Retrotransposon Marker
Encyclopedia
Retrotransposon markers are retrotransposon
s that are used as cladistic
markers.
The analysis of SINEs – Short INterspersed Elements – LINEs – Long INterspersed Elements – or truncated LTRs – Long Terminal Repeats – as molecular cladistic
markers represents a particularly interesting complement to DNA sequence
and morphological
data.
The reason for this is that retrotransposons are assumed to represent powerful noise-poor synapomorphies (Shedlock and Okada, 2000). The target sites
are relatively unspecific so that the chance of an independent integration of exactly the same element into one specific site in different taxa is not large and may even be negligible over evolutionary time scales. Retrotransposon integrations are currently assumed to be irreversible events; this might change since no eminent biological mechanisms
have yet been described for the precise re-excision of class I transposon
s, but see van de Lagemaat et al. (2005). A clear differentiation between ancestral and derived
character state at the respective locus
thus becomes possible as the absence of the introduced sequence can be with high confidence considered ancestral.
In combination, the low incidence of homoplasy together with a clear character polarity make retrotransposon integration markers ideal tools for determining the common ancestry of taxa by a shared derived
transpositional event (Hamdi et al. 1999; Shedlock and Okada 2000). The “presence” of a given retrotransposon in related taxa suggests their orthologues integration, a derived
condition acquired via a common ancestry, while the “absence” of particular elements indicates the plesiomorphic condition prior to integration in more distant taxa. The use of presence/absence analyses to reconstruct the systematic biology
of mammal
s depends on the availability of retrotransposons that were actively integrating before the divergence of a particular species
.
Examples for phylogenetic studies based on retrotransposon presence/absence data are the definition of whales as members of the order Cetartiodactyla
with hippos being their closest living relatives (Nikaido et al., 1999), hominoid relationships (Salem et al. 2003), the strepsirrhine tree (Roos et al., 2004), the marsupial
radiation from South America to Australia, and the placental mammalian evolution (Kriegs et al., 2006).
Inter-Retrotransposons Amplified Polymorphisms (IRAPs) are an alternative valuable retrotransposon-based markers. In this method, PCR oligonucleotide primers facing outwards from the LTR or other regions of retrotransposons are made and amplify between two retroelements inserted into the genome. As discussed above, the insertion of elements into the genome mean that the number of sites amplified and sizes of inter-retroelement fragments differ between different lines, and can be used as markers to detect genotypes, measure diversity or reconstruct phylogeny (see Flavell et al. 1999; Kalendar et al. 1999; Kumar & Hirochika 2001).
Retrotransposon
Retrotransposons are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. They are a subclass of transposon. They are particularly abundant in plants, where they are often a principal component of nuclear DNA...
s that are used as cladistic
Cladistics
Cladistics is a method of classifying species of organisms into groups called clades, which consist of an ancestor organism and all its descendants . For example, birds, dinosaurs, crocodiles, and all descendants of their most recent common ancestor form a clade...
markers.
The analysis of SINEs – Short INterspersed Elements – LINEs – Long INterspersed Elements – or truncated LTRs – Long Terminal Repeats – as molecular cladistic
Cladistics
Cladistics is a method of classifying species of organisms into groups called clades, which consist of an ancestor organism and all its descendants . For example, birds, dinosaurs, crocodiles, and all descendants of their most recent common ancestor form a clade...
markers represents a particularly interesting complement to DNA sequence
DNA sequence
The sequence or primary structure of a nucleic acid is the composition of atoms that make up the nucleic acid and the chemical bonds that bond those atoms. Because nucleic acids, such as DNA and RNA, are unbranched polymers, this specification is equivalent to specifying the sequence of...
and morphological
Morphology (biology)
In biology, morphology is a branch of bioscience dealing with the study of the form and structure of organisms and their specific structural features....
data.
The reason for this is that retrotransposons are assumed to represent powerful noise-poor synapomorphies (Shedlock and Okada, 2000). The target sites
Retrotransposon
Retrotransposons are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. They are a subclass of transposon. They are particularly abundant in plants, where they are often a principal component of nuclear DNA...
are relatively unspecific so that the chance of an independent integration of exactly the same element into one specific site in different taxa is not large and may even be negligible over evolutionary time scales. Retrotransposon integrations are currently assumed to be irreversible events; this might change since no eminent biological mechanisms
Biological process
A biological process is a process of a living organism. Biological processes are made up of any number of chemical reactions or other events that results in a transformation....
have yet been described for the precise re-excision of class I transposon
Transposon
Transposable elements are sequences of DNA that can move or transpose themselves to new positions within the genome of a single cell. The mechanism of transposition can be either "copy and paste" or "cut and paste". Transposition can create phenotypically significant mutations and alter the cell's...
s, but see van de Lagemaat et al. (2005). A clear differentiation between ancestral and derived
Derived
In phylogenetics, a derived trait is a trait that is present in an organism, but was absent in the last common ancestor of the group being considered. This may also refer to structures that are not present in an organism, but were present in its ancestors, i.e. traits that have undergone secondary...
character state at the respective locus
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...
thus becomes possible as the absence of the introduced sequence can be with high confidence considered ancestral.
