Syntany

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The synteny , more rarely synteny derived from the Greek σύν (syn - together) and ταινία (Tainia - Band), is a term used in comparative genomics and bioinformatics . Today, the term is mostly used for the loci of orthologous genes that are located in different biological species on chromosome sections with these species of common evolutionary descent. Originally, the term was defined differently and used for genes that, in the same species, sit on the same chromosome without necessarily always showing a linkage. This linguistic usage is still partly used in scientific journals. When the same orthologous genes are present in the same arrangement on chromosomes of different species, this is called conserved syntany. The areas for which this applies are called synthesis blocks. Instead of conserved syntany, however, the term syntany is very often only abbreviated.

Basics

In the context of comparative genomics, the genome of different species is compared with one another in order to determine their evolutionary history and relationship, to elucidate the function and functional change of various genes and, based on this, to be able to cure diseases that may be triggered or promoted by them. This comparison is made more difficult by the fact that the DNA sequences of two species diverge more or less quickly after speciation. Not only do point mutations that lead to SNPs occur, but entire sections can be lost, duplicated or profoundly remodeled through inversions , translocations and other modifications. The exact comparison of the sequences, called alignment , is therefore only possible for closely related species or over short sequence sections. However, it is often possible to detect homologous genes in a similar sequence (known as collinearity) over longer sections of a chromosome in different species, even if their sequence can differ greatly in detail. This is called conserved syntany. The sequence comparison is now computer-aided, using the methods of combinatorics . Numerous algorithms are in use for this in the context of bioinformatics , which are continuously improved.

Language history

The English term "synteny" was introduced by John H. Renwick of the London School of Hygiene and Tropical Medicine at the fourth International Congress of Human Genetics in 1971 in Paris. Originally, the term in genetics meant that syntene loci were on the same chromosome.

literature

  • Chris Bryan, Gregory Guterman, Kwan-Liu Ma, Harris Lewin, Denis Larkin, Jaebum Kim, Jian Ma, Marta Farré: Synteny Explorer: An interactive visualization application for teaching genome evolution. In: IEEE Trans Visualization Computer Graphics 23, 2017: 711-720. DOI: 10.1109 / TVCG.2016.2598789 .
  • Gene Order. In: NM van Straalen, Dick Roelofs: An Introduction to ecological Genomics. Oxford University Press, Oxford 2006, ISBN 0-19-856671-9 , pp. 68-70.
  • Synteny: The Comparative Analysis of Genomes. In: Kurt Weising: DNA Fingerprinting in Plants: Principles, Methods, and Applications. Second edition. CRC Press, Hoboken 2005, ISBN 0-8493-1488-7 , pp. 287-288.

Individual evidence

  1. Nils Stein: synteny (Syntenic Genes). In: Stanley Maloy, Kelly Hughes (eds): Brenner's Encyclopedia of Genetics (2nd ed). Elsevier, Amsterdam, Munich 2013, pp. 623–626. ISBN 978-0-08-096156-9
  2. a b Eberhard Passarge, Bernhard Horsthemke, Rosann A. Farber: Incorrect use of the term synteny. In: Nature Genetics 23 (4), 1999: p. 387.
  3. ^ Robert C. King, William D. Stansfield, Pamela K. Mulligan: A dictionary of genetics. Oxford University Press, 7th edition, 2006 ISBN 978-0-19-530762-7 . “Syntenic genes” on page 435.
  4. Haibao Tang, John E. Bowers, Xiyin Wang, Ray Ming, Maqsudul Alam, Andrew H. Paterson synteny and collinearity in plant genomes. In: Science 320, 2008: 486-488. doi : 10.1126 / science.1153917
  5. Guénola Drillon, Alessandra Carbone, Gilles Fischer: Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs. In: Journal of Logic and Computation 23 (4), 2013: 815-838. doi : 10.1093 / logcom / exr047
  6. ^ Dang Liu, Martin Hunt, Isheng J. Tsai: Inferring synteny between genome assemblies: a systematic evaluation. In Cold Spring Harbor Laboratory bioRxiv preprint server 2017. doi : 10.1101 / 149989
  7. ^ John H. Renwick: Assignment and map-positioning of human loci using chromosomal variation. In: Ann Hum Genet 35 (1), 1971: 79-97. doi: 10.1111 / j.1469-1809.1956.tb01381.x
  8. ^ John H Renwick: The mapping of human chromosomes. In: Annual Review of Genetics 5, 1971: 81-120. doi: 10.1146 / annurev.ge.05.120171.000501