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The Accidental Discovery Of Divergent DNA Is Genetic Game-Changer

The researchers were trying to sequence single cells using low input DNA levels and found that the divergent DNA signaling the end of a gene in this protist seemed to be completely distinct from other ciliates.

Author:Hajra Shannon
Reviewer:Paula M. Graham
Oct 20, 2023965 Shares60.3K Views
DNA, a molecule that stores instructions for living things, is based on the pairing of four bases: adenine (A), thymine (T), cytosine (C), and guanine (G). Scientists from the Earlham Institute and the University of Oxford discovered that the DNA code for proteins in protists, which are part of a broad group of eukaryotes, is not as ubiquitous as previously thought.
They sequenced the genome of Oligohymenophorea sp. PL0344, a tiny creature found in a pond in Oxford University Parks.
The researchers were trying to sequence single cells using low input DNA levels, and found that the divergent DNAsignaling the end of a gene in this protist seemed to be completely distinct from other ciliates. This raises questions about the complexities of DNA interpretation and the potential differences between species.

What Is Genetic Divergence?

When two or more populations of an ancestral species accrue separate genetic modifications over time, reproductive isolation occurs and the populations continue to evolve even when they are no longer in contact with one another. This may happen when a population has smaller subpopulations in more ecologically varied outlying areas or larger ranges.
Silent mutations or major physical or physiological alterations might be among the genetic variations that separate populations. The primary process behind speciation is genetic divergence, which occurs in tandem with reproductive isolation owing to innovative adaptations through selection or genetic drift.
Molecular genetics has provided evidence that speciation is the outcome of genetic divergence caused by changes in a very small number of genes within a species. Experts counter that a single dominant mutation in a critical gene is unlikely to cause divergence since a carrier of such a mutation would be unable to reproduce or pass it on to future generations.
Visualization of gene
Visualization of gene

Causes Of Genetic Divergence

Founder Effect

Genetic divergence, the process by which two or more populations of an ancestral species accumulate differences in their gene pools, can occur through various mechanisms. One such mechanism is the Founder Effect, where a small group of individuals becomes isolated from the original population.
If these individuals carry specific genetic traits, those traits become overrepresented in the new population, leading to divergence from the original population's genetic makeup.
For instance, if 10 individuals with 80% blue eyes and 20% brown eyes form a new population from an original population where only 10% had blue eyes, the new population will exhibit a higher percentage of blue-eyed individuals.

Bottleneck Effect

Another factor contributing to genetic divergence is the Bottleneck Effect. This phenomenon occurs when a catastrophic event drastically reduces the population size, leading to the overrepresentation of certain genetic patterns in the surviving individuals.
Similar to the Founder Effect, this can result in a genetic makeup in the surviving population that differs significantly from the original population.

Disruptive Selection

Moreover, genetic divergence can happen without geographical separation, a process known as Disruptive Selection. This occurs when extreme phenotypes are more advantageous than intermediate ones, leading to the splitting of a population.
For example, in Darwin's finches, birds with vastly different beak sizes are selected for based on the type of seeds they consume. Individuals with intermediate beak sizes face selection pressures, leading to minimal gene flow between the populations with different beak sizes.
This disruptive selection can create distinct niches within a population, promoting genetic divergence and potentially resulting in speciation.
Understanding these mechanisms sheds light on the intricate processes that govern genetic diversity and speciation in natural populations.

