Name: genome size and gene evolution
Uploaded: 2023-04-30T18:28:42.000Z
Duration: 3 min 21 s
Channel: JoVE

K12 Standards

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North Carolina K-12 Science Standard Course of Study

9-12

Biology

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Heredity- Inheritance and Variation of Traits

LS.Bio.6.2

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

Cell Biology

Unit 1

Cells, Genomes, and Evolution

KEY TERMS AND CONCEPTS

genome size and gene evolution

Genome size and gene evolution are linked through changes in DNA sequence and genome structure. Some genes can arise from parts of the genome that were not coding before, while others come from changes to existing genes. These shifts help explain how new genetic material can appear over time.

A genome is the full set of DNA in an organism. Its size can change as DNA is added, removed, or rearranged. The transcript highlights that genome size is not fixed, and that these changes can shape the evolution of new genes.

New genes may form by duplication and later change, or by other alterations in noncoding DNA. Over time, these changes can give rise to new functions. This process helps connect genome structure with the emergence of genetic novelty.

Genome Size and Gene Evolution

what are cells?

Cells as the Building Blocks of Life

Cells are the basic building blocks of life. A bacterium can be a single cell, while a human is made of trillions of cells. Even with this range, cells share key features that support life. A living cell has a plasma membrane. This is a bilayer of lipids that separates the cytoplasm inside the cell from the outside environment. A cell also carries genetic information in the form of DNA. In prokaryotic cells, DNA is found in a region called the nucleoid. In eukaryotic cells, DNA is enclosed...

the tree of life - bacteria, archaea, and eukaryotes

the-tree-of-life-bacteria-archaea-and-eukaryotes

Three Domains on the Tree of Life

The tree of life shows how living things are grouped into three domains: Bacteria, Archaea, and Eukaryotes. This classification helps explain the major branches of life and how they are related. Bacteria and Archaea are both single-celled organisms, but they are not the same. Eukaryotes include organisms with more complex cells, such as plants, animals, and fungi. Together, these three domains give a broad picture of life on Earth. Understanding the tree of life helps students compare cell...

prokaryotic cells

How Prokaryotes Survive Without a Nucleus

Prokaryotes are small unicellular organisms that live without a nucleus. They include the domains Archaea and Bacteria. Bacteria include common microbes such as Salmonella and E. coli, while Archaea include extremophiles that live in harsh places like volcanic springs. Prokaryotic cells still share several basic features with eukaryotic cells. They have a plasma membrane, cytoplasm, ribosomes, and genetic material in the form of single, circular DNA. Their cell parts float freely in the...

eukaryotic compartmentalization

How Organelles Keep Cells Working

Eukaryotic cells keep their organelles separate so each part can do a specific job. Organelles such as the nucleus and mitochondria are surrounded by membranes. These membranes are selectively permeable, which means they control what enters and leaves. That control creates small internal environments with conditions suited to each organelle. These controlled spaces help organelles work more efficiently. In animal cells, lysosomes keep an acidic environment that helps their enzymes digest...

eukaryotic evolution

How Eukaryotic Cells Became Complex

Eukaryotic cells became complex through a debated evolutionary path that likely involved endosymbiosis. The most accepted model is the endosymbiont theory, which explains how organelles such as mitochondria and chloroplasts may have entered an ancestral cell. Other ideas include the nucleus-first hypothesis, the mitochondria-first hypothesis, and the eukaryote-first hypothesis. The nucleus-first hypothesis says an ancestral prokaryote first formed a membrane around its DNA, creating the...

animal and plant cell structure

Plant vs Animal Cell Division and Specialization

Plant and animal cells differ in how they divide, organize into tissues, and specialize for different jobs. Both cell types divide by mitosis in non-gametic cells and by meiosis in gametic cells, but the details are not the same. These differences help explain how each cell type supports growth and reproduction. During cell division, animal cells use centrosomes to organize spindle fibers and separate chromosomes. Plant cells do not have centrosomes. Instead, they use a microtubule-organizing...

