Phene
Encyclopedia
A phene is an individual genetically determined characteristic or trait
which can be possessed by an organism
, such as eye colour, height, behavior, tooth shape or any other observable characteristic.
as Gene
is to Genotype
, and Similarly Phene is to Phenome
as Gene is to Genome
.
The term has been widely adopted by the academic community and appears in scientific literature. A quick keyword search of titles and abstracts containing "phene" at PubMed returns many articles.
It is a valuable concept in the genomic era where "phenes" or "traits" (symptoms) are used to distinguish groups with genetic disorders. Genome wide association studies are then employed to identify genes that are more common in the symptomatic group than in the astymtomatic control group. Allen et al. report that with respect to Schizophrenia "Research in molecular genetics has focused on detecting multiple genes of small effect" This indicates the importance of discovering individual traits or "phenes" that are governed by single genes. Schizophrenia or bipolar disorder may be described as a phenotype but how many individual traits or "phenes" contribute to these phenotypes? Very large genome wide association studies have not found many significant gene linkages. On the contrary the results of these studies implicate a large number of gene alleles that have a very small effect (phene).
More specifically, a Phene is an abstract concept describing a particular characteristic which can be possessed by an organism. Whereas Phenotype refers to a collection of Phenes possessed by a particular organism, and Phenome refers to the entire set of Phenes that exist within an organism or species.
It is important to note that the word phenotype
was originally used to refer to both the trait/character itself (e.g. the blue eyes phenotype) and the set of traits/characteristics possessed by the organism (clair's eye-colour phenotype is blue). While this definition is still used in many places, the lack of distinction can make indepth explanations confusing and thus use of the term Phene becomes necessary. Indeed it is extremely difficult to determine precisely what the fundamental building blocks of a phenome are. Since the term "phenotype" has been used to describe traits and syndromes and population characteristics it is not helpful in the collective search for specific traits that could be a consequence of a single gene or gene-environmental interaction. Phene has emerged as a candidate building block for the phenome.
give rise to phenes. Genes are the biochemical instructions encoding what an organism can be, while phenes are what the organism is. In general it takes a combination of particular genes, environmental influences and random variation to give rise to any one phene in an organism. Both phenes and genes are subject to evolution. However, if one defines "genes" as "DNA sequences encoding polypeptides", they are not directly accessible to natural selection
; the associated phenes are. Note that some, e.g. Richard Dawkins
, have used a wider definition of "gene" than the one used in genetics
on occasion, extending it to any DNA sequence with a function.
Due to the distinct chemical and physical properties of the nucleotides in the DNA and some mutations being "silent
" (that is, not altering gene expression
), the DNA primary sequence may also be a phene. For example, A-T and C-G base pairs are differently resistant to heat (see also DNA-DNA hybridization). In a thermophilic microorganism, "silent" mutations may have an effect on DNA stability and thus survival. While being subject to evolution
, natural selection
affects the primary sequence directly in this case, with or without it being expressed.
Consider, for example, a mutation that makes a zygote
abort development as a young embryo
. This mutation, obviously, will not spread, as it is quickly fatal. It is not the mutated nucleotide that is selected against, but the fact that due to this mutation, the phene (a key enzyme or developmental factor for example) does not get expressed.
Compare a (fictional) kind of mutation that breaks the DNA strand in a crucial position and defies all attempts to repair it, leading to cell death. Here, the mutated and unmutated DNA sequences would be phenes themselves; it is the changed primary sequence itself which by failing would cause death, not the corresponding polypeptide.
See also Dawkin's concept of extended phenotype.
, and there is some consternation amongst Australian researchers as to who first coined the term.
According to Anatoly Ruvinsky, The University of New England, Australia, the term was introduced by the influential Russian geneticist Alexander Serebrovsky in the 1920s. This assertion would seem to be supported by this article. While it is possible that the term has been coined independently several times, the basic definition of "phene is to phenotype as gene is to genotype" appears to be shared, though there is some disagreement over precisely what this phrase means.
Trait (biology)
A trait is a distinct variant of a phenotypic character of an organism that may be inherited, environmentally determined or be a combination of the two...
which can be possessed by an organism
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...
, such as eye colour, height, behavior, tooth shape or any other observable characteristic.
Phene - phenotype - phenome distinction
The term 'phene' was evidently coined as an obvious parallel construct to 'gene'. Phene is to PhenotypePhenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...
as Gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
is to Genotype
Genotype
The genotype is the genetic makeup of a cell, an organism, or an individual usually with reference to a specific character under consideration...
, and Similarly Phene is to Phenome
Phenome
A phenome is the set of all phenotypes expressed by a cell, tissue, organ, organism, or species.Just as the genome and proteome signify all of an organism's genes and proteins, the phenome represents the sum total of its phenotypic traits. Examples of human phenotypic traits are skin color, eye...
as Gene is to Genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
.
The term has been widely adopted by the academic community and appears in scientific literature. A quick keyword search of titles and abstracts containing "phene" at PubMed returns many articles.
