Retrotransposon marker

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Retrotransposon markers are components of DNA which are used as cladistic markers. They assist in determining the common ancestry, or not, of related taxa. The "presence" of a given retrotransposon in related taxa suggests their orthologous 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 mammals depends on the availability of retrotransposons that were actively integrating before the divergence of a particular species.

Details

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. [1] 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 transposons, but see van de Lagemaat et al. (2005). [2] 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. [1] [3] The "presence" of a given retrotransposon in related taxa suggests their orthologous 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 mammals depends on the availability of retrotransposons that were actively integrating before the divergence of a particular species. [4]

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, [5] hominoid relationships, [6] the strepsirrhine tree, [7] the marsupial radiation from South America to Australia, [8] and the placental mammalian evolution. [9] [10]

Inter-retrotransposons amplified polymorphisms (IRAPs) are alternative retrotransposon-based markers. In this method, PCR oligonucleotide primers face outwards from terminal retrotransposon regions. Thus, they amplify the fragment between two retrotransposon insertions. As retrotransposon integration patterns vary between genotypes, the number and size of the resulting amplicons can be used for differentiation of genotypes or cultivars, to measure genetic diversity or to reconstruct phylogenies. [11] [12] [13] SINEs, which are small in size and often integrate within or next to genes represent an optimal source for the generation of effective IRAP markers. [14]

Related Research Articles

<span class="mw-page-title-main">Retroposon</span>

Retroposons are repetitive DNA fragments which are inserted into chromosomes after they had been reverse transcribed from any RNA molecule.

An Alu element is a short stretch of DNA originally characterized by the action of the Arthrobacter luteus (Alu) restriction endonuclease. Alu elements are the most abundant transposable elements, containing over one million copies dispersed throughout the human genome. Alu elements were thought to be selfish or parasitic DNA, because their sole known function is self reproduction. However, they are likely to play a role in evolution and have been used as genetic markers. They are derived from the small cytoplasmic 7SL RNA, a component of the signal recognition particle. Alu elements are highly conserved within primate genomes and originated in the genome of an ancestor of Supraprimates.

<span class="mw-page-title-main">Euarchontoglires</span> Superorder of mammals

Euarchontoglires, synonymous with Supraprimates, is a clade and a superorder of mammals, the living members of which belong to one of the five following groups: rodents, lagomorphs, treeshrews, primates, and colugos.

<span class="mw-page-title-main">Retrotransposon</span> Type of genetic component

Retrotransposons are a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through the reverse transcription process using an RNA transposition intermediate.

Interspersed repetitive DNA is found in all eukaryotic genomes. They differ from tandem repeat DNA in that rather than the repeat sequences coming right after one another, they are dispersed throughout the genome and nonadjacent. The sequence that repeats can vary depending on the type of organism, and many other factors. Certain classes of interspersed repeat sequences propagate themselves by RNA mediated transposition; they have been called retrotransposons, and they constitute 25–40% of most mammalian genomes. Some types of interspersed repetitive DNA elements allow new genes to evolve by uncoupling similar DNA sequences from gene conversion during meiosis.

<span class="mw-page-title-main">Laurasiatheria</span> Clade of mammals

Laurasiatheria is a superorder of placental mammals that groups together true insectivores (eulipotyphlans), bats (chiropterans), carnivorans, pangolins (pholidotes), even-toed ungulates (artiodactyls), odd-toed ungulates (perissodactyls), and all their extinct relatives. From systematics and phylogenetic perspectives, it is subdivided into order Eulipotyphla and clade Scrotifera. It is a sister group to Euarchontoglires with which it forms the magnorder Boreoeutheria. Laurasiatheria was discovered on the basis of the similar gene sequences shared by the mammals belonging to it; no anatomical features have yet been found that unite the group, although a few have been suggested such as a small coracoid process, a simplified hindgut and allantoic vessels that are large to moderate in size. The Laurasiatheria clade is based on DNA sequence analyses and retrotransposon presence/absence data. The superorder originated on the northern supercontinent of Laurasia, after it split from Gondwana when Pangaea broke up. Its last common ancestor is supposed to have lived between ca. 76 to 90 million years ago.

<span class="mw-page-title-main">Epitheria</span> Clade of mammals

Epitherians comprise all the placental mammals except the Xenarthra. They are primarily characterized by having a stirrup-shaped stapes in the middle ear, which allows for passage of a blood vessel. This is in contrast to the column-shaped stapes found in marsupials, monotremes, and xenarthrans. They are also characterized by having a shorter fibula relative to the tibia.

<span class="mw-page-title-main">Pegasoferae</span> Group of mammals comprising horses, bats, carnivores, and pangolins, among others

Pegasoferae is a proposed clade of mammals based on genomic research in molecular systematics by Nishihara, Hasegawa and Okada (2006).

The Ty5 is a type of retrotransposon native to the Saccharomyces cerevisiae organism.

<span class="mw-page-title-main">Heat shock factor</span> Transcription factor

In molecular biology, heat shock factors (HSF), are the transcription factors that regulate the expression of the heat shock proteins. A typical example is the heat shock factor of Drosophila melanogaster.

<span class="mw-page-title-main">PASK</span> Protein-coding gene in the species Homo sapiens

PAS domain-containing serine/threonine-protein kinase is an enzyme that in humans is encoded by the PASK gene.

<span class="mw-page-title-main">ESD (gene)</span> Protein-coding gene in the species Homo sapiens

S-formylglutathione hydrolase is an enzyme that in humans is encoded by the ESD gene.

<span class="mw-page-title-main">EIF5B</span> Protein-coding gene in the species Homo sapiens

Eukaryotic translation initiation factor 5B is a protein that in humans is encoded by the EIF5B gene.

