Synteny
Encyclopedia
In classical genetics
Classical genetics
Classical genetics consists of the technique and methodologies of genetics that predate the advent of molecular biology. A key discovery of classical genetics in eukaryotes was genetic linkage...

, synteny describes the physical co-localization of genetic loci
Locus (genetics)
In the fields of genetics and genetic computation, a locus is the specific location of a gene or DNA sequence on a chromosome. A variant of the DNA sequence at a given locus is called an allele. The ordered list of loci known for a particular genome is called a genetic map...

 on the same chromosome
Chromosome
A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...

 within an individual or species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...

. The concept is related to genetic linkage
Genetic linkage
Genetic linkage is the tendency of certain loci or alleles to be inherited together. Genetic loci that are physically close to one another on the same chromosome tend to stay together during meiosis, and are thus genetically linked.-Background:...

: Linkage between two loci is established by the observation of lower-than-expected recombination
Genetic recombination
Genetic recombination is a process by which a molecule of nucleic acid is broken and then joined to a different one. Recombination can occur between similar molecules of DNA, as in homologous recombination, or dissimilar molecules, as in non-homologous end joining. Recombination is a common method...

 frequencies between them. In contrast, any loci on the same chromosome are by definition syntenic, even if their recombination frequency cannot be distinguished from unlinked loci by practical experiments. Thus, in theory, all linked loci are syntenic, but not all syntenic loci are necessarily linked. Similarly, in genomics
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...

, the genetic loci on a chromosome are syntenic regardless of whether this relationship can be established by experimental methods such as DNA sequencing
DNA sequencing
DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....

/assembly, genome walking, physical localization or hap-mapping
Happy mapping
HAPPY Mapping, by Paul H. Dear and Peter R. Cook in 1989, is a method used in molecular biology to study the linkage between two or more DNA sequences. According to the , it is "Mapping based on the analysis of approximately HAPloid DNA samples using the PolYmerase chain reaction"...

.

Students of genetics employ the term synteny to describe the situation in which two genetic loci have been assigned to the same chromosome but still may be separated by a large enough distance in map units that genetic linkage has not been demonstrated.

The Encyclopædia Britannica gives the following description of synteny:

Shared synteny

Shared synteny (also known as conserved synteny) describes preserved co-localization of genes on chromosomes of different species. During 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...

, rearrangements to the genome such as chromosome translocations may separate two loci apart, resulting in the loss of synteny between them. Conversely, translocations can also join two previously separate pieces of chromosomes together, resulting in a gain of synteny between loci. Stronger-than-expected shared synteny can reflect selection for functional relationships between syntenic genes, such as combinations of alleles that are advantageous when inherited together, or shared regulatory mechanisms.

The term is sometimes also used to describe preservation of the precise order of genes on a chromosome passed down from a common ancestor, although many geneticists reject this use of the term. The analysis of synteny in the gene order sense has several applications in genomics. Shared synteny is one of the most reliable criteria for establishing the orthology of genomic regions in different species. Additionally, exceptional conservation of synteny can reflect important functional relationships between genes. For example, the order of genes in the "Hox cluster
Homeobox
A homeobox is a DNA sequence found within genes that are involved in the regulation of patterns of anatomical development in animals, fungi and plants.- Discovery :...

", which are key determinants of the animal
Animal
Animals are a major group of multicellular, eukaryotic organisms of the kingdom Animalia or Metazoa. Their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later on in their life. Most animals are motile, meaning they can move spontaneously and...

 body plan
Body plan
A body plan is the blueprint for the way the body of an organism is laid out. An organism's symmetry, its number of body segments and number of limbs are all aspects of its body plan...

 and which interact with each other in critical ways, is essentially preserved throughout the animal kingdom. Patterns of shared synteny or synteny breaks can also be used as characters
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...

 to infer the phylogenetic relationships among several species, and even to infer the genome organization of extinct ancestral species. A qualitative distinction is sometimes drawn between macrosynteny, preservation of synteny in large portions of a chromosome, and microsynteny, preservation of synteny for only a few genes at a time.

Etymology

Synteny is a neologism meaning "on the same ribbon"; Greek
Ancient Greek
Ancient Greek is the stage of the Greek language in the periods spanning the times c. 9th–6th centuries BC, , c. 5th–4th centuries BC , and the c. 3rd century BC – 6th century AD of ancient Greece and the ancient world; being predated in the 2nd millennium BC by Mycenaean Greek...

: , syn = along with + , tainiā = band.

External links

  • Synteny server Server for Synteny Identification and Analysis of Genome Rearrangement—the Identification of synteny and calculating reversal distances.
  • Comparative Maps NIH's National Library of Medicine NCBI link to Gene Homology resources, and Comparative Chromosome Maps of the Human, Mouse, and Rat.
  • NCBI Home Page NIH's National Library of Medicine NCBI (National Center for Biotechnology Information) link to a tremendous number of resources.
  • ACT (Artemis Comparison Tool) — Probably the most used synteny software program used in comparative genomics.
The source of this article is wikipedia, the free encyclopedia.  The text of this article is licensed under the GFDL.
 
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