The role of understanding the genome rearrangement is becoming more and more crucial in the modern life sciences. The new, alternative model explaining the process of genome rearrangement as well as the relationships between diverged gene-order sequences is proposed. The main characteristic feature of the model is its evolutionary nature: the gene-order sequences are viewed as the result of evolutionary genome development, that is, consecutive transformation of the ancestral genome via non-local genome mutations of two types, insertion and reversal. The close relationship of the above evolutionary-based mutations in the proposed model and “traditional” genome rearrangement mutations, such as, reversal and transposition, is discussed. A new, multiple longest common subsequence-based, method for extraction the evolutionary processes directly related to genome rearrangement is presented. Its advantages, disadvantages and future enhancements are outlined.
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