Satellite DNA as a driver of population divergence in the red flour beetle tribolium castaneum

Genome Biology and Evolution

Volumn 7, Issue 1, 2014, Pages 228-239

  Feliciello, Isidoro ^a,b   Akrap, Ivana ^a   Brajkovi, Josip ^a   Zlatar, Ivo ^a   Ugarkovic, Durdica ^a  

^a RUDER BO KOVI INSTITUTE   (Croatia)

^b UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

genome evolution; heterochromatin; population divergence; repetitive DNA; Satellite DNA; Tribolium castaneum

Indexed keywords

EUKARYOTA; TRIBOLIUM CASTANEUM;

HETEROCHROMATIN; SATELLITE DNA;

ANIMAL; CENTROMERE; CHROMOSOME; GENETIC VARIABILITY; GENETICS; HETEROCHROMATIN; INSECT GENOME; NUCLEOTIDE REPEAT; POPULATION GENETICS; TRIBOLIUM;

ANIMALS; CENTROMERE; CHROMOSOMES; DNA, SATELLITE; GENETIC VARIATION; GENETICS, POPULATION; GENOME, INSECT; HETEROCHROMATIN; REPETITIVE SEQUENCES, NUCLEIC ACID; TRIBOLIUM;

EID: 84928256552     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu280     Document Type: Article

References (48)

