Analysis of SINE and LINE repeat content of Y chromosomes in the platypus, Ornithorhynchus anatinus

Reproduction, Fertility and Development

Volumn 21, Issue 8, 2009, Pages 964-975

  Kortschak, R Daniel ^a   Tsend Ayush, Enkhjargal ^a   Grützner, Frank ^a  

^a UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

Genome evolution; Repetitive element; Y chromosome evolution

Indexed keywords

ARTICLE; AUTOSOME; CHROMOSOME ISOLATION; DNA BASE COMPOSITION; EVOLUTION; GENOME; LONG INTERSPERSED REPEAT; MONOTREMATE; NONHUMAN; ORNITHORHYNCHUS ANATINUS; PLATYPUS; SHORT INTERSPERSED REPEAT; X CHROMOSOME; Y CHROMOSOME;

ANIMALS; CELLS, CULTURED; CHROMOSOME MAPPING; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; MALE; PLATYPUS; SEQUENCE ANALYSIS, DNA; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS; Y CHROMOSOME;

AVES; MONOTREMATA; ORNITHORHYNCHUS ANATINUS; THERIA;

EID: 71049118748     PISSN: 10313613     EISSN: None     Source Type: Journal    
DOI: 10.1071/RD09084     Document Type: Article

References (34)

1. Ashley,T. (2005). Chromosome chains and platypus sex: kinky connections. Bioessays 27, 681-684. doi:10.1002/BIES.20265
2. Birney, E., Andrews, T. D., Bevan, P., Caccamo, M., Chen,Y., et al. (2004). An overview of Ensembl. Genome Res. 14, 925-928. doi:10.1101/GR.1860604
3. Charlesworth, B. (1991). The evolution of sex chromosomes. Science 251, 1030-1033. doi:10.1126/SCIENCE.1998119
4. Crollius, H. R., Jaillon, O., Dasilva, C., Ozouf-Costaz, C., Fizames, C., et al. (2000). Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis. Genome Res. 10, 939-949. doi:10.1101/GR.10.7.939
5. Edgar, R. C., and Myers, E. W. (2005). PILER: identification and classification of genomic repeats. Bioinformatics 21(Suppl. 1), i152-i158. doi:10.1093/BIOINFORMATICS/BTI1003
6. Ellegren, H. (2007). Characteristics, causes and evolutionary consequences of male-biased mutation. Proc. Biol. Sci. 274, 1-10. doi:10.1098/RSPB.2006.3720 (Pubitemid 47055489)
7. Ewing, B., and Green, P. (1998). Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186-194. (Pubitemid 28177230)
8. Ewing, B., Hillier, L.,Wendl, M., and Green, P. (1998). Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175-185. (Pubitemid 28177229)
9. Gordon, D., Abajian, C., and Green, P. (1998). Consed: a graphical tool for sequence finishing. Genome Res. 8, 195-202. (Pubitemid 28177231)
10. Grützner, F., Rens,W.,Tsend-Ayush, E., El-Mogharbel,N., O'Brien, P. C. M., Jones, R. C., Ferguson-Smith, M. A., and Graves, J. A. M. (2004). In the platypus a meiotic chain of ten sex chromosomes shares genes with the bird Z and mammal X chromosomes. Nature 432, 913-917. doi:10.1038/NATURE03021 (Pubitemid 40037154)
11. Grüzner, F., Ashley, T., Rowell, D. M., and Graves, J. A. M. (2006). How did the platypus get its sex chromosome chain?A comparison of meiotic multiples and sex chromosomes in plants and animals. Chromosoma 115, 75-88. doi:10.1007/S00412-005-0034-4
12. Jurka, J. (1998). Repeats in genomic DNA: mining and meaning. Curr. Opin. Struct. Biol. 8, 333-337. doi:10.1016/S0959-440X(98)80067-5
13. Jurka, J., Krnjajic, M., and Kapitonov, V. V. (2002). Active Alu elements are passed primarily through paternal germlines. Theor. Popul. Biol. 61, 519-530. doi:10.1006/TPBI.2002.1602
14. Jurka, J., Kohany, O., Pavlicek, A., Kapitonov, V. V., and Jurka, M. V. (2004). Duplication, coclustering, and selection of humanAlu retrotransposons. Proc. Natl Acad. Sci. USA 101, 1268-1272. doi:10.1073/PNAS. 0308084100 (Pubitemid 38182678)
15. Jurka, J.,Kohany,O., Pavlicek, A., Kapitonov,V.V., and Jurka, M.V. (2005a). Clustering, duplication and chromosomal distribution of mouse SINE retrotransposons. Cytogenet. Genome Res. 110, 117-123. doi:10.1159/000084943