Unexpected Genetic Discovery Of Divergent DNA In Protists

DNA and genetics have long been the building blocks of life, the intricate code that governs our existence. Yet, every so often, nature surprises us with a twist, revealing how much we are yet to grasp about the complex world of genetic information.
In a recent exploration at the Earlham Institute, scientists embarked on a mission to test a new method of sequencing single cells. Little did they know that this venture would unearth an unexpected genetic revelation in a tiny but remarkable organism – a protist known as Oligohymenophorea sp. PL0344.
Dr. Jamie McGowan, a postdoctoral scientist, led this scientific odyssey. The team initially aimed to perfect a DNA sequencing pipeline capable of handling minuscule amounts of genetic material, such as that extracted from a single cell. But what they discovered was nothing short of astounding.
Oligohymenophorea sp. PL0344, a type of ciliate, exhibited a genetic anomaly. It defied the conventional understanding of how DNA is translated into proteins. In most organisms, specific sequences of DNA, known as stop codons, signify the end of a gene.
However, in this particular ciliate, one stop codon, TGA, served its usual purpose while another, TAA, took on the role of specifying lysine, and TAG was suddenly designating glutamic acid. This unexpected genetic variation challenges our prior knowledge about gene translation.
Protists like Oligohymenophorea sp. PL0344 belong to a diverse group, ranging from microscopic single-celled creatures to larger multicellular organisms like kelp and slime molds. Dr. McGowan highlights the diversity within the protist category, stating that some are more closely related to animals, others to plants, and their ecological roles encompass hunters, prey, parasites, and hosts.
Intriguingly, the genetic code variations found in ciliates like Oligohymenophorea sp. PL0344 are a rare phenomenon. Stop codons, TAA, TAG, and TGA, almost universally share the same translation. This genetic discovery reminds us of the boundless mysteries lurking within the natural world, underscoring how little we truly comprehend about the genetics of these remarkable protists.
This serendipitous revelation is a testament to the idea that science often stumbles upon groundbreaking discoveries when we least expect them. It highlights the need to explore the intricate world of genetic information with an open mind and a readiness to embrace the unexpected revelations that nature has in store for us.

Why Is This Discovery Important?

The finding of the divergent genetic coding of Oligohymenophorea sp. PL0344 is significant for various reasons. First, it calls into question genetics' established laws, demonstrating that there is more variability and complexity in how organisms read and interpret their DNA than previously imagined.
Second, it offers up new study routes into the genesis and development of this divergence, as well as its implications for the biology and ecology of this protist and other similar species.
Third, it highlights the ability and promise of single-cell sequencing technologies to uncover unique genomic characteristics and events that traditional approaches would otherwise overlook.
The researchers hope that their findings will spur more research into the genetics and genomes of protists, which are often ignored and understudied despite their variety and significance to the biosphere. They also hope that their research will increase understanding and appreciation for the beauty and wonder of life's variety and complexity.

What Are Protists?

Protists are an extremely varied collection of creatures that defy easy categorization as either animals, plants, bacteria, or fungus. Unicellular organisms are often microbes that only have one cell. Protists are eukaryotes because their organelles are contained inside a lipid bilayer like a cell's nucleus.
Protista was the traditional kingdom for single-celled creatures like amoebas and single-cell algae. However, improved genomic data has allowed for a deeper comprehension of the evolutionary connections between the various classes of protists. Depending on the level of cellular complexity, all forms of life fall into one of two categories: prokaryotes and eukaryotes.
Prokaryotes, which include bacteria and archaea, lack the cellular organization seen in eukaryotic cells. Algae, amoebas, and ciliates are only few of the many different types of protists. Protists are all eukaryotic species outside of the animal, plant, and fungal kingdoms, according to Dalhousie University professor Alastair Simpson.

What Is A Stop Codon?

A gene is a DNA segment that encodes a protein or a functioning RNA molecule. A gene has a beginning and an end point, which are indicated by specific sequences known as start and stop codons. ATG is a common start codon that also codes for the amino acid methionine. A stop codon may be one of three different combinations: TAA, TAG, or TGA. These codons do not encode any amino acids, but rather mark the end of protein production.
The start and stop codons are recognized by ribosomes, which are the cell's protein manufacturers. Ribosomes bind to the start codon and proceed along the gene, reading each triplet of bases (called a codon) and adding the matching amino acid to the developing protein chain. They detach off the gene and release the finished protein when they reach a stop codon.
The start and stop codons are part of the genetic code, which is a collection of instructions that governs the translation of DNA into proteins. The genetic code is thought to be universal, which means that it is shared by almost all living things on Earth. Some exceptions exist, such as bacteria and mitochondria, which have somewhat different coding. These alterations, however, are generally small and include just one or two codons.

Causes Of Oligohymenophorea Sp. PL0344 Diverge From The Genetic Code

The genetic coding of Oligohymenophorea sp. PL0344 was determined to be significantly different from that of other organisms. As a stop codon, TGA was employed exclusively in place of TAA, TAG, and TGA. TAA and TAG, which would ordinarily code for a different amino acid (CAA and CAG, respectively), were reallocated to represent glutamine.
This indicates that the genes of this protist were terminated and proteins were synthesized in a manner distinct from the norm. It also suggests that it had more opportunities to code for glutamine, which might affect the variety and function of its proteins.
This discovery surprised the researchers since they had not seen this kind of divergence in any other ciliate or protist genome. They suggested that this protist may have acquired this variation from an unknown source through horizontal gene transfer, or that it could have developed this divergence independently of other species.
When one creature acquires genetic material from another without becoming its child, this is called horizontal gene transfer. Virus infection, plasmid exchange, and endosymbiosis are just a few examples of the many ways this may occur.
The evolution and adaption of a species may be influenced by the introduction of new genes or variants into its genome via horizontal gene transfer.

