Tandem repeat-containing MITEs in the clam Donax trunculus

Genome Biology and Evolution

Volumn 5, Issue 12, 2013, Pages 2549-2559

  Šatović, Eva ^a   Plohl, Miroslav ^a  

^a RUDER BO KOVI INSTITUTE   (Croatia)

Author keywords

Evolution; MITE; Mobile element; Satellite DNA; Sequence rearrangements; Tandem repeats

Indexed keywords

SATELLITE DNA;

ANIMAL; ARTICLE; BIVALVE; DNA SEQUENCE; EVOLUTION; GENETIC VARIABILITY; GENETICS; INVERTED REPEAT; MITE; MOBILE ELEMENT; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE REARRANGEMENTS; TANDEM REPEATS; TRANSPOSON;

EVOLUTION; MITE; MOBILE ELEMENT; SATELLITE DNA; SEQUENCE REARRANGEMENTS; TANDEM REPEATS;

ANIMALS; BASE SEQUENCE; BIVALVIA; DNA TRANSPOSABLE ELEMENTS; DNA, SATELLITE; EVOLUTION, MOLECULAR; GENETIC VARIATION; INVERTED REPEAT SEQUENCES; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 84892541773     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evt202     Document Type: Article

References (50)

1. Alkan C, et al. 2007. Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data. PLoS Comput Biol. 3(9):1807-1818.
2. Biscotti MA, et al. 2007. Repetitive DNA, molecular cytogenetics and genome organization in the King scallop (Pecten maximus). Gene 406:91-98.
3. Brajković J, Feliciello I, Bruvo-Madaric B, Ugarković D. 2012. Satellite DNAlike elements associated with genes within euchromatin of the beetle Tribolium castaneum. G3 2:931-941.
4. Bureau TE, Wessler SR. 1992. Tourist: a large family of small inverted repeat elements frequently associated with maize genes. Plant Cell 4:1283-1294.
5. Cafasso D, Cozzolino S, De Luca P, Chinali G. 2003. An unusual satellite DNA from Zamia paucijuga (Cycadales) characterised by two different organisations of the repetitive unit in the plant genome. Gene 311: 71-79.
6. Canapa A, Barucca M, Cerioni PN, Olmo E. 2000. A satellite DNA containing CENP-B box-like motifs is present in the antarctic scallop Adamussium colbecki. Gene 247:175-180.
7. Casola C, Hucks D, Feschotte C. 2008. Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals. Mol Biol Evol. 25:29-41.
8. Coates BS, Kroemer JA, Sumerford DV, Hellmich RLL. 2011. A novel class of miniature inverted repeat transposable elements (MITEs) that contain hitchhiking (GTCY)n microsatellites. Insect Mol Biol. 20: 15-27.
9. Cohen JB, Hoffman-Liebermann B, Kedes L. 1985. Structure and unusual characteristics of a new family of transposable elements in the sea urchin Strongylocentrotus purpuratus. Mol Cell Biol. 5: 2804-2813.
10. Craig NL. 1995. Unity in transposition reactions. Science 270:253-254.
11. Dover GA. 1986. Molecular drive in multigene families: How biological novelties arise, spread and are assimilated. Trends Genet. 2: 159-165.
12. Feschotte C, Mouchès C. 2000. Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon. Mol Biol Evol. 17:730-737.
13. Feschotte C, Zhang X, Wessler S. 2002. Miniature inverted-repeat transposable elements (MITEs) and their relationship with established DNA transposons. In: Craig N, editor. Mobile DNA II. Washington (DC): ASM Press. p. 1147-1158.
14. Finnegan DJ. 1989. Eukaryotic transposable elements and genome evolution. Trends Genet. 5:103-107.
15. Fleetwood DJ, et al. 2011. Abundant degenerate miniature invertedrepeat transposable elements in genomes of epichloid fungal endophytes of grasses. Genome Biol Evol. 3:1253-1264.
16. Gaffney PM, Pierce JC,MackinleyAG, TitchenDA, GlennWK. 2003. Pearl, a novel family of putative transposable elements in bivalve mollusks. J Mol Evol. 56:308-316.
17. Hall SE, Kettler G, Preuss D. 2003. Centromere satellites from Arabidopsis populations: maintenance of conserved and variable domains. Genome Res. 13:195-205.
18. Heikkinen E, Launonen V, Muller E, Bachmann L. 1995. The pvB370 BamHI satellite DNA family of the Drosophila virilis group and its evolutionary relation to mobile dispersed genetic pDv elements. J Mol Evol. 41:604-614.
19. Henikoff S, Ahmad K, Malik HS. 2001. The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293: 1098-1102.
20. Hikosaka A, Kawahara A. 2004. Lineage-specific tandem repeats riding on a transposable element of MITE in Xenopus evolution: a new mechanism for creating simple sequence repeats. J Mol Evol. 59: 738-746.
21. Hinegardner R. 1974. Cellular DNA content of the Mollusca. Comp Biochem Physiol A Comp Physiol. 47:447-460.
22. Izsvák Z, et al. 1999. Short inverted-repeat transposable elements in teleost fish and implications for a mechanism of their amplification. J Mol Evol. 48:13-21.