<span class="mw-page-title-main">CD248</span> Protein-coding gene in the species Homo sapiens

Endosialin is a protein that in humans is encoded by the CD248 gene.

<span class="mw-page-title-main">Alkaline phosphatase, placental type</span> Protein-coding gene in the species Homo sapiens

Alkaline phosphatase, placental type also known as placental alkaline phosphatase (PLAP) is an allosteric enzyme that in humans is encoded by the ALPP gene.

<span class="mw-page-title-main">Exafroplacentalia</span> Proposed clade of placental mammals

Exafroplacentalia or Notolegia is a clade of placental mammals proposed in 2001 on the basis of molecular research.

<span class="mw-page-title-main">GNAT3</span> Protein-coding gene in the species Homo sapiens

Guanine nucleotide-binding protein G(t) subunit alpha-3, also known as gustducin alpha-3 chain, is a protein subunit that in humans is encoded by the GNAT3 gene.

A transpoviron is a plasmid-like genetic element found in the genomes of giant DNA viruses.

<span class="mw-page-title-main">Long interspersed nuclear element</span>

Long interspersed nuclear elements (LINEs) are a group of non-LTR retrotransposons that are widespread in the genome of many eukaryotes. LINEs contain an internal Pol II promoter to initiate transcription into mRNA, and encode one or two proteins, ORF1 and ORF2. The functional domains present within ORF1 vary greatly among LINEs, but often exhibit RNA/DNA binding activity. ORF2 is essential to successful retrotransposition, and encodes a protein with both reverse transcriptase and endonuclease activity.

References

  1. 1 2 Shedlock AM, Okada N (February 2000). "SINE insertions: powerful tools for molecular systematics". BioEssays. 22 (2): 148–60. doi:10.1002/(SICI)1521-1878(200002)22:2<148::AID-BIES6>3.0.CO;2-Z. PMID   10655034.
  2. ↑ van de Lagemaat LN, Gagnier L, Medstrand P, Mager DL (September 2005). "Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates". Genome Res. 15 (9): 1243–9. doi:10.1101/gr.3910705. PMC   1199538 . PMID   16140992.
  3. ↑ Hamdi H, Nishio H, Zielinski R, Dugaiczyk A (June 1999). "Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates". J. Mol. Biol. 289 (4): 861–71. doi:10.1006/jmbi.1999.2797. PMID   10369767.
  4. ↑ Nishihara H, Okada N (2008). "Retroposons: Genetic Footprints on the Evolutionary Paths of Life". Phylogenomics. Methods in Molecular Biology. Vol. 422. pp. 201–225. doi:10.1007/978-1-59745-581-7_13. ISBN   978-1-58829-764-8. PMID   18629669.{{cite book}}: |journal= ignored (help)
  5. ↑ Nikaido M, Rooney AP, Okada N (August 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 (18): 10261–6. Bibcode:1999PNAS...9610261N. doi: 10.1073/pnas.96.18.10261 . PMC   17876 . PMID   10468596.
  6. ↑ Salem AH, Ray DA, Xing J, et al. (October 2003). "Alu elements and hominid phylogenetics". Proc. Natl. Acad. Sci. U.S.A. 100 (22): 12787–91. Bibcode:2003PNAS..10012787S. doi: 10.1073/pnas.2133766100 . PMC   240696 . PMID   14561894.
  7. ↑ Roos C, Schmitz J, Zischler H (July 2004). "Primate jumping genes elucidate strepsirrhine phylogeny". Proc. Natl. Acad. Sci. U.S.A. 101 (29): 10650–4. Bibcode:2004PNAS..10110650R. doi: 10.1073/pnas.0403852101 . PMC   489989 . PMID   15249661.
  8. ↑ Nilsson, M. A.; Churakov, G.; Sommer, M.; Van Tran, N.; Zemann, A.; Brosius, J.; Schmitz, J. (2010-07-27). Penny, David (ed.). "Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions". PLOS Biology . 8 (7): e1000436. doi: 10.1371/journal.pbio.1000436 . PMC   2910653 . PMID   20668664.
  9. ↑ Kriegs JO, Churakov G, Kiefmann M, Jordan U, Brosius J, Schmitz J (April 2006). "Retroposed elements as archives for the evolutionary history of placental mammals". PLOS Biol. 4 (4): e91. doi: 10.1371/journal.pbio.0040091 . PMC   1395351 . PMID   16515367.
  10. ↑ Nishihara H, Hasegawa M, Okada N (2006). "Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions". Proc. Natl. Acad. Sci. U.S.A. 103 (26): 9929–9934. Bibcode:2006PNAS..103.9929N. doi: 10.1073/pnas.0603797103 . PMC   1479866 . PMID   16785431.
  11. ↑ Kalendar R, Grob T, Regina M, Suomeni A, Schulman A (April 1999). "IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques". Theoretical and Applied Genetics. 98 (5): 704–711. doi:10.1007/s001220051124. S2CID   28784368.
  12. ↑ Flavell AJ, Knox MR, Pearce SR, Ellis TH (December 1998). "Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis". Plant J. 16 (5): 643–50. doi: 10.1046/j.1365-313x.1998.00334.x . PMID   10036780.
  13. ↑ Kumar A, Hirochika H (March 2001). "Applications of retrotransposons as genetic tools in plant biology". Trends Plant Sci. 6 (3): 127–34. doi:10.1016/s1360-1385(00)01860-4. PMID   11239612.
  14. ↑ Seibt, KM; Wenke, T; Wollrab, C; Junghans, H; Muders, K; Dehmer, KJ; Diekmann, K; Schmidt, T (June 2012). "Development and application of SINE-based markers for genotyping of potato varieties". Theoretical and Applied Genetics. 125 (1): 185–96. doi:10.1007/s00122-012-1825-7. PMID   22371142. S2CID   15776815.
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