18.4 Genomes and Genome Evolution

Introduction

A genome is the complete set of genetic material in an organism. It includes all of the organism’s DNA (or RNA in some viruses), encompassing all of its genes as well as non-coding sequences. The genome contains the instructions needed for the growth, development, functioning, and reproduction of the organism. In eukaryotes (like plants, animals, and fungi), the genome is found mostly in the nucleus, with some DNA also present in mitochondria (and in chloroplasts in plants). In prokaryotes (like bacteria), the genome is typically a single circular DNA molecule located in the cytoplasm, and often includes the DNA sequence in the cell as well as any DNA sequences of plasmids, which are extra pieces of DNA that are not essential for normal growth.

In eukaryotes, DNA is bound with proteins to form complexes called chromosomes.  Each species of eukaryote has a characteristic number of chromosomes in the nuclei of its cells. For example, human body cells (somatic cells) have 46 chromosomes. A somatic cell contains two matched sets of chromosomes, a configuration known as diploid (symbol is 2n). Human cells that contain one set of 23 chromosomes are called gametes, or sex cells; these eggs and sperm are designated n, or haploid. The genome of organisms consists of DNA that contains both exons, which code for proteins, and introns, referred to as repetitive DNA.  All species have a characteristic genome size ranging from several thousand in bacteria to 20 – 30 thousand in more complex organisms (Fig 1).

Figure 1: Gene counts in a variety of species.  Viruses, the simplest particles, have only a handful of genes.  Bacteria such as Escherichia coli have a few thousand genes, and multicellular plants and animals have two to ten times more (Image Credit: https://commons.wikimedia.org/wiki/File:Gene_counts_in_a_variety_of_species.png).

Genome evolution refers to the process of changes in the genetic material (DNA) of an organism over time. Several key mechanisms contribute to genome evolution, including mutation, natural selection, genetic drift, horizontal gene transfer, and gene duplication.  Mutation, natural selection, and genetic drift have been discussed in previous chapters.  This chapter will discuss additional concepts, including gene transfer and gene duplication.

Sources of New Genes

Within One Organism

There are surprisingly more ways to create a new gene besides DNA mutation, although a change in a DNA sequence that leads to a change in the protein is one way to find a new gene or trait (Fig 2).

Figure 2: A section of DNA showing the replacement of a single nucleotide from adenine to cytosine, a point mutation, leading to a different and incorrect amino acid (shown in orange) being incorporated into the protein sequence (Image Credit: U.S. National Library of Medicine, Public domain, via Wikimedia Commons. https://commons.wikimedia.org/wiki/File:Missense_Mutation_Example.jpg).

Recall that non-coding or repetitive sections of DNA called introns can mutate without consequence and can do so at a predictable rate (i.e. molecular clock).  These non-coding regions do not code for a particular protein and therefore any change in them is unusually not impactful.  Again, this is inconsequential because the introns do not code for a specific protein.  Changes to the intron sequence should not have an effect, until they do influence the expression of the exons or if enough changes occur that the intron is no longer an intron and acts as an exon.  The scientific community has discovered at least 155 human genes that have evolved from introns.  Because these new genes are so small in length (about 300 nucleotides long) they are called microgenes which likely explains why they were overlooked for so long (Vakirlis et al 2022).

Not only can genes evolve, but so too can chromosomes.  Whole chromosomes or segments of chromosomes may be duplicated, or segments flipped around and inverted, thereby changing messages and genes.  Such interchromosomal rearrangements can lead to speciation events in a variety of organisms, such as fish.  Research has shown that eight major interchromosomal rearrangements occurred soon after fish-specific whole genome duplication in an ancestor that led to species of pufferfish, zebrafish, and medaka fish (Kasahara et al 2007).

Genes can also get flipped or rearranged on a chromosome or even jump from one section of a chromosome to another section or a different chromosome altogether.  These genes are commonly referred to as jumping genes for their behavior or transposons.  You may also hear these jumping genes called transposable elements.  In some cases, the transposons affect gene expression but they can also create a new gene if the transposon stays in place and serves a new function.

The first transposons were discovered in the 1940s by Barbara McClintock who worked with maize (Zea mays corn). She found that they were responsible for a variety of types of gene mutations. In developing somatic tissues like corn kernels, a mutation (e.g., “c” mutation) that alters color will be passed on to all the descendant cells. This produces the variegated pattern which is so prized in “Indian corn” (Fig 3). It took about 40 years for other scientists to fully appreciate the significance of Barbara McClintock’s discoveries. She was finally awarded a Nobel Prize in 1983. You can learn more about this amazing scientist here.

Figure 3:  Indian corn.  The color of the kernels is the result of transposons or jumping genes. (Image Credit: Sam Fentress, CC BY-SA 2.0 <https://creativecommons.org/licenses/by-sa/2.0>, via Wikimedia Commons.  https://commons.wikimedia.org/wiki/File:Corncobs.jpg).

Transposons are activated by stress, such as changes in temperature, oxygen, toxins, or nutrients, which can result in new genetic variations.  This new variation can lead to the evolution of traits.  For example, transposons account for at least half of all phenotype-altering mutations in flies where infected with the pathogen stressor of Pseudomonas.  Once the transposable elements moved, variant flies were produced that could survive in this environment (Rech et al 2019).  In another example, Anopheles coluzzii mosquitoes in new habitats with new stressors, have been found to show transposable elements inserted near genes involved in insecticide resistance and immunity, helping to drive the mosquitoes’ ecological flexibility and their ability to live in these new environments (Vargas-Chavez et al. 2021).