In combination, the low incidence of homoplasy together with a clear character polarity make retrotransposon integration markers ideal tools for determining the common ancestry of taxa by a shared derived
Derived
In phylogenetics, a derived trait is a trait that is present in an organism, but was absent in the last common ancestor of the group being considered. This may also refer to structures that are not present in an organism, but were present in its ancestors, i.e. traits that have undergone secondary...
transpositional event (Hamdi et al. 1999; Shedlock and Okada 2000). The “presence” of a given retrotransposon in related taxa suggests their orthologues integration, a derived
Derived
In phylogenetics, a derived trait is a trait that is present in an organism, but was absent in the last common ancestor of the group being considered. This may also refer to structures that are not present in an organism, but were present in its ancestors, i.e. traits that have undergone secondary...
condition acquired via a common ancestry, while the “absence” of particular elements indicates the plesiomorphic condition prior to integration in more distant taxa. The use of presence/absence analyses to reconstruct the systematic biology
Cladistics
Cladistics is a method of classifying species of organisms into groups called clades, which consist of an ancestor organism and all its descendants . For example, birds, dinosaurs, crocodiles, and all descendants of their most recent common ancestor form a clade...
of mammal
Mammal
Mammals are members of a class of air-breathing vertebrate animals characterised by the possession of endothermy, hair, three middle ear bones, and mammary glands functional in mothers with young...
s depends on the availability of retrotransposons that were actively integrating before the divergence of a particular 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...
.
Examples for phylogenetic studies based on retrotransposon presence/absence data are the definition of whales as members of the order Cetartiodactyla
Cetartiodactyla
Cetartiodactyla is the clade in which whales and even-toed ungulates have currently been placed. The term was coined by merging the name for the two orders, Cetacea and Artiodactyla, into a single word. The term Cetartiodactyla reflects the idea that whales evolved within the artiodactyls...
with hippos being their closest living relatives (Nikaido et al., 1999), hominoid relationships (Salem et al. 2003), the strepsirrhine tree (Roos et al., 2004), the marsupial
Marsupial
Marsupials are an infraclass of mammals, characterized by giving birth to relatively undeveloped young. Close to 70% of the 334 extant species occur in Australia, New Guinea, and nearby islands, with the remaining 100 found in the Americas, primarily in South America, but with thirteen in Central...
radiation from South America to Australia, and the placental mammalian evolution (Kriegs et al., 2006).
Inter-Retrotransposons Amplified Polymorphisms (IRAPs) are an alternative valuable retrotransposon-based markers. In this method, PCR oligonucleotide primers facing outwards from the LTR or other regions of retrotransposons are made and amplify between two retroelements inserted into the genome. As discussed above, the insertion of elements into the genome mean that the number of sites amplified and sizes of inter-retroelement fragments differ between different lines, and can be used as markers to detect genotypes, measure diversity or reconstruct phylogeny (see Flavell et al. 1999; Kalendar et al. 1999; Kumar & Hirochika 2001).
Notations
- Flavell AJ, Knox MR, Pearce SR and Ellis THN. (1999) Retrotransposon-based insertion polymorphisms (RBIP) for high-throughput marker analysis. Plant J. 16: 643-650
- Hamdi H, Nishio H, Zielinski R, Dugaiczyk A (1999) Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates. J Mol Biol 289: 861–871. GS
- Kalendar R, Grob T, Regina M, Suomeni A, Schulman A. 1999. IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theoretical and Applied Genetics 98: 704–711
- Kumar A, Hirochika H. 2001. Applications of retrotransposons as genetic tools in plant biology. Trends in Plant Sciences 6: 127–134
- Shedlock AM, Okada N (2000) SINE insertions: Powerful tools for molecular systematics. Bioessays 22: 148–160. GS
- van de Lagemaat LN, Gagnier L, Medstrand P, Mager DL (2005) Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. Genome Res 15: 1243–1249. GS
- Nikaido M, Rooney AP, Okada N (1999) Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: Hippopotamuses are the closest extant relatives of whales. Proc Natl Acad Sci U S A 96: 10261–10266. GS
- Salem AH, Ray DA, Xing J, Callinan PA, Myers JS, Hedges DJ, Garber RK, Witherspoon DJ, Jorde LB, Batzer MA (2003) Alu elements and hominid phylogenetics. Proc Natl Acad Sci U S A 100: 12787–12791. GS
- Roos C, Schmitz J, Zischler H (2004) Primate jumping genes elucidate strepsirrhine phylogeny. Proc Natl Acad Sci U S A 101: 10650–10654. GS
- Kriegs JO, Churakov G, Kiefmann M, Jordan U, Brosius J, Schmitz J. (2006) Retroposed Elements as Archives for the Evolutionary History of Placental Mammals. PLoS Biol 4(4): e91.http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040091