Single-cell Sequencing Method

Nucleic acid sequences, such as DNA or RNA, offer genetic instructions for life. Walter Fiers, Frederick Sanger, and Ray Wu pioneered the development of sequencing methods in the 1970s. The genomes of individual cells from a cell population are measured using single cell sequencing, a kind of single cell RNA sequencing.
It has been used to discover new mutations in cancer cells, investigate epigenome changes during embryonic development, and determine how an apparently uniform cell population expresses certain genes.
Isolation of single cells, extraction, processing, amplification of genetic material, development of a sequencing library, and sequencing of the library using a next-generation sequencer are the four basic processes in single cell sequencing technology.
Magnetic-activated cell sorting (MACS) tags particular proteins on target cells using antibody-mediated superparamagnetic nanoparticles, while laser capture microdissection (LCM) separates target cells from solid tissue samples.
Manual cell picking, also known as micromanipulation, requires the use of an inverted microscope and micro-pipettes to select and isolate target cells. Before preparing a sequencing library, the quality of cell isolation is examined, and viability is determined using imaging.
The resultant DNA or RNA is extracted and amplified for further analysis. Sequencing libraries are created from single-stranded DNA fragments that have been barcoded and amplified. Synthesis, pyrosequencing, reversible terminator sequencing, proton detection sequencing, and ligation are all techniques used by commercial sequencing systems.
Quality controls are in place to guarantee that the original cell's condition is accurately replicated. Synthesis, pyrosequencing, and ligation sequencing are less prevalent yet produce reliable readings.

FAQs - Divergent DNA

What Does Divergent Mean In Genetics?

In genetics, "divergent" refers to the process by which two or more populations of a common ancestor accumulate genetic differences over time. These differences can lead to variations in traits, gene frequencies, and ultimately, the formation of distinct species.

What Is An Example Of Divergence In Biology?

An iconic example of divergence in biology is Charles Darwin's observations of finches in the Galápagos Islands. These finches exhibited variations in beak size and shape due to differences in their diets. Over time, these variations contributed to the evolution of separate species adapted to specific niches, showcasing the concept of adaptive radiation and genetic divergence.

What Is The First Great Discovery Of Genetics?

One of the earliest significant discoveries in genetics was Gregor Mendel's work on the inheritance of traits in pea plants, which laid the foundation for understanding the principles of heredity. Mendel's experiments in the mid-19th century revealed the concepts of dominant and recessive traits and the inheritance of genetic factors from generation to generation.

Who Discovered Genetics?

While many scientists have contributed to the field of genetics, Gregor Mendel is often recognized as the father of modern genetics. His pioneering work on pea plants and the principles of inheritance became the cornerstone of genetic research.

When Were Genes First Discovered?

Genes, as discrete units of heredity, were not explicitly discovered until the 20th century. The term "gene" was introduced by Danish botanist Wilhelm Johannsen in the early 1900s.
Prior to this, Gregor Mendel's work on heredity (mid-19th century) laid the groundwork for understanding genetic principles, although the word "gene" had not yet been coined. The true nature of genes and their molecular structure was unraveled later in the 20th century with the advent of molecular genetics and DNA research.

Final Words

Oligohymenophorea sp. PL0344 is a stunning illustration of the variety and complexity of life that may be uncovered by chance. The divergent DNA of this protist is read and interpreted in a manner that is distinct from the universal genetic code used by the vast majority of Earth's living creatures.
This variation questions long-held genetic principles and paves the way for novel investigations into the phenomenon's genesis, history, and impact.
It also exemplifies the promise and utility of single-cell sequencing approaches for illuminating hitherto unsuspected characteristics and phenomena of the genome. There is still so much to learn and discover about the fascinating world of protists, and this research is a reminder of that.
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Hajra Shannon

Hajra Shannon

Paula M. Graham

Paula M. Graham

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