It is a valuable concept in the genomic era where "phenes" or "traits" (symptoms) are used to distinguish groups with genetic disorders. Genome wide association studies are then employed to identify genes that are more common in the symptomatic group than in the astymtomatic control group. Allen et al. report that with respect to Schizophrenia "Research in molecular genetics has focused on detecting multiple genes of small effect" This indicates the importance of discovering individual traits or "phenes" that are governed by single genes. Schizophrenia or bipolar disorder may be described as a phenotype but how many individual traits or "phenes" contribute to these phenotypes? Very large genome wide association studies have not found many significant gene linkages. On the contrary the results of these studies implicate a large number of gene alleles that have a very small effect (phene).
More specifically, a Phene is an abstract concept describing a particular characteristic which can be possessed by an organism. Whereas Phenotype refers to a collection of Phenes possessed by a particular organism, and Phenome refers to the entire set of Phenes that exist within an organism or species.
It is important to note that the word phenotype
Phenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...
was originally used to refer to both the trait/character itself (e.g. the blue eyes phenotype) and the set of traits/characteristics possessed by the organism (clair's eye-colour phenotype is blue). While this definition is still used in many places, the lack of distinction can make indepth explanations confusing and thus use of the term Phene becomes necessary. Indeed it is extremely difficult to determine precisely what the fundamental building blocks of a phenome are. Since the term "phenotype" has been used to describe traits and syndromes and population characteristics it is not helpful in the collective search for specific traits that could be a consequence of a single gene or gene-environmental interaction. Phene has emerged as a candidate building block for the phenome.
Phene - gene distinction
GenesGênes
Gênes is the name of a département of the First French Empire in present Italy, named after the city of Genoa. It was formed in 1805, when Napoleon Bonaparte occupied the Republic of Genoa. Its capital was Genoa, and it was divided in the arrondissements of Genoa, Bobbio, Novi Ligure, Tortona and...
give rise to phenes. Genes are the biochemical instructions encoding what an organism can be, while phenes are what the organism is. In general it takes a combination of particular genes, environmental influences and random variation to give rise to any one phene in an organism. Both phenes and genes are subject to evolution. However, if one defines "genes" as "DNA sequences encoding polypeptides", they are not directly accessible to natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....
; the associated phenes are. Note that some, e.g. Richard Dawkins
Richard Dawkins
Clinton Richard Dawkins, FRS, FRSL , known as Richard Dawkins, is a British ethologist, evolutionary biologist and author...
, have used a wider definition of "gene" than the one used in genetics
Genetics
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
on occasion, extending it to any DNA sequence with a function.
Due to the distinct chemical and physical properties of the nucleotides in the DNA and some mutations being "silent
Silent mutation
Silent mutations are DNA mutations that do not result in a change to the amino acid sequence of a protein. They may occur in a non-coding region , or they may occur within an exon in a manner that does not alter the final amino acid sequence...
" (that is, not altering gene expression
Gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
), the DNA primary sequence may also be a phene. For example, A-T and C-G base pairs are differently resistant to heat (see also DNA-DNA hybridization). In a thermophilic microorganism, "silent" mutations may have an effect on DNA stability and thus survival. While being subject to evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
, natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....
affects the primary sequence directly in this case, with or without it being expressed.
Consider, for example, a mutation that makes a zygote
Zygote
A zygote , or zygocyte, is the initial cell formed when two gamete cells are joined by means of sexual reproduction. In multicellular organisms, it is the earliest developmental stage of the embryo...
abort development as a young embryo
Embryo
An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination...
. This mutation, obviously, will not spread, as it is quickly fatal. It is not the mutated nucleotide that is selected against, but the fact that due to this mutation, the phene (a key enzyme or developmental factor for example) does not get expressed.
Compare a (fictional) kind of mutation that breaks the DNA strand in a crucial position and defies all attempts to repair it, leading to cell death. Here, the mutated and unmutated DNA sequences would be phenes themselves; it is the changed primary sequence itself which by failing would cause death, not the corresponding polypeptide.
See also Dawkin's concept of extended phenotype.
Origin
The term is sometimes thought to be recently (past decade or so) derived from the term phenotypePhenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...
, and there is some consternation amongst Australian researchers as to who first coined the term.
According to Anatoly Ruvinsky, The University of New England, Australia, the term was introduced by the influential Russian geneticist Alexander Serebrovsky in the 1920s. This assertion would seem to be supported by this article. While it is possible that the term has been coined independently several times, the basic definition of "phene is to phenotype as gene is to genotype" appears to be shared, though there is some disagreement over precisely what this phrase means.
Usages
"Phene" is used as to refer to relevant phenotypic traits in the OMIA (Online Mendelian Inheritance in Animals) database. One of the objectives of the OMIA is to match genotypes to phenotypes. Lenffer et al. (2006) describe the OMIA as a "comparative biology resource" "(The) OMIA is a comprehensive resource of phenotypic information on heritable animal traits and genes in a strongly comparative context, relating traits to genes where possible. OMIA is modelled on and is complementary to Online Mendelian Inheritance in Man (OMIM)." The term "phene" is equated with "trait".See also
- PhenotypePhenotypeA phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...
- OMIA (a database of animal Phenes)
- OMIM (a database of human Phenes)
- MLC (a database of mouse phenes)