Bioinformatics Evolution Genome Analysis

Evolution of Genomes

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Genome evolution is a process in which a genome changes in structure, sequence or size over time. The study of genome evolution includes multiple fields such as structural analysis of the genome, the study of genomic parasites, gene and ancient genome  duplications, polyploidy, and comparative genomics.

The Evolution of the Genome gives a much needed overview of genomic study through clear, detailed, expert-authored discussions of the key areas in genome biology. 

The evolution of the genome is identified by the accumulation of changes. The analysis of genomes and their changes in sequence or size over time involves certain fields. There are many mechanisms that have contributed to genome evolution and these include gene and genome duplications, polyploidy, mutation rates, transposable elements, pseudogenes, exon shuffling and genomic reduction and gene loss. 

Transposable Elements

These are regions of DNA that can be inserted into the genetic code through one of two mechanisms. These mechanisms work similarly to “cut-and-paste” and “copy-and-paste” functionalities in word processing programs. The “cut-and-paste” mechanism works by excising DNA from one place in the genome and inserting itself into another location in the code. 

Pseudogenes

Often a result of spontaneous mutation, pseudogenes are dysfunctional genes derived from previously functional gene relatives. There are many mechanisms by which a functional gene can become a pseudogene including the deletion or insertion of one or multiple nucleotides. This can result in a shift of reading frame, causing the gene to longer code for the expected protein, a premature stop codon or a mutation in the promoter region. 

Exon Shuffling

Exon shuffling is a mechanism by which new genes are created. This can occur when two or more exons from different genes are combined together or when exons are duplicated. Exon shuffling results in new genes by altering the current intron-exon structure. 

Genome Reduction and Gene Loss

Many species have genome reduction when subsets of their genes are not needed anymore. This typically happens when organisms adapt to a parasitic lifestyle, e.g. when their nutrients are supplied by a host. As a result, they lose the genes need to produce these nutrients. In many cases, there are both free living and parasitic species that can be compared and their lost genes identified. 

Whole-Genome Duplication

Whole-genome duplication is characterized by an organism’s entire genetic information being copied once or multiple times. As well as the generation of new genes by duplication followed by mutation, novel protein functions can also be produced by rearranging existing genes. This is possible because most proteins are made up of structural domains.

Domain duplication happens when the gene segment coding for a structural domain is duplicated by unequal crossing-over, replication slippage or one of the other methods that we have considered for duplication of DNA sequences.

Domain shuffling happens when segments coding for structural domains from completely different genes are joined together to form a new coding sequence that specifies a hybrid or mosaic protein, one that would have a novel combination of structural features and might provide the cell with an entirely new biochemical function 

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