23. Jurka J, Kapitonov VV, Kohany O, JurkaMV. 2007. Repetitive sequences in complex genomes: structure and evolution. Annu Rev Genomics Hum Genet. 8:241-259.
24. Jurka J, et al. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 110:462-467.
25. Kazazian HH. 2004. Mobile elements: drivers of genome evolution. Science 303:1626-1632.
26. Kipling D, Warburton PE. 1997. Centromeres, CENP-B and Tigger too. Trends Genet. 13:141-145.
27. Kourtidis A, Drosopoulou E, Pantzartzi CN, Chintiroglou CC, Scouras ZG. 2006. Three new satellite sequences and a mobile element found inside HSP70 introns of the Mediterranean mussel (Mytilus galloprovincialis). Genome 49:1451-1458.
28. Kuhn GCS, Heslop-Harrison JS. 2011. Characterization and genomic organization of PERI, a repetitive DNA in the Drosophila buzzatii cluster related to DINE-1 transposable elements and highly abundant in the sex chromosomes. Cytogenet Genome Res. 132: 79-88.
29. Kuhn GCS, Küttler H, Moreira-Filho O, Heslop-Harrison JS. 2012. The 1.688 repetitive DNA of Drosophila: concerted evolution at different genomic scales and association with genes. Mol Biol Evol. 29:7-11.
30. Locke J, Howard LT, Aippersbach N, Podemski L, Hodgetts RB. 1999. The characterization of DINE-1, a short, interspersed repetitive element present on chromosome and in the centric heterochromatin of Drosophila melanogaster. Chromosoma 108:356-366.
31. López-Flores I, Garrido-Ramos MA. 2012. The repetitive DNA content of eukaryotic genomes. In: Garrido-Ramos MA, editor. Repetitive DNA VII. Basel (Switzerland): Karger Publishers. p. 1-28.
32. López-Flores I, et al. 2004. The molecular phylogeny of oysters based on a satellite DNA related to transposons. Gene 339:181-188.
33. Macas J, Koblízková A, Navrá tilová A, Neumann P. 2009. Hypervariable 3' UTR region of plant LTR-retrotransposons as a source of novel satellite repeats. Gene 448:198-206.
34. Masumoto H, Masukata H, Muro Y, Nozaki N, Okazaki T. 1989. A human centromere antigen (CENP-B) interacts with a short specific sequence in alphoid DNA, a human centromeric satellite. J Cell Biol. 109: 1963-1973.
35. Meštrović N, Castagnone-Sereno P, Plohl M. 2006. Interplay of selective pressure and stochastic events directs evolution of the MEL172 satellite DNA library in root-knot nematodes. Mol Biol Evol. 23: 2316-2325.
36. Meštrović N, et al. 2013. Conserved DNA motifs, including the CENP-B box-like, are possible promoters of satellite DNA array rearrangements in nematodes. PLoS One 8:e67328.
37. Miller WJ, Nagel A, Bachmann J, Bachmann L. 2000. Evolutionary dynamics of the SGM transposon family in the Drosophila obscura species group. Mol Biol Evol. 17:1597-1609.
38. Mravinac B, Plohl M. 2010. Parallelism in evolution of highly repetitive DNAs in sibling species. Mol Biol Evol. 27:1857-1867.
39. Noma K, Ohtsubo E. 2000. Tnat1 and Tnat2 from Arabidopsis thaliana: novel transposable elementswith tandem repeat sequences. DNA Res. 7:1-7.
40. Ohzeki J, NakanoM, Okada T,Masumoto H. 2002. CENP-B box is required for de novo centromere chromatin assembly on human alphoid DNA. J Cell Biol. 159:765-775.
41. Petrović V, Plohl M. 2005. Sequence divergence and conservation in organizationally distinct subfamilies of Donax trunculus satellite DNA. Gene 362:37-43.
42. Petrović V, et al. 2009. A GC-rich satellite DNA and karyology of the bivalve mollusk Donax trunculus: a dominance of GC-rich heterochromatin. Cytogenet Genome Res. 124:63-71.
43. Plohl M, Cornudella L. 1996. Characterization of a complex satellite DNA in the mollusc Donax trunculus: analysis of sequence variations and divergence. Gene 169:157-164.
44. Plohl M, Cornudella L. 1997. Characterization of interrelated sequence motifs in four satellite DNAs and their distribution in the genome of the mollusc Donax trunculus. J Mol Evol. 44:189-198.
45. Plohl M, Luchetti A, Mestrović N, Mantovani B. 2008. Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene 409: 72-82.
46. Plohl M, et al. 2010. Long-term conservation vs high sequence divergence: the case of an extraordinarily old satellite DNA in bivalve mollusks. Heredity 104:543-551.
47. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497.
48. Wang S, Zhang L, Meyer E, Matz MV. 2010. Characterization of a group of MITEs with unusual features from two coral genomes. PLoS One 5: e10700.
49. Wilder J, Hollocher H. 2001. Mobile elements and the genesis of microsatellites in dipterans. Mol Biol Evol. 18:384-392.
50. Yang H-P, Barbash DA. 2008. Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes. Genome Biol. 9:R39