IScan. In addition to identifying 18 112 ISfinder elements, OASIS found 19 365 new ISs, indicating the advantage of OASIS in finding novel ISs.
Mentions: A total number of 41 821 copies representing 6829 unique IS sets were identified by OASIS in 1240 genomes out of the 1737 analyzed (Table 1 and Figure 2). Among those, 16.4% of the unique IS sets are single-copy ISs. The remaining sets belong to multicopy ISs and comprise 97.3% of the total copies, with the largest multicopy set in a single genome containing 232 elements. OASIS took a total of 9 h and 40 min to annotate all 1737 genomes on a 4-core 2.8-Ghz processor, with a maximum per-genome running time of 6 min.Figure 2.

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