Name: how genome size shapes new genes
Uploaded: 2020-11-23T11:47:33.000Z
Duration: 3 min 21 s
Channel: JoVE

K12 Standards

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NC K-12 Science Standard Course of Study

9-12

Biology

Biological Evolution- Unity and Diversity

LS.Bio.9.2

genome-size-and-the-evolution-of-new-genes

Genome Size and the Evolution of New Genes

Despite the simple nature of the genetic code, there is considerable variation in terms of genome size, from the smallest known genomes - including the proteobacterium Candidatus Carsonella ruddii at less than 160 thousand base pairs, to the largest, such as the Japanese flowering plant Paris japonica at around 150 billion. 
&#160; 
Despite these extremes, bacteria and archaea generally have around 3,000 genes within their genomes. Because prokaryotes have almost no non-coding sequences, this means that their genomes can be relatively small compared to those of eukaryotes. Smaller genomes also mean less to replicate at each round of cell division - which makes logistical sense for fast reproduction.
Eukaryotes typically have somewhere in the region of 20,000 genes, but their genomes are punctuated by long stretches of non-coding sequence - meaning their genome size does not necessarily translate to complexity.&#160;
Paris japonica&#8217;s genome may be over fifty times the size of the human genome - but this is due at least in part to vast amounts of non-coding sequence and probably high levels of duplication - not necessarily more novel genes.
So how do organisms evolve new genes? The answer is typically by modifying the sequence that already exists.
One of the primary resources for new genes to evolve is through gene duplication. Imagine a section of DNA containing a gene is accidentally duplicated. Now the organism has a second copy of an existing gene.&#160;
Such new gene copies are free from the constraints placed on the original to maintain function, and so they can diverge - potentially evolving a novel role or a modified function of the original.&#160;
Another way to create new genes is DNA shuffling - where segments of an existing gene or gene copy are separated and moved to join those of a different gene - making a hybrid gene that can take on a new function.
Intragenic mutation - the changes in a gene sequence introduced by mutations over time, accounts for many &#8220;new&#8221; genes. This divergence which is most noticeable when comparing species or lineages which are themselves diverging independently. Once this divergence is beyond a certain point, or one gene takes on a novel function, they may be classified as different genes entirely.
Finally, horizontal gene transfer brings in novel genes and sequences to the genome from external sources - such as other individuals and even other species. This type of novel gene acquisition is most common in prokaryotes and archaea, with the transfer of antibiotic resistance genes being a well-known example.&#160;
While rare in eukaryotes, it is still considered to be an essential source of genetic novelty, and genetic material can even come from distantly related species, such as the bacteria and fungi in this example.

genome size and the evolution of new genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence. Overall, this contributes to the phenomena that prokaryotic genomes tend to be smaller (i.e. contain fewer bases) on average than those of eukaryotes.
Unsurprisingly, given this observation, the smallest known genomes are mostly prokaryotes. Candidatus Carsonella rudii, for example, is a highly simplified proteobacterium which has a genome size of just 160 thousand base-pairs. Having lost many genes that it needed to synthesize life-essential proteins, it has evolved to be an obligate intracellular symbiont. At the opposite end of the spectrum, the eukaryote Japanese flowering plant Paris japonica is one of the largest known genomes, at around 150 billion base-pairs. Although the number of genes this encodes isn&#8217;t known, the genome shows vast amounts of duplication and non-coding sequence.
Within the genome of an average prokaryote there are roughly 3,000 genes. The average eukaryote has somewhere in the region of 20,000. But the genome size, especially in eukaryotes, is wildly variable - in large part due to the amount of non-coding sequence.
The Creation of New Genes
In order to evolve new genes, organisms have a few main options. The one thing most of these have in common is that they modify sequences that already exist.
Duplication plays an important role in creating new genes, and there are a few types of duplication that can result in these novel sequences. In gene duplication, a section of DNA containing a gene is duplicated. This second copy does not face the selection pressure which constrains the first, and so it can diverge. In time, this can lead to the evolution of novel genes, with new roles.
Another type of duplication - DNA shuffling - can result in just a section of a gene being duplicated and joining another gene. This can result in the creation of novel genes, with novel products.
Sometimes new genes simply evolve from accumulated mutations over time. This is known as intragenic mutation, and is most noticeable when comparing across species or divergent populations.
Finally, it is also possible to obtain new genes from external sources, in a process known as horizontal gene transfer. This means genetic material can be incorporated from other individuals, sometimes of the same species, but also potentially from another species entirely. This is a frequent source of novel genes in prokaryotes and archaea. It is less common in eukaryotes, but has been shown to occur, and eukaryotes can even pick up genetic information from sources as distant as bacteria or fungi.

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major ...

Education

JoVE Core

Molecular Biology

Unit 1

DNA, Cells, and Evolution

KEY TERMS AND CONCEPTS

how genome size shapes new genes

Genome size can vary widely, and it also helps show how new genes form. Every living organism has a genome, whether it uses RNA or DNA. Yet the size of that genome can be very different from one organism to another.

One major difference is whether the organism is prokaryotic or eukaryotic. Prokaryotic genomes usually have little to no non-coding sequence, which means genes are packed closely together in operons along the chromosome. Eukaryotic genomes contain long stretches of non-coding DNA between genes. This helps explain why prokaryotic genomes are often smaller than eukaryotic genomes.

