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The evolution of genomes

How did genomes evolve and why junk DNA is our gold?

The vast majority of Eukaryotic genomes consists of junk DNA, which has function. Yet, the nucleotides of this junk DNA exhibit a non-random organization and the question is why. A deeper analysis of the architecture of genomes shows that they possess a complex architecture, in which the GC nucleotides are organized into homogeneous and nonhomogeneous domains of varying lengths and GC composition. By large, many genic features, like richness of genes and regulatory elements, are correlated with GC richness, yes these structures stretch beyond the coding regions and raise many evolutionary questions, such as, why do they exist? Why did they not disappear throughout evolution? What maintains these domains? What benefits to they provide genes and regulatory elements? Can they be used to address open phylogenetic and evolutionary questions.

The first question that we must ask ourselves is how to find these regions. Numerous methods for segmenting DNA sequences into contiguous compositionally-coherent domains (some of which were termed “isochores”) have been proposed in the literature. These methods differ from one another in the number and types of parameters used in the segmentation process, as well as in the levels of user intervention. Unfortunately, even methods that limit user input to a few parameters yield incongruent results with one another. We developed IsoPlotter a robust and unsupervised segmentation methods and validated it through benchmark simulations. IsoPlotter has since been adopted by over a dozen genome sequencing projects to resolve the genomic compositions of various species, allowing us to characterize and carry out evolutionary comparative analyses while addressing evolutionary questions.

Research illustration with different sized bars.
Genomic coverage of four compositional domain types.

In the above illustration homogeneous domains are in blue shades; nonhomogeneous domains are in green shades. Domains longer than 300 kb are in dark shades; domains shorter than 300 kb are inlight shades. Compositionally homogeneous domains longer than 300 kb(i.e., isochoric domains) are in dark blue. From Elhaik and Graur (2014, at PLOS Computational Biology's website).

With the availability of IsoPlotter, we can now investigate the genome architecture in various organisms and develop methods to track the evolutionary changes in genomes. The composition and organization of the compositional domains were likely shaped by different evolutionary processes that either fused or broke down the domains.  For example, in Simola et al. (2012) we showed that unlike other Hymenopterans, long domains have been rapidly accumulated along the ant linage with the leaf-cutter ants having the largest domains among all fully sequenced insect genomes. Yet, the evolutionary mechanisms that shaped the transitions that affected these genomes remain unclear. Understanding these biological mechanisms and their evolutionary implications is a key factor in reconstructing the evolutionary history of genome evolution. 


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