cytoplasm

Cytoplasm and the Cell’s Internal Support

The cytoplasm is the cell’s internal space that holds organelles and the cytoskeleton. It is suspended in the cytosol, an aqueous fluid made of water, ions, salts, and many organic molecules. This fluid helps keep the cell organized and supports many cellular activities. The cytoplasm is also where protein synthesis and protein folding take place. The watery cytosol helps proteins fold correctly. In a folded protein, hydrophobic amino acid side chains tend to stay buried in the core, while...

the nucleus

Nuclear DNA, Chromatin, and Nucleoli

The nucleus is a membrane-bound organelle that stores chromosomal DNA and helps control what proteins a eukaryotic cell makes. It acts as the cell’s control center. DNA in mitochondria and chloroplasts is different because it mainly supports functions specific to those organelles. Inside the nucleus, DNA is wrapped around proteins called histones. This DNA-protein complex is called chromatin. During interphase, when the cell is not dividing, chromatin stays loosely arranged so the DNA is easy...

the dna helix

How DNA Structure Was Discovered

DNA is the genetic material that passes traits from one generation to the next in organisms and most viruses. It is made of two strands of nucleotides that twist into a spring-like double helix. The shape is not perfectly even. It also has repeating grooves called the major groove and the minor groove. The major groove forms where the sugar-phosphate backbones are farther apart. This wider space gives DNA-binding proteins, including transcription factors, better access to the bases. The minor...

the central dogma

DNA to Protein: RNA’s Role

DNA to protein flow depends on RNA as the link between genetic information and the amino acids that build proteins. Early scientists knew that DNA stores the information for cell functions and that proteins carry out most of those functions. For a long time, they did not know how the code in DNA became a working protein. At first, many people thought one gene was changed directly into its protein. Two findings in eukaryotic cells challenged that idea. Protein production does not happen in the...

mutations

Mutations in DNA and Inherited Disease

Mutations are changes in the DNA sequence. They can happen on their own during DNA copying, or they can be caused by environmental factors. Scientists describe mutations in several ways, including whether they change the amino acid sequence of a protein, how much DNA they affect, and whether they occur in somatic cells or germline cells. Some mutations are point mutations. A point mutation changes a single nucleotide in DNA. Other mutations are chromosomal alterations, which change the number...

Genome size and gene evolution are linked through changes in DNA sequence and genome structure. Some genes can arise from parts of the genome that were not coding before, while others come from changes to existing genes. These shifts help explain how new genetic material can appear over time. A genome is the full set of DNA in an organism. Its size can change as DNA is added, removed, or rearranged. The transcript highlights that genome size is not fixed, and that these changes can shape the...

gene families

Shared Origins of Gene Families

Gene families are groups of related genes that share a common origin. They form when genes are copied and then change over time. These related genes can be found within the same genome. The video also connects gene families to homologous genes and orthologous genes. Homologous genes are genes with a shared evolutionary origin. Orthologous genes are homologous genes found in different species. Gene families help show how these relationships are used to study evolution and related gene functions.

gene evolution - fast or slow?

Gene Evolution Rates and Selection

Gene evolution can happen at different rates, and natural selection helps shape those changes. Some genes change slowly because important DNA changes are removed over time. Other genes can change more quickly when different mutations are kept in a population. The rate of evolution depends on how a gene is used and how strongly it is affected by selection. Genes with essential jobs often stay more similar across species. Genes under weaker pressure may show more variation and may evolve faster.<br...

types of genetic transfer between organisms

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Vertical and Horizontal Gene Transfer

Genetic transfer between organisms happens in two main ways: vertical gene transfer and horizontal gene transfer. These two routes explain how hereditary material moves from one generation to the next or between organisms that are not parent and offspring. Vertical gene transfer passes genes from parent to offspring during reproduction. This is the usual way genetic information is inherited in living things. Horizontal gene transfer moves genetic material between organisms outside of...

key terms and concepts

Explore how genome size changes can shape gene evolution, including gene duplication, DNA rearrangement, and the rise of new genetic functions.

Genome Size and Gene Evolution | JoVE K12

cell biology

JoVE Core Cell Biology illustrates complex cellular processes in easy-to-understand yet comprehensive animated video lessons. This collection focuses on the essential components and functions of cells, including organelles and membranes, cellular transport, and cell energetics. It is complemented by scientist-in-action videos that demonstrate the application of cell biology in real-world research experiments.