1. Alvarez-Fuster A, Juan C, Petitpierre E. 1991. Genome size in Tribolium flour-beetles: inter-and intraspecific variation. Genet Res. 58:1-5.
2. Assum G, Fink T, Steinbeisser T, Fisel KJ. 1993. Analysis of human extrachromosomal DNA elements originating from different beta-satellite subfamilies. Hum Genet. 91:489-495.
3. Bachmann L, Venanzetti F, Sbordoni V. 1994. Characterization of a species-specific satellite DNA of Dolichopoda schiavazzi (Orthoptera, Rhaphidophoridae) cave crickets. J Mol Evol. 39:274-281.
4. Bosco G, Campbell P, Leiva-Neto JT, Markow TA. 2007. Analysis of Drosophila species genome size and satellite DNA content reveals significant differences among strains as well as between species. Genetics 177:1277-1290.
5. Brajković J, Feliciello I, Bruvo-Mad-arić B, Ugarković D-. 2012. Satellite DNAlike elements associated with genes within euchromatin of the beetle. Tribolium castaneum. G3. 2:931-941.
6. Brown JD, Mitchell SE, O'Neill RJ. 2012. Making a long story short: noncoding RNAs and chromosome change. Heredity 108:42-49.
7. Cabrero J, Perfectti F, Gomez R, Camacho JP, Lopez-Leon MD. 2003.Population variation in the A chromosome distribution of satellite DNA and ribosomal DNA in the grasshopper Eyprepocnemis plorans. Chromosome Res. 11:375-381.
8. Cardone DE, Feliciello I, Marotta M, Rosati C, Chinali G. 1997. A family of centromeric satellite DNAs from the European brown frog Rana graeca italica. Genome 40:774-781.
9. de Franco FF, Kuhn GC, Sene FM, Manfrin MH. 2006. Conservation of pBuM-2 satellite DNA sequences among geographically isolated Drosophila gouveai populations from Brazil. Genetica 128:287-295.
10. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
11. Elder FJ, Turner BJ. 1994. Concerted evolution at the population level: pupfish HindIII satellite DNA sequences. Proc Natl Acad Sci USA. 91:994-998.
12. Ellegren H, et al. 2012. The genomic landscape of species divergence in Ficedula flycatchers. Nature 491:756-776.
13. Feliciello I, Chinali G, Ugarković D-. 2011. Structure and evolutionary dynamics of the major satellite in the red flour beetle Tribolium castaneum. Genetica 139:999-1008.
14. Feliciello I, Parazajder J, Akrap I, Ugarković D-. 2013. First evidence of DNA methylation in insect Tribolium castaneum-environmental regulation of DNA methylation within heterochromatin. Epigenetics 8:534-541.
15. Feliciello I, Picariello O, Chinali G. 2005. The first characterization of the overall variability of repetitive units in a species reveals unexpected features of satellite DNA. Gene 349:153-164.
16. Feliciello I, Picariello O, Chinali G. 2006. Intra-specific variability and unusual organization of the repetitive units in a satellite DNA from Rana dalmatina: molecular evidence of a new mechanism of DNA repair acting on satellite DNA. Gene 383:81-92.
17. Ferree PM, Barbash DA. 2009. Species-specific heterochromatin prevents mitotic chromosome segregation to cause hybrid lethality in Drosophila. PLoS Biol. 7:e1000234.
18. Ferree PM, Prasad S. 2012. How can satellite DNA divergence cause reproductive isolation Let us count the chromosomal ways. Genet Res Int. 2012:430136.
19. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52: 696-704.
20. Hollister JD, et al. 2011. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc Natl Acad Sci USA. 108:2322-2327.
21. Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
22. Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH. 2000. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci USA. 97:6603-6609.
23. Kanizay LB, Albert PS, Birchler JA, Dawe RK. 2013. Intragenomic conflict between the two major knob repeats of maize. Genetics 194:81-89.
24. Kohany O, Gentles AJ, Hankus L, Jurka J. 2006. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7:474.
25. Kuhn GC, Franco FF, Silva WA Jr, Martinez-Rossi NM, Sene FM. 2003. On the pBuM189 satellite DNA variability among South American populations of Drosophila buzzatti. Hereditas 139:161-166.
26. Kuhn GC, Sene FM. 2004. Characterization and interpopulation variability of a complex HpaI satellite DNA of Drosophila seriema (repleta group). Genetica 121:241-249.
27. Lorite P, Carrillo JA, Garneria I, Petitpierre E, Palomeque T. 2002. Satellite DNA in the elm leaf beetle Xanthogaleruca luteola (Coleoptera, Chrysomelidae): characterization, interpopulation analysis and chromosomal location. Cytogenet Genome Res. 98:302-307.
28. Ma J, Jackson SA. 2006. Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice. Genome Res. 16:251-259.
29. Malik HS, Henikoff S. 2009. Major evolutionary transitions in centromere complexity. Cell 138:1067-1082.
30. Mestrović N, PlohlM, Mravinac B, Ugarković D-. 1998. Evolution of satellite DNAs from the genus Palorus-experimental evidence for the "library" hypothesis. Mol Biol Evol. 15:1062-1068
31. Navrátilová A, Kobĺzková A, Macas J. 2008. Survey of extrachromosomal circular DNA derived from plant satellite repeats. BMC Plant Biol. 8:90
32. Pezer Z , , Brajković J, Feliciello I, Ugarković D-. 2012. Satellite DNA-mediated effects on genome regulation. Genome Dyn. 7:153-169.
33. Pezer Z Ugarković D (2008) Role of non-coding RNA and heterochromatin in aneuploidy and cancer. Semin Cancer Biol. 18. 123-130
34. PezerZ, Ugarković D-2012. Satellite DNA-associated siRNAs as mediators of heat shock response in insects. RNA Biol. 9. 587-595.
35. Picariello O, Feliciello I, Bellinello R, Chinali G. 2002. S1 satellite DNA as a taxonomic marker in brown frogs: molecular evidence that Rana graeca graeca and Rana graeca italica are different species. Genome 45:63-70.
36. Pons J, et al. 2004. Complex structural features of satellite DNA sequences in the genus Pimelia (Coleoptera: Tenebrionidae): random differential amplification from a common "satellite DNA library". Heredity 92: 418-428.
37. Raskina O, Brodsky L, Belyayev A. 2011. Tandem repeats on an ecogeographical scale: outcomes from the genome of Aegilops speltoides. Chromosome Res. 19:607-623.
38. Richards S, et al. 2008. The genome of the model beetle and pest Tribolium castaneum. Nature 452:949-955.
39. Ruijter JM, et al. 2009. Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res. 37:e45.
40. Ruijter JM, et al. 2013. Evaluation of qPCR curve analysis methods for reliable biomarker discovery: bias, resolution, precision, and implications. Methods 59:32-46.
41. Stuart JJ, Mocelin G. 1995. Cytogenetics of chromosome rearrangements in Tribolium castaneum. Genome 38:673-680.
42. Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56:564-577.
43. Tamura K, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739.
44. Ugarković D-, Plohl M. 2002. Variation in satellite DNA profiles-causes and effects. EMBO J. 21:5955-5959.
45. Ugarković D-, Podnar M, Plohl M. 1996. Satellite DNA of the red flour beetle Tribolium castaneum-comparative study of satellites from the genus Tribolium. Mol Biol Evol. 13:1059-1066.
46. Vieira P, et al. 2014. Sequence variability of the MspI satellite DNA family of the pinewood nematode Bursaphelenchus xylophilus at different geographic scales. Mol Phylogenet Evol. 70:120-129.
47. Wang S, Lorenzen MD, Beeman RW, Brown SJ. 2008. Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome. Genome Biol. 9:R61.
48. White BJ, Cheng C, Simard F, Costantini C, Besansky NJ. 2010. Genetic association of physically unlinked islands of genomic divergence in incipient species of Anopheles gambiae. Mol Ecol. 19:925-939.