The smallest known genomes are mostly prokaryotic. One example is Candidatus Carsonella rudii, a highly simplified proteobacterium with a genome of only 160 thousand base-pairs. It has lost many genes needed to make life-essential proteins, so it now lives as an obligate intracellular symbiont. On the other end of the range, the Japanese flowering plant Paris japonica has one of the largest known genomes, at about 150 billion base-pairs. Its genome contains extensive duplication and non-coding sequence, and the number of genes it encodes is not known.

Gene counts also differ between these groups. An average prokaryote has roughly 3,000 genes. An average eukaryote has around 20,000 genes. Even so, genome size in eukaryotes can vary a great deal because of how much non-coding DNA they contain.

New genes usually arise by changing sequences that already exist. Gene duplication copies a DNA segment that contains a gene. The extra copy is not under the same selection pressure as the original, so it can change over time and take on a new role. DNA shuffling can duplicate only part of a gene and join it to another gene, which can create a new gene product.

New genes can also appear through intragenic mutation, which means mutations build up within a gene over time. This is often seen when comparing different species or populations that have diverged. Another source is horizontal gene transfer, where genetic material comes from another individual or even another species. This is a common way for prokaryotes and archaea to gain novel genes, although it can also happen in eukaryotes, including gene transfers from bacteria or fungi.

How Genome Size Shapes New Genes

the dna helix

DNA Structure and Base Pairing

DNA has a helical structure that helps store genetic information. The double helix is the shape formed by two strands that twist around each other. This structure is a key feature of DNA in cells. The two strands are held together by base pairing. Bases on one strand match with bases on the other strand in a regular way. This pairing helps keep the DNA molecule stable and organized. The helix shape also helps explain how DNA fits into chromosomes and carries instructions for living things. By...

the central dogma

DNA to Protein: Central Dogma Steps

The central dogma explains how genetic information moves from DNA to RNA to protein. This flow is a key idea in molecular biology. It helps show how cells use genes to make the molecules that carry out work. DNA stores the instructions for making proteins. During transcription, a gene in DNA is copied into RNA. The RNA then carries that message to the next stage. In translation, the RNA message is used to build a protein. Proteins do much of the cell’s work, so this process connects genes to...

prokaryotic cells

Inside Prokaryotic Cell Structure

Prokaryotic cells have a simple internal structure compared with many other cells. They are usually divided into two groups: bacteria and archaea. These cells have no nucleus, so their DNA is not enclosed in a membrane-bound compartment. Instead, the genetic material is found in the nucleoid, a region where the DNA is located in the cell. Some prokaryotic cells also contain plasmids, which are small extra DNA molecules. A capsule may surround the cell and provide an additional outer layer. <br...

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Cell Compartments in Eukaryotes

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the tree of life - bacteria, archaea, eukaryotes

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Mutations are changes in DNA. They can alter the genetic code and affect how genes work. In high school biology, students often study mutations to understand how DNA changes can influence traits. The transcript focuses on two common mutation types: point mutations and frameshift mutations. A point mutation changes one nucleotide, which is one DNA building block. A frameshift mutation happens when nucleotides are added or removed and the reading frame shifts. These changes matter because they...

gene evolution - fast or slow?

Why Some Gene Regions Evolve Faster

Gene regions do not all change at the same rate. In eukaryotes, long stretches of DNA do not code for proteins or RNAs. Some of these non-coding regions include important regulatory sequences, but most have no known function. Because little or no selection pressure acts on them, they often change the fastest over evolutionary time. Protein-coding regions usually evolve more slowly. A change in a coding sequence can alter a protein and make it less effective at doing its job. That creates...

Genome size can vary widely, and it also helps show how new genes form. Every living organism has a genome, whether it uses RNA or DNA. Yet the size of that genome can be very different from one organism to another. One major difference is whether the organism is prokaryotic or eukaryotic. Prokaryotic genomes usually have little to no non-coding sequence, which means genes are packed closely together in operons along the chromosome. Eukaryotic genomes contain long stretches of non-coding DNA...

gene families

How Gene Families Evolve and Diversify

Gene families are groups of genes that are thought to come from a shared ancestor. They usually form when a gene is copied by mistake during cell division. The original gene stays under selection pressure to keep its job, while the extra copy can change more quickly over time. Some copied genes gain a new role in the organism. When that happens, they are called paralogs, which are two genes in the same species that evolved from one common ancestral gene. Gene families also include orthologs,...

types of genetic transfer between organisms

types-of-genetic-transfer-between-organisms

How Genes Move Within and Across Generations

Genetic transfer is the movement of genetic information from one organism to another. It happens in two main ways: vertical gene transfer and horizontal gene transfer. Vertical gene transfer moves genes from one generation to the next. It is much more common than horizontal gene transfer. Vertical gene transfer happens during both sexual reproduction and asexual reproduction. In both cases, one or more organisms pass some or all of their genome to their offspring. This kind of transfer occurs...

key terms and concepts

Compare prokaryotic and eukaryotic genome sizes, then see how gene duplication, DNA shuffling, mutation, and horizontal gene transfer create new genes.

How Genome Size Shapes New Genes | JoVE K12

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Heredity: Inheritance and Variation of Traits

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Understand natural selection as a mechanism for biological evolution.

How Genome Size Shapes New Genes

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