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The limitations of draft assemblies for understanding prokaryotic adaptation and evolution
N Ricker1, H Qian, R R Fulthorpe
1Department of Physical and Environmental Sciences, University of Toronto Scarborough, Canada.
Genomics
|July 4, 2012
Summary
De novo genome assembly is challenging due to repeats and transposable elements. Genomic islands significantly impact assembly quality, hindering understanding of bacterial adaptations.
Area of Science:
- Genomics
- Bioinformatics
- Microbial Ecology
Background:
- De novo genome assembly of next-generation sequencing data is complex.
- Genomic repeats and transposable elements frequently interrupt genome assemblies.
- This leads to a high number of draft assemblies rather than fully finished genomes.
Purpose of the Study:
- To investigate factors affecting de novo genome assembly quality.
- To determine the impact of genomic repeats, transposable elements, and genomic islands on assembly fragmentation.
- To assess the utility of finished genomes for understanding bacterial adaptations.
Main Methods:
- Creation and assembly of idealized sequence datasets for five bacterial strains: Cupriavidus metallidurans CH34, Caulobacter sp. K31, Gramella forsetii KT0803, Rhodobacter sphaeroides 2.4.1, and Bordetella bronchiseptica RB50.
- Analysis of assembly fragmentation in relation to transposable elements and known/predicted genomic islands.
- Correlation analysis between assembly quality metrics and genomic features.
Main Results:
- Transposable elements were confirmed to interrupt genome assemblies.
- A strong association was found between highly fragmented regions and genomic islands.
- Putative genomic island content was a more significant factor in assembly quality than other examined factors.
Conclusions:
- Draft genome assemblies are limited in their ability to reveal the genomic context of bacterial adaptations.
- Finishing bacterial genomes, despite increased effort, yields valuable information for future research.
- Understanding genomic islands is crucial for improving de novo assembly strategies.
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