Abstract
BackgroundGenome rearrangement describes gross changes of chromosomal regions, plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. With more and more complete genomes accomplished, lots of genomic comparisons have been conducted in order to find genome rearrangements and the mechanisms which underlie the rearrangement events. In our opinion, genomic comparison of different individuals/strains within the same species (pan-genome) is more helpful to reveal the mechanisms for genome rearrangements since genomes of the same species are much closer to each other.ResultsWe study the mechanism for inversion events via core-genome scaffold comparison of different strains within the same species. We focus on two kinds of bacteria, Pseudomonas aeruginosa and Escherichia coli, and investigate the inversion events among different strains of the same species. We find an interesting phenomenon that long (larger than 10,000 bp) inversion regions are flanked by a pair of Inverted Repeats (IRs). This mechanism can also explain why the breakpoint reuses for inversion events happen. We study the prevalence of the phenomenon and find that it is a major mechanism for inversions. The other observation is that for different rearrangement events such as transposition and inverted block interchange, the two ends of the swapped regions are also associated with repeats so that after the rearrangement operations the two ends of the swapped regions remain unchanged. To our knowledge, this is the first time such a phenomenon is reported for transposition event.ConclusionsIn both Pseudomonas aeruginosa and Escherichia coli strains, IRs were found at the two ends of long sequence inversions. The two ends of the inversion remained unchanged before and after the inversion event. The existence of IRs can explain the breakpoint reuse phenomenon. We also observed that other rearrangement operations such as transposition, inverted transposition, and inverted block interchange, had repeats (not necessarily inverted) at the ends of each segment, where the ends remained unchanged before and after the rearrangement operations. This suggests that the conservation of ends could possibly be a popular phenomenon in many types of chromosome rearrangement events.
Highlights
Genome rearrangement describes gross changes of chromosomal regions, plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans
The other explanation is that the inverted transposition can be replaced by two inversions: the first inversion is from Blocks 16 to -15 and the second inversion is from Blocks -19 to -16. Both of these two inversions are flanked by a pair of Inverted repeat (IR) (+Q/-Q). For both Pseudomonas aeruginosa and Escherichia coli strains, IRs were found at the two ends of long sequence inversions
We observed that other rearrangement operations such as transposition, inverted transposition, and inverted block interchange, had repeats at the ends of each segment, where the ends remained unchanged before and after the rearrangement operations
Summary
Genome rearrangement describes gross changes of chromosomal regions, plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. We study the mechanism for inversion events via core-genome scaffold comparison of different strains within the same species. Armengol et al observed that nine primary regions involved in human genomic disorders which show changes in the order or the orientation of mouse/human synteny segments were often flanked by segmental duplications in the human sequence [11]. They found that 53% of all evolutionary rearrangement breakpoints associate with segmental duplications, as compared with 18% expected in a random location of breaks along the chromosome (P < 10−4)
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