Pennsylvania State Academic Standards

Life Science

Inheritance and Variation of Traits

3.1.9-12.P

3.1.9-12.Q

Louisiana Student Standards for Science

High School

Life Sciences

Biological Evolution: Unity And Diversity

HS-LS4-1

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Ohio’s Learning Standards and Model Curriculum

Heredity

Mutations

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BIO.5

BIO.5.b

Arizona Science Standards

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HS+B.L3U1.12

Next Generation Science Standards

Heredity: Inheritance and Variation of Traits

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New York State Science Learning Standards

HS-LS3-1.

What is Meiosis?

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Meiosis I

Meiosis II

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Crossing Over

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Oogenesis

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Use models to explain how DNA is passed from parents to offspring through the processes of meiosis and fertilization in sexual reproduction.

LS.Bio.6.1

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations ...

Types of Genetic Transfer Between Organisms

Base-pairing and DNA Repair

The DNA Replication Fork

Lagging Strand Synthesis

The Replisome

Proofreading

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Replication in Prokaryotes

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Replication in Eukaryotes

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Overview of DNA Repair

Base Excision Repair

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DNA Distortion and Damage
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Fixing Double-strand Breaks

Homologous Recombination

Gene Conversion

Restarting Stalled Replication Forks

Construct an explanation to summarize how inheritable genetic variations may result from: new genetic combinations in meiosis, mutations during replication, or mutations caused by environmental factors.

An Overview of Genetic Analysis

An organism&#8217;s physical traits, or phenotype, are a product of its genotype, which is the combination of alleles (gene variants) inherited from its ...

Genetic Crosses

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Punnett Squares

Monohybrid Crosses

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Law of Independent Assortment

Chi-square Analysis

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Pedigree Analysis

Multiple Allele Traits

Incomplete Dominance

Gregor Mendel&#39;s work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid ...

Lethal Alleles

Agouti: A Lethal Allele
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Polygenic Traits

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Background and Environment Affect Phenotype

Although the genetic makeup of an organism plays a major role in determining the phenotype, there are also several environmental factors, such as ...

Use mathematics and computational thinking to predict the variation and distribution of expressed traits based on: Mendelian inheritance, co-dominance, incomplete dominance, multiple alleles, and sex-linked inheritance.

LS.Bio.7.1

Overview

A pedigree is a diagram displaying a family&#x2019;s history of a trait. Analyzing pedigrees can reveal (1) whether a trait is dominant or ...

Probability Laws

Overview

The probability of inheriting a trait can be calculated using the sum and product rules. The sum rule is used to calculate the probability of ...

The Concept of Multiple Allelism

Multiple allelism describes genes that exist in three or more allelic forms. Although diploid organisms, like humans, ...

Analyze and interpret data to explain how polygenic traits result in a wide range of phenotypes.

LS.Bio.7.2

Pleiotropy

Pleiotropy is the phenomenon in which a single gene impacts multiple, seemingly unrelated phenotypic traits. For example, defects in the SOX10 gene cause ...

Nature and Nurture

Many human characteristics, like height, are shaped by both nature&mdash;in other words, by our genes&mdash;and by nurture, or our environment. For ...

Construct an explanation to summarize how traits result from interactions of genetic factors (multiple genes and/or alleles) and environmental factors.

LS.Bio.7.3

PCR: The Polymerase Chain Reaction

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DNA Gel Electrophoresis

DNA gel electrophoresis is a technique used for the detection and separation of DNA molecules. An electric field is applied to a gel matrix comprised of ...

DNA Isolation

DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further ...

Restriction Enzymes

Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called ...

DNA Agarose Gel Electrophoresis

Agarose gel electrophoresis is a laboratory technique commonly used to separate DNA fragments by size. However, it can also be used to isolate and purify ...

dna-isolation-and-restriction-enzyme-analysis

DNA Isolation and Restriction Enzyme Analysis

The revelation of DNA as the hereditary molecule in all organisms has led to enormous scientific and medical breakthroughs and significantly enhanced our ...

Analyze and interpret data to compare DNA samples.

LS.Bio.8.1

Understand genetic mechanisms for variation.

Genome Size and Gene Evolution

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