Genes can not only move from one location to another, parts of them, that is their exons, can also get shuffled within their original location to produce new combinations of messages and therefore new traits or proteins.  This exon recombination has led to the production of a variety of antibodies, proteins that can attach to foreign pathogens such as viruses in human cells and thereby render them ineffective (until the rest of the immune system can destroy the pathogens).

Susumu Tonegawa was awarded the Nobel Prize in Physiology or Medicine for this discovery of the genetic principle for the generation of antibody diversity.  In 1983 he published his research showing how bone marrow-derived lymphocytes (white blood cells) use segments of DNA that have been recombined in ways to make a new complete gene, which contributes to increasing the diversity of antibodies that can be produced by a single organism (Tonegawa 1983).

Between Organisms

Horizontal gene transfer is the process by which genetic material (DNA or sometimes RNA) is transferred between different, often unrelated, organisms. Unlike the more common vertical gene transfer, which occurs from parent to offspring during reproduction, horizontal gene transfer allows for the exchange of genetic material between individuals that may not be directly related by descent.

Horizontal gene transfer can happen between organisms of the same species (intraspecific) or between different species (interspecific). It is most prevalent in prokaryotes, such as bacteria and archaea, but has also been observed in some eukaryotic organisms.  It is quite common for virus DNA to be interspecifically transferred to another species.

There are several mechanisms through which horizontal gene transfer can occur between species:

• Transformation: In transformation, bacteria or other organisms take up free DNA from their surroundings. This DNA can come from dead or lysed cells, and if it contains functional genes, it may be integrated into the recipient organism’s genome.
• Transduction: Transduction is a process in which genetic material is transferred from one bacterium to another through a bacteriophage (a type of virus that infects bacteria). During the viral replication cycle, the phage may accidentally package a fragment of the host’s DNA and transfer it to another bacterium when it infects it.

Horizontal gene transfer has significant implications for the evolution and diversification of organisms. It allows for the rapid acquisition of new traits and genes, enabling species to adapt to changing environments or new ecological niches more efficiently. In prokaryotes, horizontal gene transfer has played a crucial role in the spread of antibiotic resistance genes, making it a critical concern in the context of antibiotic resistance in pathogens.

In eukaryotes, horizontal gene transfer is relatively less common but still occurs, particularly in simpler organisms like fungi, plants, and protists. While it might not be as prevalent or significant as in prokaryotes, the transfer of genes between eukaryotic species can still influence their evolutionary trajectories and contribute to the genetic diversity observed in these organisms.

Duplication of Genes & Pseudogenes

Gene duplication occurs when a segment of DNA is copied, resulting in multiple copies of a gene within a genome. These duplicated genes can diverge over time, leading to the evolution of new functions or specialization, contributing to the complexity and diversity of organisms.

We can also see what looks to be a new gene, say a copy or duplication of an existing gene, but then it doesn’t do anything.  When you look closer at this “new” gene, you can see what appears to be exons and introns (sections of repetitive DNA); however, it turns out that this gene doesn’t work.  This would be a pseudogene.

Because pseudogenes do not affect function, mutations in pseudogenes tend to be neutral and they can accumulate rapidly over evolutionary time (the molecular clock).

The scientific community continues to learn more about pseudogenes and we are learning that in some cases, pseudogenes are not as inactive as we thought.  It has been shown that pseudogenes are capable of dampening cancer-causing genes, called oncogenes, and therefore suppressing tumors (Pink et al 2011).

Summary 

Genome evolution refers to the process of changes in the genetic material (DNA) of an organism over time and is a fundamental aspect of biological evolution, playing a crucial role in shaping the diversity of life on Earth. Several key mechanisms contribute to genome evolution, including jumping genes, horizontal gene transfer, and gene duplication. Genome evolution plays a crucial role in the adaptation of organisms to changing environments and ecological niches. It drives speciation, the process by which new species arise, and is responsible for the vast array of life forms found on our planet. The study of genome evolution helps us understand the genetic basis of traits, diseases, and the relationships between different species, providing valuable insights into the history and mechanisms of life’s development. Advances in genomics and bioinformatics have significantly improved our understanding of genome evolution and continue to unravel the complexities of this fascinating field.

Questions

Glossary

References

Kasahara, M., Naruse, K., Sasaki, S. et al. 2007. The medaka draft genome and insights into vertebrate genome evolution. Nature 447, 714–719. https://doi.org/10.1038/nature05846

Pink RC, Wicks K, Caley DP, Punch EK, Jacobs L, & DRF Carter. 2011. Pseudogenes: Pseudo-functional or key regulators in health and disease? RNA 17(5): 792-798.

Rech GE, Bogaerts-Marquez M, Barron MG, Merenciano M, Villanueva-Canas JL, Horvath V, Fiston-Lavier AS,, Luyten I, Venkataram S, Quesneville H, & DA Petrov. 2019. Stress response, behavior and development are shaped by transposable element-induced mutations in Drosophila. PLoS Genetics 15(2): e1007900 https://doi.org/10.1371/journal.pgen.1007900

Tonegawa, S. 1983. Somatic generation of antibody diversity. Nature 302: 575-581.

Vakirlis N, Vane Z, Duggan KM, & A McLysaght. 2022. De novo birth of functional microproteins in the human lineage. Cell Reports 41 (12): 111808. https://doi.org/10.1016/j.celrep.2022.111808.

Vargas-Chavez C, Long Pendy NM, Nsango SE, Aguilera L, Ayala D, & J. Gonzalez. 2021. Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii. Genome Research 32: 189-202.  doi:10.1101/gr.275761.121

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