16. Jurka, J., Kapitonov, V. V., Pavlicek, A., Klonowski, P., Kohany, O., and Walichiewicz, J. (2005b). Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462-467. doi:10.1159/000084979
17. Jurka, J., Kapitonov, V. V., Kohany, O., and Jurka, M. V. (2007). Repetitive sequences in complex genomes: structure and evolution. Annu. Rev. Genomics Hum. Genet. 8, 241-259. doi:10.1146/ANNUREV.GENOM. 8.080706.092416
18. Kejnovsky, E., Hobza, R., Cernak, T., Kubat, Z., and Vyskot, B. (2009). The role of repetitive DNA in structure and evolution of sex chromosomes in plants. Heredity 102, 533-541. doi:10.1038/HDY.2009.17
19. Kriegs, J. O., Matzke, A., Churakov, G., Kuritzin, A., Mayr, G., Brosius, J., and Schmitz, J. (2007).Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes). BMC Evol. Biol. 7, 190. doi:10.1186/1471-2148-7-190
20. Kuroki, Y., Toyoda, A., Noguchi, H., Taylor, T. D., Itoh, T., et al. (2006). Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. Nat. Genet. 38, 158-167. doi:10.1038/NG1729
21. Mandal, P. K., and Kazazian, H. H. Jr. (2008). SnapShot: vertebrate transposons. Cell 135, 192-192.e1. doi:10.1016/J.CELL.2008.09.028
22. Mariotti, B., Manzano, S., Kejnovský, E., Vyskot, B., and Jamilena, M. (2009). Accumulation of Y-specific satellite DNAs during the evolution of Rumex acetosa sex chromosomes. Mol. Genet. Genomics 281, 249-259. doi:10.1007/S00438-008-0405-7
23. Montgomery, E., Charlesworth, B., and Langley, C. H. (1987). A test for the role of natural selection in the stabilization of transposable element copy number in a population of Drosophila melanogaster. Genet. Res. 49, 31-41.
24. Murtagh, C. E. (1977). A unique cytogenetics system in monotremes. Chromosoma 65, 37-57. doi:10.1007/BF00293129
25. Ohno, S. (1967). 'Chromosomes and Sex-Linked Genes.'(Springer: Berlin.)
26. Rens,W., Grüzner, F., O'Brian, P. C., Fairclough, H., Graves, J. A. M., and Ferguson-Smith, M. A. (2004). Resolution and evolution of the duckbilled platypus karyotype with an X1Y1X2Y2X3Y3X4Y4X5Y5 male sex chromosome constitution. Proc. Natl Acad. Sci. USA 101, 16 257-16 261. doi:10.1073/PNAS. 0405702101
27. Rens, W., O'Brien, P. C. M., Grützner, F., Clarke, O., Graphodatskaya, D., et al. (2007). The multiple sex chromosomes of platypus and echidna are not completely identical and several share homology with the avian Z. Genome Biol. 8, R243. doi:10.1186/GB-2007-8-11-R243 (Pubitemid 351917501)
28. Scott, D.W. (1992). 'Multivariate Density Estimation. Theory, Practice and Visualization.' (Wiley: NewYork.)
29. Skaletsky, H., Kuroda-Kawaguchi, T., Minx, P. J., Cordum, H. S., Hillier, L., et al. (2003). The male-specific region of the human Y chromosome: a mosaic of discrete sequences. Nature 423, 825-837. doi:10.1038/NATURE01722
30. Smit, A. F. A., Hubley, R., and Green, P. (1996-2004). RepeatMasker Open-3.0. 〈/www.repeatmasker.org〉
31. Steinemann, S., and Steinemann, M. (2005). Y chromosomes: born to be destroyed. Bioessays 27, 1076-1083. doi:10.1002/BIES.20288
32. Veyrunes, F.,Waters, P.D.,Miethke, P., Rens,W.,McMillan,D., et al. (2008). Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes. Genome Res. 18, 965-973. doi:10.1101/GR.7101908
33. Warren, W. C., Hillier, L. W., Graves, J. A. M., Birney, E., Ponting, C. P., et al. (2008). Genome analysis of the platypus reveals unique signatures of evolution. Nature 453, 175-183. doi:10.1038/NATURE06936
34. Weiner, A. M. (2002). SINEs and LINEs: the art of biting the hand that feeds you. Curr. Opin. Cell Biol. 14, 343-350. doi:10.1016/S0955-0674(02)00338-1