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5.6: Mechanisms of Genome Evolution

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    40940
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    Once we have alignments of large genomic regions (or whole genomes) across multiple related species, we can begin to make comparisons in order to infer the evolutionary histories of those regions.

    Rates of evolution vary across species and across genomic regions. In S. cerevisiae, for example, 80% of ambiguities are found in 5% of the genome. Telomeres are repetitive DNA sequences at the end of chromosomes which protect the ends of the chromosomes from deterioration. Telomere regions are inherently unstable, tending to undergo rapid structural evolution, and the 80% of variation corresponds to 31 of the 32 telomeric regions. Gene families contained within these regions such as HXT, FLO, COS, PAU, and YRF show significant evolution in number, order, and orientation. Several novel and protein-coding sequences can be found in these regions. Since very few genomic rearrangements are found in S. cerevisiae aside from the telomeric regions, regions of rapid change can be identified by protein family expansions in chromosome ends.

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    Figure 5.22: Dynamic view of a changing gene.

    Geness evolve at different rates. For example as illustrated in Figure 5.22, on one extreme, there is YBR184W in yeast which shows unusually low sequence conservation and exhibits numerous insertions and deletions across species. On the other extreme there is MatA2, which shows perfect amino acid and nu- cleotide conservation. Mutation rates often also vary by functional classification. For example, mitochondrial ribosomal proteins are less conserved than ribosomal proteins.

    The fact that some genes evolve more slowly in one species versus another may be due to factors such as longer life cycles. Lack of evolutionary change in specific genes, however, suggests that there are additional biological functions which are responsible for the pressure to conserve the nucleotide sequence. Yeast can switch mating types by switching all their A and α genes and MatA2 is one of the four yeast mating-type genes (MatA2, Matα2, MatA1, Matα1). Its role could potentially be revealed by nucleotide conservation analysis.

    Fast evolving genes can also be biologically meaningful. Mechanisms of rapid protein change include:

    • Protein domain creation via stretches of Glutamine (Q) and Asparagine (N) and protein-protein inter- actions,
    • Compensatory frame-shifts which enable the exploration of new reading frames and reading/creation of RNA editing signals,
    • Stop codon variations and regulated read-through where gains enable rapid changes and losses may result in new diversity
    • Inteins, which are segments of proteins that can remove themselves from a protein and then rejoin the remaining protein, gain from horizontal transfers of post-translationally self-splicing inteins.

      We now look at differences in gene content across different species (S.cerevisiae, S.paradoxus, S.mikatae, and S.bayanus.) A lot can be revealed about gene loss and conversion by observing the positions of paralogs across related species and observing the rates of change of the paralogs. There are 8-10 genes unique to each genome which are involved mostly with metabolism, regulation and silencing, and stress response. In addition, there are changes in gene dosage with both tandem and segment duplications. Protein family expansions are also present with 211 genes with ambiguous correspondence. All in all however, there are few novel genes in the different species.

    Chromosomal Rearrangements

    These are often mediated by specific mechanisms as illustrated for Saccharomyces in Figure 5.23. [MattFox]Fig11ChromEvolImageissuperblurryasfarasIcansee.Whereeverthiswasfound,itshouldbereplacedwithahigh

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    Figure 5.23: Mechanisms of chromosomal evolution.

    Translocations across dissimilar genes often occur across transposable genetic elements (Ty elements in yeast for example). Transposon locations are conserved with recent insertions appearing in old locations and long terminal repeat remnants found in other genomes. They are evolutionarily active however (for example with Ty elements in yeast being recent), and typically appear in only one genome. The evolution- ary advantage of such locationally conserved transposons may lie in the possibility of mediating reversible arrangements. Inversions are often flanked by tRNA genes in opposite transcriptional orientation. This may suggest that they originate from recombination between tRNA genes.


    This page titled 5.6: Mechanisms of Genome Evolution is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by Manolis Kellis et al. (MIT OpenCourseWare) via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.